diff --git a/CHANGELOG.md b/CHANGELOG.md index 64f7744..2fbce82 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,16 @@ ## Unreleased +- Add the Cell Ontology definition check (`definitions`): the presence and absence marker axioms of a + claimed term, own and inherited, mapped to genes and compared with the subject's measurements; a + contradiction sends the record to review (BEV026). `Ontology` now reads logical-definition relations + and gene names of protein terms. The single-cell case adds per-cluster definition panels and an + external split of six datasets from other studies (81 clusters). Run there with thresholds frozen on + the first six datasets (protocol 3), the check did not transfer. It flagged wrong annotations no better + than chance (47% against 42%), because several protein definitions (mast cell CCR3, neutrophil + CEACAM8, NK cells lacking CD3 epsilon) do not hold for transcripts. Fed back in the loop, its findings + turned 15 correct answers into wrong ones. Identifier errors (70 of 479 answers) were still all caught. + The check is marked experimental; its findings still go back to the proposer in the feedback loop. - Add the single-cell cell-type annotation case (`examples/singlecell_celltype`): marker tables derived from six CELLxGENE datasets annotated by their authors, with the Cell Ontology, HGNC and ASCT+B pinned. Benchmark scenario 3 runs six models on it, alone and in the feedback loop. In the pilot, 35 of 138 first diff --git a/docs/ENGINEERING.md b/docs/ENGINEERING.md index 1cdcc98..14437d9 100644 --- a/docs/ENGINEERING.md +++ b/docs/ENGINEERING.md @@ -47,6 +47,7 @@ evidence items), and duplicate source/item/line/adjudication IDs cannot be admit | BEV023 | Grounding: a cited identifier is obsolete, withdrawn, or not its current name (a previous gene symbol or alias) | Reject | | BEV024 | Grounding: a cited identifier is malformed, or of the wrong kind for its place (e.g. not a cell type) | Reject | | BEV025 | Cross-check: a pinned reference resource contradicts the claim or its supporting evidence | Review | +| BEV026 | Definition check: measurements contradict a marker the ontology defines the claimed term to have or lack | Review | A human acceptance does not erase contradictions, missing evidence, source mismatches, or other human rejection/deferral. Low-strength extraction permissions are explicit @@ -181,6 +182,47 @@ bioevidence validate record.json --ontology cl-basic.obo --term-root cell_type=C `TableGrounder` and `ReferenceGrounder` need their configuration (evidence types, keys, relation) and are used from Python. +### Ontology definitions as checks + +Many Cell Ontology terms are defined by marker proteins. A CD8-positive, alpha-beta T cell `has plasma membrane +part` the CD8 co-receptor and `lacks plasma membrane part` CD4; a natural killer cell lacks CD3 epsilon. These +axioms belong to a pinned release, not to a judgment about one dataset, so they can be checked against +measurements without knowing the right answer. + +- `MarkerDefinitions` (`definitions`) collects each term's presence and absence axioms, its own and inherited + through `is_a`. It maps each protein to HGNC genes: + - by its PRO short label or gene-based synonym; + - as a family (`Fcgr3` is FCGR3A and FCGR3B); + - through the components of a complex (the CD8 co-receptor is CD8A and CD8B); + - or through the protein a modified form belongs to. +- It leaves some axioms out: + - isoform-specific markers (CD45RA), which gene-level counts cannot see; + - axioms about relative amounts, which compare with another cell type rather than with the rest of a + dataset. + + It needs the full `cl.obo`, which keeps the logical definitions. +- `DefinitionGrounder` compares the claimed term with `measure(record)`, which gives each gene's detection rate + and log fold change for the record's subject. It raises BEV026 in two cases: + - **presence:** every gene of a defining protein is detected in fewer than 10% of the cells; + - **absence:** a gene of an excluded protein is detected in at least half of them and more than elsewhere. + + The thresholds were set on the single-cell case's first six datasets, before it was run on six others. + +BEV026 sends a record to review and does not reject it, because a transcript is not a protein and some +definitions are written for one species. In the feedback loop it goes back to the proposer together with the +measurement. The proposer cannot make the finding go away by leaving evidence out, because the check reads the +data, not the evidence the proposer cites. The check is **experimental**. + +**It did not transfer to new data.** On the single-cell case's external split, the thresholds set on the +first six datasets flagged wrong annotations no better than chance (47% against 42%). The cause was definitions +that do not hold for transcripts: +- mast cells defined by CCR3, and neutrophils by CEACAM8, whose transcripts are not detected; +- NK cells defined as lacking CD3 epsilon, although their CD3E transcripts are. + +Fed back to models, these findings turned correct answers into wrong ones (see the benchmark README). Use it +on transcript data only with markers validated at the mRNA level, since the loop passes its findings to the +proposer as they are. + ### The feedback loop `feedback.revise(propose, validator)` runs the loop around any proposer: a model call, an agent or a person. diff --git a/evaluation/llm_benchmark/README.md b/evaluation/llm_benchmark/README.md index e071365..7548ec8 100644 --- a/evaluation/llm_benchmark/README.md +++ b/evaluation/llm_benchmark/README.md @@ -345,6 +345,59 @@ Limits: "wrong" is partly label noise; exact plus coarser plus finer is the fairer measure of agreement. - One run per split. The test split has 46 clusters from the same six datasets as the pilot. +### External split (protocol 3): the definition check did not transfer + +Protocol 3 adds the Cell Ontology definition check (`bioevidence_validator.definitions`, BEV026) to +protocol 2. The check compares the markers a claimed term is defined to have or lack with the cluster's +measurements: +- a defining marker detected in under 10% of cells is a contradiction; +- an excluded marker detected in half or more, and higher than elsewhere, is a contradiction. + +The thresholds were set on the 70 clusters of the first six datasets. There, the 20 first answers the check +flagged were wrong 70% of the time, against 38% overall. Protocol 3 was committed before it was run on six +datasets from other studies, 81 clusters, mostly immune ([results](results/celltype-external/summary.md)). +The gate is reported both with and without the check, on the same first answers. + +| Configuration | Annotated | Compatible (exact + coarser + finer) | Exact | Wrong or invalid | Routed to a person | +|---|---:|---:|---:|---:|---:| +| Model alone | 479/486 | 278 | 169 | 201 | 0 | +| Model + gate without the definition check | 362/486 | 242 | 154 | 120 | 117 | +| Model + gate with it | 302/486 | 202 | 114 | 100 | 177 | +| Model + feedback loop with it | 390/486 | 242 | 125 | 148 | 89 | + +**What this shows: a negative result.** + +- **On new data the check flagged answers no better than chance.** It flagged 88 first answers: 41 wrong, + 43 exactly the authors' term and 4 finer. That is 47% wrong, against 42% wrong overall. Behind the gate it + stopped 20 more wrong answers and 40 more correct ones, and left the error rate of what was admitted + unchanged (33% with and without it). +- **It pushed models away from correct answers.** In the loop, the check's findings go back to the model, + and models believed them. Of 40 answers that matched the authors' term exactly and were revised: + - 15 were changed to a wrong term, 8 of which were then admitted; + - 12 became coarser or finer; + - 13 stayed exact. + + As a result, compatible answers in the loop (242) fell below the model alone (278). +- **The cause is transcripts against proteins.** The Cell Ontology defines cell types by surface proteins, + and several definitions do not hold at the mRNA level: + - a mast cell is defined by CCR3, detected in 0% of all four mast cell clusters; + - a neutrophil is defined by CEACAM8 (CD66b), also undetected; + - a natural killer cell is defined as lacking CD3 epsilon, yet CD3E transcripts are detected in 50–68% of + NK and ILC3 cells. + + These rules fire on the authors' own labels: 11 of 81 external clusters. The development datasets had + almost no mast cells or neutrophils, so the problem did not show before. +- **The identifier layer held.** 70 of 479 first answers had an identifier error (GPT-5.6-Luna 33, + Claude Haiku 4.5 23), and none was admitted. + +Two lessons: +- **Feed back only findings that are facts.** An identifier that belongs to another term is a fact. A + definition that may not hold for transcripts is not, and a model in a feedback loop treats any finding as + an instruction. A finding of uncertain precision belongs with a person, not in the model's next prompt. +- **Validate before transferring.** A protein-level definition can become a transcript-level check only for + markers shown to be reliable at the mRNA level, for example against CITE-seq data that measures both. + That needs its own validation on data not used to choose the markers. + ## Semantic checks (#31) Grounding cannot tell whether a verbatim quote supports the claim, so two semantic layers were diff --git a/evaluation/llm_benchmark/celltype_loop.py b/evaluation/llm_benchmark/celltype_loop.py index ecd68fa..bfdd0a2 100644 --- a/evaluation/llm_benchmark/celltype_loop.py +++ b/evaluation/llm_benchmark/celltype_loop.py @@ -18,6 +18,10 @@ against the answer and cross-checked supporting markers with ASCT+B. Protocol 2 (the held-out test split), from what the pilot showed, asks for contradicting markers only when some clearly point to another cell type (a mixed cluster, doublets), and leaves out the ASCT+B cross-check, whose biomarker lists are not specificity statements. +Protocol 3 (the external split, six datasets from other studies) keeps protocol 2 and adds the Cell Ontology +definition check (`bioevidence_validator.definitions`): a claimed term whose defining markers the cluster's +measurements contradict (a CD8 T cell in which CD4 is detected in most cells) goes back to the model with the +measurement, as a finding to review (BEV026). Its thresholds were set on the first six datasets. One run gives three views: the model alone (its first answer as given), behind a bioevidence gate (its first answer, validated) and in the feedback loop (its last answer, validated). Scoring is independent of the @@ -27,6 +31,7 @@ from __future__ import annotations import argparse +import collections import concurrent.futures import datetime as dt import hashlib @@ -40,6 +45,7 @@ from bioevidence_validator import feedback from bioevidence_validator.crosscheck import ReferenceGrounder +from bioevidence_validator.definitions import DefinitionGrounder, MarkerDefinitions from bioevidence_validator.engine import RecordValidator from bioevidence_validator.grounding import SnapshotStore, SourceBytesGrounder from bioevidence_validator.identifiers import GeneGrounder, Genes, Ontology, OntologyGrounder, _label_key @@ -91,7 +97,7 @@ different cell type, for example in a mixed cluster or doublets, list those with stance "contradicts". If the \ markers do not identify a cell type, set "decision" to "uncertain". Answer from what you know: do not run \ commands, search the web or read files.""" -PROMPTS = {1: PROMPT_V1, 2: PROMPT} +PROMPTS = {1: PROMPT_V1, 2: PROMPT, 3: PROMPT} REVISION = """{prompt} Your previous answer: @@ -121,6 +127,16 @@ def __init__(self) -> None: self.tasks = {t["task_id"]: t for t in load_jsonl(SOURCES / "tasks.jsonl")} self.versions = {d["markers_sha256"]: d["dataset_version_id"] for d in self.manifest["datasets"]} self.tables = {sha: parse_table(self.store.get(sha) or b"")[1] for sha in self.versions} + self.panels: dict[str, dict[str, dict[str, tuple[float, float]]]] = {} + for dataset in self.manifest["datasets"]: + for row in parse_table(self.store.get(dataset["panel_sha256"]) or b"")[1]: + cluster = self.panels.setdefault(dataset["name"], {}).setdefault(row["cluster"], {}) + cluster[row["gene"]] = (float(row["pct_in"]), float(row["logfc"])) + + def measure(self, record: dict) -> dict[str, tuple[float, float]] | None: + """The definition panel of the record's cluster (`cluster:/`).""" + dataset, _, cluster = record["statement"]["subject"]["id"].removeprefix("cluster:").partition("/") + return self.panels.get(dataset, {}).get(cluster) def validator(self, protocol: int = 2) -> RecordValidator: grounders: list = [SourceBytesGrounder(self.store), TableGrounder(self.store, ["marker_gene"]), @@ -129,6 +145,8 @@ def validator(self, protocol: int = 2) -> RecordValidator: grounders.append(ReferenceGrounder.from_table(self.reference, label="ASCT+B", evidence_key="gene", relation="marker_of", ontology=self.ontology, conflict="disjoint")) + if protocol >= 3: + grounders.append(DefinitionGrounder(MarkerDefinitions(self.ontology, self.genes), self.measure)) return RecordValidator(profile=CASE / "profile.yaml", grounders=grounders) def markers(self, task: dict) -> set[str]: @@ -294,6 +312,12 @@ def problems(case: Case, task: dict, answer: dict) -> list[str]: VIEWS = [("model", "Model alone (first answer)"), ("gate", "Model + bioevidence gate (first answer)"), ("loop", "Model + bioevidence feedback loop (last answer)")] +# Protocol 3 only: the gate as protocol 2 would have it, on the same first answers (the prompts are the same). +WITHOUT_DEFINITIONS = ("gate_without_definitions", "Model + gate without the definition check (first answer)") + + +def views_for(protocol: int) -> list[tuple[str, str]]: + return VIEWS[:2] + [WITHOUT_DEFINITIONS] + VIEWS[2:] if protocol >= 3 else VIEWS def view(row: dict, name: str) -> dict: @@ -305,10 +329,11 @@ def view(row: dict, name: str) -> dict: return {"answer": first if first and first["decision"] == "annotate" else None, "routed": False, "expert": False} if not attempts: return {"answer": None, "routed": False, "expert": False} - chosen = attempts[0] if name == "gate" else attempts[-1] - index = 0 if name == "gate" else len(attempts) - 1 + first = name in ("gate", WITHOUT_DEFINITIONS[0]) + chosen = attempts[0] if first else attempts[-1] + index = 0 if first else len(attempts) - 1 annotating = [a for a in answered if a["decision"] == "annotate" and a["cell_type_id"].strip()] - if chosen["status"] == "admitted": + if chosen["status"] == "admitted" or (name == WITHOUT_DEFINITIONS[0] and set(chosen["codes"]) == {"BEV026"}): return {"answer": annotating[index], "routed": False, "expert": False} return {"answer": None, "routed": True, "expert": chosen["to_expert"]} @@ -337,15 +362,23 @@ def metrics(mine: list[dict], name: str) -> dict: split = case.tasks[rows[0]["task_id"]]["split"] if rows else "pilot" protocol = rows[0].get("protocol", 1) if rows else 2 + names = views_for(protocol) summary = {"benchmark": f"singlecell-celltype-v{protocol}", "split": split, - "results": {m: {n: metrics([r for r in rows if r["model"] == m], n) for n, _ in VIEWS} for m in models}, - "pooled": {n: metrics(rows, n) for n, _ in VIEWS}, "episodes": len(rows), + "results": {m: {n: metrics([r for r in rows if r["model"] == m], n) for n, _ in names} for m in models}, + "pooled": {n: metrics(rows, n) for n, _ in names}, "episodes": len(rows), "calls": sum(len(r["calls"]) for r in rows), "failed_calls": sum(c["error"] is not None for r in rows for c in r["calls"]), "revised": sum(len(r["attempts"]) > 1 for r in rows), "codes": {c: sum(c in a["codes"] for r in rows for a in r["attempts"]) for c in sorted({c for r in rows for a in r["attempts"] for c in a["codes"]})}, "episodes_sha256": hashlib.sha256((results / "episodes.jsonl").read_bytes()).hexdigest()} + if protocol >= 3: # first answers the definition check flagged, by how they compare with the authors' term + flagged = collections.Counter() + for r in rows: + got = [c["answer"] for c in r["calls"] if c["answer"] and c["answer"]["decision"] == "annotate"] + if r["attempts"] and "BEV026" in r["attempts"][0]["codes"]: + flagged[outcome(case, truth[r["task_id"]]["term"], got[0])] += 1 + summary["definition_flags_on_first_answers"] = dict(sorted(flagged.items())) (results / "summary.json").write_text(json.dumps(summary, indent=2, sort_keys=True) + "\n", encoding="utf-8", newline="\n") (results / "summary.md").write_text(render(summary), encoding="utf-8", newline="\n") @@ -365,7 +398,7 @@ def render(summary: dict) -> str: "or marker error | Routed to a person |", "|---|---|---:|---:|---:|---:|---:|---:|---:|---:|"] blocks = [(score_claims.MODEL_NAMES[m], v) for m, v in summary["results"].items()] + [("All models", summary["pooled"])] for name, views in blocks: - for key, label in VIEWS: + for key, label in views_for(protocol): m = views[key] lines.append(f"| {name} | {label} | {f(m['answered'])} | {f(m['exact'])} | {f(m['coarser'])} | " f"{f(m['finer'])} | {f(m['wrong'])} | {f(m['invalid'])} | " @@ -377,6 +410,9 @@ def render(summary: dict) -> str: "", f"{summary['episodes']} episodes, {summary['calls']} model calls ({summary['failed_calls']} failed), " f"{summary['revised']} revised after feedback. Rule codes raised across all records: " + ", ".join(f"{c} {n}" for c, n in summary["codes"].items()) + ".", ""] + if "definition_flags_on_first_answers" in summary: + lines[-1:] = ["", "First answers the definition check flagged, by comparison with the authors' term: " + + ", ".join(f"{k} {n}" for k, n in summary["definition_flags_on_first_answers"].items()) + ".", ""] return "\n".join(lines) @@ -385,11 +421,11 @@ def main(argv: list[str] | None = None) -> int: steps = parser.add_subparsers(dest="step", required=True) r = steps.add_parser("run") r.add_argument("--output", type=Path, required=True) - r.add_argument("--split", choices=["pilot", "test"], default="pilot") + r.add_argument("--split", choices=["pilot", "test", "external"], default="pilot") r.add_argument("--models", nargs="+", choices=list(run_models.MODELS), default=list(run_models.MODELS)) r.add_argument("--workers", type=int, default=2) r.add_argument("--limit", type=int) - r.add_argument("--protocol", type=int, choices=sorted(PROMPTS), default=2) + r.add_argument("--protocol", type=int, choices=sorted(PROMPTS), default=3) c = steps.add_parser("collect") c.add_argument("--output", type=Path, required=True) c.add_argument("--results", type=Path, required=True) diff --git a/evaluation/llm_benchmark/results/celltype-external/episodes.jsonl b/evaluation/llm_benchmark/results/celltype-external/episodes.jsonl new file mode 100644 index 0000000..1c01221 --- /dev/null +++ b/evaluation/llm_benchmark/results/celltype-external/episodes.jsonl @@ -0,0 +1,486 @@ +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}], "rationale": "This marker profile is characteristic of classical monocytes. CD14 is a canonical monocyte surface antigen, and the combination of S100A8, S100A9 (highly co-expressed innate immune proteins), FCN1 (ficolin-1, a pattern recognition receptor), LYZ (lysozyme), and myeloid markers like TYROBP, FCER1G, and CSF3R all strongly support classical monocyte identity. The high pct_in values (>0.98) and elevated logfc values indicate these genes are specifically and highly expressed in this cluster. No contradictory markers are present; all top markers are consistent with monocyte biology."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-0094010baa"} +{"attempts": [{"codes": ["BEV004"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "ITGA2B", "stance": "contradicts"}, {"gene": "NFE2", "stance": "contradicts"}], "rationale": "This is a mast cell cluster, clearly identified by the top marker genes. HDC (histidine decarboxylase) and FCER1A (high-affinity IgE receptor) are diagnostic mast cell markers. PRG2, CLC, and CPA3 are additional well-established mast cell-specific proteins. SRGN (serglycin) is also found in mast cells. The presence of ITGA2B and NFE2 (megakaryocyte/platelet markers) suggests possible contamination or doublets, but the overwhelming preponderance of mast cell markers supports the primary annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-0224ef5d63"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'endometrial fibroblast' is not the name of CL:0002076 ('endo-epithelial cell'). Closest names: CL:4033025 (perichondrial fibroblast); CL:4023054 (mesothelial fibroblast); CL:4052030 (adventitial fibroblast).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002076", "cell_type_label": "endometrial fibroblast", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "LMNA", "stance": "supports"}, {"gene": "FOSB", "stance": "supports"}, {"gene": "JUN", "stance": "supports"}, {"gene": "FOS", "stance": "supports"}, {"gene": "HSP90AA1", "stance": "supports"}, {"gene": "PPP1R15A", "stance": "supports"}, {"gene": "ZFP36", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}], "rationale": "The marker profile is dominated by fibroblast-lineage genes (TAGLN, TPM2, LMNA) and stress/activation response genes (JUN, FOS, FOSB, HSP90AA1, PPP1R15A, ZFP36), consistent with activated endometrial fibroblasts. TPSB2 (tryptase beta) is a mast cell-specific marker and contradicts the primary fibroblast identity, likely representing contamination or a minor population within the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.7}, {"answer": {"cell_type_id": "CL:UNKNOWN", "cell_type_label": "endometrial fibroblast (cell type identified; CL ID unknown)", "decision": "uncertain", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "LMNA", "stance": "supports"}, {"gene": "JUN", "stance": "supports"}, {"gene": "FOS", "stance": "supports"}, {"gene": "FOSB", "stance": "supports"}, {"gene": "HSP90AA1", "stance": "supports"}, {"gene": "PPP1R15A", "stance": "supports"}, {"gene": "ZFP36", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}], "rationale": "Marker profile is consistent with activated endometrial fibroblasts: contractile proteins (TAGLN, TPM2, LMNA), immediate early genes (JUN, FOS, FOSB), and stress response genes support fibroblast identity. TPSB2 (mast cell tryptase) contradicts this, likely representing contamination. The cell type is confidently identified as fibroblast/myofibroblast, but the correct Cell Ontology identifier cannot be reliably determined without access to the pinned release."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'endometrial fibroblast' is not the name of CL:0002076 ('endo-epithelial cell'). Closest names: CL:4033025 (perichondrial fibroblast); CL:4023054 (mesothelial fibroblast); CL:4052030 (adventitial fibroblast)."], "seconds": 26.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-027de551e6"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "SEC61B", "stance": "supports"}, {"gene": "GZMB", "stance": "contradicts"}], "rationale": "Strong, consistent markers of antibody-secreting cells: immunoglobulin chains (JCHAIN, IGKC, IGLC2) are highly specific for plasma cells; MZB1, BCL11A, and IRF7 support B cell and plasma cell identity. SEC61B (ER protein translocation) supports the secretory phenotype. GZMB (granzyme B) is atypical for plasma cells and suggests possible minor contamination from cytotoxic lymphocytes, but does not override the dominant plasma cell signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.5}, {"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "uncertain", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}], "rationale": "Immunoglobulin chain genes (JCHAIN, IGKC, IGLC2) and B cell identity markers (MZB1, BCL11A, IRF7) confirm B lineage origin. However, the complete absence of SDC1 (0% in cluster) excludes plasma cell classification, which requires surface syndecan-1. The marker profile suggests activated or proliferating B cells engaged in antibody production rather than post-mitotic plasma cells. Specific B cell subtype cannot be confidently determined without additional discriminatory markers."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 0% of the cluster's cells."], "seconds": 28.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-0460394dc8"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "This cluster shows a clear B cell signature with high expression of canonical B cell markers (CD79A, CD79B, MS4A1/CD20, CD37, BANK1) and strong immunoglobulin gene expression (IGKC, IGHA1, IGLC2, IGHG1) indicating antibody-secreting or differentiated B cells. The elevated HLA class II expression (CD74, HLA-DRA, HLA-DRB1, etc.) is consistent with activated B cells. The combination of these markers—particularly the B cell-specific CD79 complex and MS4A1 alongside immunoglobulin production—confidently identifies this as a B cell population, likely activated or plasma cell-differentiated B cells in the kidney immune infiltrate."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-04f3e6a976"} +{"attempts": [{"codes": ["BEV023"], "evidence": 8, "findings": [{"message": "CL:0000293 (obsolete structural cell) is obsolete in the pinned CL release. Closest names: CL:0002504 (enteric smooth muscle cell); CL:1000979 (ureter smooth muscle cell); CL:0002598 (bronchial smooth muscle cell).", "rule_id": "BEV023", "where": "object id"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000293", "cell_type_label": "myometrial smooth muscle cell", "decision": "annotate", "markers": [{"gene": "ACTA2", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}], "rationale": "This cluster has a strong and consistent smooth muscle transcriptional signature. ACTA2 and MYH11 are canonical markers of smooth muscle cells. Additional structural proteins (TPM1, TPM2, MYL9, CALD1) and smooth muscle-associated genes (TAGLN, SPARCL1) further confirm this identification. The tissue context (endometrium/myometrium) and expression profile are consistent with myometrial smooth muscle cells. Heat shock proteins and immune markers present are secondary/stress-related and do not contradict the primary smooth muscle identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.3}, {"answer": {"cell_type_id": "", "cell_type_label": "smooth muscle cell", "decision": "uncertain", "markers": [{"gene": "ACTA2", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}], "rationale": "The cluster has a definitive smooth muscle transcriptional signature. ACTA2, MYH11, TAGLN, TPM1, TPM2, MYL9, and CALD1 are canonical smooth muscle markers; SPARCL1 is also smooth muscle-associated. The tissue origin (human endometrium) points specifically to myometrial smooth muscle, but CL:0000293 is obsolete in the current Cell Ontology release. The correct current CL term for myometrial smooth muscle cells cannot be reliably identified without access to the current pinned CL release. The biological identity is unambiguous; only the precise CL term is uncertain."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000293 (obsolete structural cell) is obsolete in the pinned CL release. Closest names: CL:0002504 (enteric smooth muscle cell); CL:1000979 (ureter smooth muscle cell); CL:0002598 (bronchial smooth muscle cell)."], "seconds": 30.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-0919bb7151"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "This cluster is a CD8+ T cell population. The top markers include the definitive markers for cytotoxic T lymphocytes: CD8A and CD8B (the CD8 heterodimer marking cytotoxic T cells), CD3E (T cell receptor complex component), and TRAC (T cell receptor alpha). Supporting evidence includes IL7R (T cell marker, especially memory T cells), CD2 (pan-T cell marker), CD27 (memory T cell marker), and IL32 (T cell cytokine). The high specificity (pct_in > 85% for most top markers) and strong fold changes (CD8A logfc 3.365, TRAC 3.169, CD3E 2.578, CD8B 2.512) firmly establish this as a CD8+ T cell cluster with no contradicting markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-15649bcc33"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'myeloid dendritic cell' is not the name of CL:0000458 ('serotonin secreting cell'). 'myeloid dendritic cell' is the name of CL:0000782 (myeloid dendritic cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000458", "cell_type_label": "myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "CLEC10A", "stance": "supports"}], "rationale": "The cluster is characterized by exceptionally high and nearly ubiquitous expression of MHC class II genes (HLA-DR, HLA-DP, HLA-DQ), which are the hallmark of professional antigen-presenting cells. CD74 (MHC II invariant chain) is essential for peptide loading onto MHC II. CD83 is a canonical marker of mature dendritic cells, and CLEC10A (DCIR) is a dendritic cell-specific C-type lectin receptor. Together, these genes define the myeloid dendritic cell subset. The high expression frequency (pct_in 0.87–1.0) and strong fold-changes of these markers, combined with their specificity, make myeloid dendritic cell the definitive classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.3}, {"answer": {"cell_type_id": "CL:0000782", "cell_type_label": "myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "CLEC10A", "stance": "supports"}], "rationale": "The cluster is characterized by exceptionally high and nearly ubiquitous expression of MHC class II genes (HLA-DR, HLA-DP, HLA-DQ), which are the hallmark of professional antigen-presenting cells. CD74 (MHC II invariant chain) is essential for peptide loading onto MHC II. CD83 is a canonical marker of mature dendritic cells, and CLEC10A (DCIR) is a dendritic cell-specific C-type lectin receptor. Together, these genes define the myeloid dendritic cell subset. The high expression frequency (pct_in 0.87–1.0) and strong fold-changes of these markers, combined with their specificity, make myeloid dendritic cell the definitive classification."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'myeloid dendritic cell' is not the name of CL:0000458 ('serotonin secreting cell'). 'myeloid dendritic cell' is the name of CL:0000782 (myeloid dendritic cell)."], "seconds": 11.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-18bf2c5651"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 16, "findings": [{"message": "The label 'tissue resident memory T cell, CD8-positive' is not the name of CL:0002416 ('mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte').", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0002416 (mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte) is defined as lacking T cell receptor co-receptor CD8 (CD8A), but CD8A is detected in 50% of the cluster's cells, more than in the others (logfc 0.85).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017", "BEV026"], "evidence": 15, "findings": [{"message": "The label 'tissue resident memory T cell, CD8-positive' is not the name of CL:0002449 ('CD94-positive Ly49CI-positive natural killer cell, mouse').", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0002449 (CD94-positive Ly49CI-positive natural killer cell, mouse) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.93).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002416", "cell_type_label": "tissue resident memory T cell, CD8-positive", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The cluster exhibits a classic CD8+ T cell transcriptional profile with strong T cell identity markers (CD3D, CD3E, TRAC, TRBC1/2) and CD8 lineage markers (CD8A, CD8B). High expression of CD69, a hallmark tissue-resident marker, combined with robust effector molecules (GZMA, GZMK, CST7) and chemokine production (CCL5, CCL4), indicates activated, cytotoxic CD8+ T cells residing in the kidney tissue. The high pct_in and differential expression of CD69, CD8A, and CD8B strongly support tissue resident memory T cell identity. No markers contradict this assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.8}, {"answer": {"cell_type_id": "CL:0002449", "cell_type_label": "tissue resident memory T cell, CD8-positive", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "CD8+ alpha-beta T cell identity is established by CD3D, CD3E, TRAC, TRBC1/2, with strong CD8 lineage markers (CD8A at 50.2% pct_in, CD8B at 46.4%). High CD69 expression (0.938 logfc, 81.2% pct_in) is the hallmark of tissue residency. Robust cytotoxic effector molecules (GZMA, GZMK, CST7) and chemokine production (CCL5, CCL4) indicate an activated, cytotoxic phenotype. The tissue context (kidney cortex) combined with CD69-high, CD8+, TCR+ profile supports tissue-resident memory T cell classification. CXCR4 and JUN show high background expression (pct_out high) and are not discriminative."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'tissue resident memory T cell, CD8-positive' is not the name of CL:0002416 ('mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte').", "object id: CL:0002416 (mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte) is defined as lacking T cell receptor co-receptor CD8 (CD8A), but CD8A is detected in 50% of the cluster's cells, more than in the others (logfc 0.85)."], "seconds": 21.3}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "CD8-positive, alpha-beta T cell identity confirmed by CD3D/E (T cell markers), CD8A/B (CD8 lineage), TRAC/TRBC1/2 (alpha-beta TCR). Robust cytotoxic and activation markers (GZMA, GZMK, CST7, CD69, CCL5, CCL4) indicate an activated/effector phenotype consistent with CD8+ T cells in kidney tissue. CXCR4 and JUN show high background (pct_out high) and are not discriminative."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'tissue resident memory T cell, CD8-positive' is not the name of CL:0002449 ('CD94-positive Ly49CI-positive natural killer cell, mouse').", "object id: CL:0002449 (CD94-positive Ly49CI-positive natural killer cell, mouse) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.93)."], "seconds": 25.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-1c3cf91fbc"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'basophil' is not the name of CL:0000236 ('B cell'). 'basophil' is the name of CL:0000767 (basophil).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000767 (basophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000767 (basophil) is defined as having ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP3) on the membrane, but ENPP3 is detected in only 7% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}, {"gene": "RGS2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "Strong mast cell signature with canonical tryptase genes (TPSAB1, TPSB2, CPA3) showing highest logfc and near-universal cluster expression. MS4A2 encodes the FcεRI-β chain. HPGDS, CD63, and ALOX5AP reflect mast cell mediator production and degranulation biology. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.8}, {"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "Basophils, not mast cells. Both cell types share tryptase genes (TPSAB1, TPSB2), CPA3, MS4A2 (FcεRI-β), and mediator-related genes (HPGDS, ALOX5AP, CD63). However, the absence of CCR3 (0% detection) rules out mast cells, which require CCR3 membrane expression by Cell Ontology definition. Basophils lack this requirement. GATA2 is a key regulator of basophil development, and CD69 reflects basophil activation. RGS1/RGS2/RGS13 regulate G-protein signaling in these cells. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 14.8}, {"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "Basophils are identified by high expression of tryptase genes (TPSAB1, TPSB2), CPA3, and MS4A2 (FcεRI-β subunit), which are hallmark markers of basophil lineage. HPGDS and ALOX5AP reflect basophil-specific mediator synthesis pathways (prostaglandins and leukotrienes). CD63 marks granules and activation. GATA2 is a key transcription factor for basophil development. CD69 indicates activation state. RGS13 regulates basophil signaling. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'basophil' is not the name of CL:0000236 ('B cell'). 'basophil' is the name of CL:0000767 (basophil)."], "seconds": 11.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-1cdfab3be0"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "RETN", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}], "rationale": "This cluster shows a definitive classical monocyte signature. S100A9 and S100A8 (calprotectin subunits) are hallmark monocyte markers with high logFC and specificity (high pct_in, very low pct_out). Supporting markers include lysozyme, Ficolin-1, and multiple S100 family proteins, all consistent with the pro-inflammatory gene expression profile of classical monocytes. No contradicting markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-1dc66b7bae"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}], "rationale": "This cluster is definitively a B lymphocyte population. The top markers are B-cell-specific transcripts: immunoglobulin genes (IGHM, IGHD, IGKC) are only expressed in B cells; CD79A and CD79B encode core components of the B cell receptor complex; MS4A1 (CD20) is the canonical pan-B cell marker; TCL1A is highly specific to B cells; VPREB3 is a pre-B cell marker; CD19 is a pan-B cell antigen; and FCMR is the B cell-specific Fc receptor. Additional markers like CD37, CD24, CD72, and ITM2C further support B cell identity. MHC class II genes (HLA-DRA, HLA-DRB1, HLA-DRB5) are expected in B cells due to their role in antigen presentation. No markers contradict B cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-1fdfebb69c"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster is dominated by canonical NK cell markers. NKG7 and the cytotoxic granule proteins (GZMA, GNLY, CST7, CTSW) are highly expressed and abundant in the cluster. The NK cell receptors KLRB1, KLRK1, KLRF1, and KLRD1 are prominent, along with FCGR3A (CD16), which is characteristically high on NK cells. HOPX and HCST are transcriptional and signaling molecules associated with NK cells. While TRDC and TRGC2 (gamma-delta TCR markers) are present, they have lower logfc and their moderate prevalence is consistent with a primarily NK cell population, possibly with minor gamma-delta T cell contribution or cross-reactivity rather than a mixed identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-21afd5c734"} +{"attempts": [{"codes": ["BEV004"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "LTB", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "Strong concordance of T cell receptor genes (TRBC1, TRDC), IL-7 signaling (IL7R), lymphotoxin (LTB), activation markers (CD69, CD52, KLRB1), and T cell differentiation factors (RORA). These markers consistently identify this as a T lymphocyte cluster from colon tissue. KRT86 (keratin) is atypical for T cells and may reflect intraepithelial localization or minor contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.2}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-227cbde019"} +{"attempts": [{"codes": ["BEV004"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "TCF4", "stance": "contradicts"}, {"gene": "IRF7", "stance": "contradicts"}, {"gene": "PLD4", "stance": "contradicts"}, {"gene": "FCER1A", "stance": "contradicts"}], "rationale": "The cluster is dominated by immunoglobulin genes (JCHAIN, IGKC, IGHM) and plasma cell-specific markers (MZB1, ITM2C), all expressed in 95.7–100% of cells with high log fold changes. JCHAIN (J chain) in particular is diagnostic for plasma cells, being required for IgM/IgA assembly. The presence of TCF4, IRF7, PLD4 (dendritic cell markers) and FCER1A (basophil/mast cell marker) suggests this may be a mixed cluster or contain doublets, but the immunoglobulin signature clearly identifies the dominant cell type as plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-26fda93c9c"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "CD8A and CD8B are the signature markers of cytotoxic T lymphocytes, showing exceptionally high logfc (3.357 and 3.275) and high pct_in (0.945 and 0.915) with excellent discrimination (low pct_out: 0.145 and 0.073). TRAC, CD3E, CD2, and CD27 confirm T cell lineage. CCR7 and IL7R indicate a naive or central memory phenotype. KLRK1 and CTSW further support cytotoxic T cell identity. No contradicting markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-28eb7ea379"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "CD163", "stance": "supports"}, {"gene": "MRC1", "stance": "supports"}, {"gene": "F13A1", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "STAB1", "stance": "supports"}, {"gene": "MERTK", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}], "rationale": "The cluster shows the canonical macrophage signature with strong, highly specific expression of CD163 (M2/alternative macrophage marker), MRC1, F13A1, and complement components (C1QA/C1QB). LYVE1 and STAB1 expression indicates tissue-resident origin. All top 10 markers are macrophage-associated. No contradictory markers present; markers are highly enriched in this cluster (pct_in: 0.79–0.99) and depleted outside it (pct_out: 0.04–0.51), confirming a homogeneous macrophage population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-302af8ae13"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000556", "cell_type_label": "megakaryocyte", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "FERMT3", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PDLIM1", "stance": "supports"}, {"gene": "GUCY1B1", "stance": "supports"}], "rationale": "This cluster is dominated by megakaryocyte-specific markers. ITGA2B (CD41) is expressed in 93% of cells with 3.91 logfc, the highest marker. PPBP, PLEK, and FERMT3 are canonical megakaryocyte/platelet proteins. NFE2 and TAL1 are transcription factors essential for megakaryocyte differentiation. CD34 presence indicates early-stage or progenitor megakaryocytes. The consistent high pct_in values and high logfc values across multiple megakaryocyte-specific genes strongly support this classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-3775a26491"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "This cluster is clearly a mast cell cluster. TPSB2 and TPSAB1 are highly specific mast cell tryptase genes with the highest log fold changes (2.98 and 2.68), expressed in >78% of cells with minimal expression outside the cluster. CPA3 (carboxypeptidase A3) is another canonical mast cell marker with high logfc. KIT (c-KIT receptor) is essential for mast cell development and is strongly expressed (98% of cells). HPGDS encodes hematopoietic prostaglandin D synthase, a mast cell-specific enzyme involved in mediator synthesis. IL33R reflects mast cell responsiveness to IL-33 signaling. These six markers together provide definitive evidence for mast cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.6}, {"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [], "rationale": "The marker profile strongly suggests a mast cell or basophil (high tryptase expression: TPSB2, TPSAB1; CPA3; KIT; and cytokine receptors), but the complete absence of CCR3 expression (0% of cluster cells) disqualifies this from the mast cell definition in the pinned Cell Ontology release. While basophils also express these markers, the extremely high tryptase fold-changes are more typical of mast cells. Without additional discriminating markers (e.g., CD123 for basophils, or the presence of CCR3), the cell type identity cannot be confidently assigned."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 29.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-3959f97db0"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "DEPTOR", "stance": "supports"}], "rationale": "FCER1A (logfc 4.022, 100% in cluster) and CPA3 (logfc 3.101, 91.4% in) are highly specific and diagnostic markers of mast cells. SLC40A1, CD34, IL1B, CRHBP, NFE2, and DEPTOR provide additional support for mast cell identity. CD34 expression suggests an immature mast cell population or mast cell progenitors. No markers contradict mast cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-3b8c7f5246"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'CD8-positive, alpha-beta cytotoxic T cell' is not the name of CL:0001049 ('activated CD8-positive, alpha-beta T cell, human'). 'CD8-positive, alpha-beta cytotoxic T cell' is the name of CL:0000794 (CD8-positive, alpha-beta cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001049", "cell_type_label": "CD8-positive, alpha-beta cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "S100A10", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD99", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}], "rationale": "GZMK (granzyme K) is the defining marker—a cytotoxic granule protein expressed in cytotoxic T lymphocytes. The cluster also shows strong expression of S100A proteins (A4, A6, A10), markers of activated/effector T cells, plus CD99 (pan-leukocyte) and notably high CD74 (HLA-DR invariant chain), which distinguishes T cells from NK cells. Proliferation markers (STMN1, HMGB2, TYMS) indicate active cycling. VIM expression is consistent with effector/migratory phenotype. The tonsil tissue context and this marker combination strongly support activated cytotoxic CD8+ T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.7}, {"answer": {"cell_type_id": "CL:0001049", "cell_type_label": "activated CD8-positive, alpha-beta T cell, human", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "S100A10", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}], "rationale": "GZMK (granzyme K) is the defining marker of cytotoxic CD8+ T cells. The high expression of S100A proteins (A4, A6, A10) and proliferation markers (STMN1, HMGB2, TYMS) with strong log fold changes and high pct_in values specifically indicate an activated/effector state rather than quiescent CD8+ T cells. VIM expression supports the activated, migratory phenotype. Together, these markers characterize activated CD8+ cytotoxic T lymphocytes in tonsil tissue."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD8-positive, alpha-beta cytotoxic T cell' is not the name of CL:0001049 ('activated CD8-positive, alpha-beta T cell, human'). 'CD8-positive, alpha-beta cytotoxic T cell' is the name of CL:0000794 (CD8-positive, alpha-beta cytotoxic T cell)."], "seconds": 12.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-3daee1395a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'CD8-positive, alpha-beta T cell' is not the name of CL:0000911 ('effector T cell'). 'CD8-positive, alpha-beta T cell' is the name of CL:0000625 (CD8-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000911", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}], "rationale": "The cluster is defined by CD8A, CD8B, and T cell receptor components (TRAC, TRGC2, CD3E, CD3G), establishing it as CD8+ T cells. High expression of cytotoxic granule proteins (GZMA, CTSW, CST7), NKG7, and KLRK1 indicates an activated/effector phenotype. All markers are consistent with CD8+ alpha-beta T lymphocytes; no contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.8}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}], "rationale": "The cluster is defined by CD8A, CD8B, and T cell receptor components (TRAC, CD3E, CD3G), establishing it as CD8-positive, alpha-beta T cells. High expression of cytotoxic effector molecules (NKG7, GZMA, CTSW, CST7, KLRK1, GNLY) indicates an activated/effector phenotype consistent with CD8+ T lymphocytes. All markers support this lineage; no contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD8-positive, alpha-beta T cell' is not the name of CL:0000911 ('effector T cell'). 'CD8-positive, alpha-beta T cell' is the name of CL:0000625 (CD8-positive, alpha-beta T cell)."], "seconds": 10.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-4b8439fcc9"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV026"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'pro-B cell' is not the name of CL:0000818 ('transitional stage B cell'). 'pro-B cell' is the name of CL:0000826 (pro-B cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000818 (transitional stage B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 6% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000818 (transitional stage B cell) is defined as having membrane-spanning 4-domains subfamily A member 1 (MS4A1) on the membrane, but MS4A1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000818", "cell_type_label": "pro-B cell", "decision": "annotate", "markers": [{"gene": "IGLL1", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "CDCA7", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "MPO", "stance": "contradicts"}, {"gene": "CSF3R", "stance": "contradicts"}, {"gene": "AZU1", "stance": "contradicts"}, {"gene": "CPA3", "stance": "contradicts"}], "rationale": "The near-universal IGLL1 expression (99.1% of cells, high logfc) is essentially diagnostic for pro-B cells at this developmental stage. CD34 confirms progenitor status, and XBP1 supports B cell development. However, the cluster shows strong myeloid contamination signals (MPO as top marker, high CSF3R, AZU1), suggesting either doublets, multipotent progenitors with multi-lineage gene expression, or contaminating myeloid cells in the sort/capture. The B-cell identity is warranted based on IGLL1 dominance."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 66.7}, {"answer": {"cell_type_id": "–", "cell_type_label": "–", "decision": "uncertain", "markers": [], "rationale": "The cluster shows conflicting lineage signals that prevent confident annotation. IGLL1 (99.1% of cells, logfc 3.772) and CD34 (80.2%, logfc 2.334) indicate early B cell development, supported by XBP1 and CDCA7. However, MPO is the dominant marker (82.1%, logfc 4.591), and CSF3R, AZU1, and CPA3 are highly expressed—indicating myeloid lineage. Critically, CD19 and MS4A1, which define pro-B and transitional B cells, are detected in only 6% and 8% respectively. This pattern is inconsistent with any single annotated cell type: too myeloid to be B-lineage (lacks CD19/MS4A1), too lymphoid to be myeloid (IGLL1 near-universal), suggesting either a multipotent progenitor, doublet cluster, or sorting/capture artifact."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pro-B cell' is not the name of CL:0000818 ('transitional stage B cell'). 'pro-B cell' is the name of CL:0000826 (pro-B cell).", "object id: CL:0000818 (transitional stage B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 6% of the cluster's cells.", "object id: CL:0000818 (transitional stage B cell) is defined as having membrane-spanning 4-domains subfamily A member 1 (MS4A1) on the membrane, but MS4A1 is detected in only 8% of the cluster's cells."], "seconds": 41.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-4e9d71ecad"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "PLAUR", "stance": "supports"}, {"gene": "AQP9", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "CTSL", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "MT2A", "stance": "supports"}, {"gene": "FTH1", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "S100A10", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "CCL20", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}], "rationale": "This cluster shows a classic activated macrophage transcriptomic signature. PLAUR and AQP9 are particularly diagnostic for macrophages. The elevated iron metabolism genes (ferritins, metallothioneins) and inflammatory chemokines (CXCL8, CCL20) suggest tissue-resident macrophages in an inflammatory state. The consistent high expression across the cluster (pct_in 0.73–1.0) and low expression outside (pct_out <0.7 for most markers) confirms this is a distinct, homogeneous population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-5169234be6"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "DUSP2", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}], "rationale": "This cluster is identified as gamma-delta T cells. The presence of TRDC (T cell receptor delta constant region) and TRGC2 (T cell receptor gamma constant region 2) as top markers definitively indicates γδ T cells, which express TCR composed of gamma and delta chains rather than the alpha-beta chains of conventional T cells. The cluster shows a characteristic cytotoxic phenotype with high expression of granzymes (GZMA), cathepsins (CTSW, CST7), and granulysin (GNLY). NK-associated receptors (KLRB1, KLRK1, KLRD1) and NKG7 are frequently expressed in γδ T cells. Pan-T cell markers (CD3E, CD2, IL7R) confirm T cell identity. No contradicting markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-56d8f3ebbf"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "SEC61B", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}], "rationale": "The cluster is characterized by extremely high expression of immunoglobulin genes (IGKC, JCHAIN, IGLL1), indicating an antibody-producing population. XBP1, a key plasma cell differentiation factor, is prominently elevated. The presence of multiple ER chaperones and protein secretion machinery components (HSP90B1, SEC11C, SEC61B, FKBP11, HERPUD1) reflects the intense protein synthesis and secretion characteristic of plasma cells. CD38 and CD27 are activation markers typical of plasma cells, and CD19 confirms B cell lineage. The combination of immunoglobulin production machinery with XBP1-driven transcriptional programming definitively identifies this as a plasma cell cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-62995bbc69"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 8, "findings": [{"message": "The label 'natural killer T cell' is not the name of CL:0002415 ('immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0002415 (immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte) is defined as lacking CD4 molecule (CD4), but CD4 is detected in 55% of the cluster's cells, more than in the others (logfc 0.47).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002415", "cell_type_label": "natural killer T cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "LAG3", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}], "rationale": "KLRB1 as the top marker gene is highly specific for natural killer T cells. RORA is essential for NKT cell development and differentiation. CD2 confirms T lymphocyte identity. LAG3, TNFRSF4 (OX40), and TNFRSF18 (GITR) are activation markers consistent with effector NKT cells. IL32 and S100A4 further support an activated T cell phenotype. No markers clearly contradict NKT cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.5}, {"answer": {"cell_type_id": "CL:0000912", "cell_type_label": "helper T cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "LAG3", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}], "rationale": "CD4 presence in 55% of cells confirms CD4+ helper T cells. KLRB1 (CD161) as the top marker identifies CD161+ helper T cells, predominantly Th17-skewed. RORA is the master regulator of Th17 differentiation. IL32 is a key Th17-associated cytokine. Strong expression of activation markers (LAG3, TNFRSF4/OX40, TNFRSF18/GITR, CTLA4) and S100A4 indicate activated effector helper T cells, likely with Th17 polarization in this tonsil population."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'natural killer T cell' is not the name of CL:0002415 ('immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell).", "object id: CL:0002415 (immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte) is defined as lacking CD4 molecule (CD4), but CD4 is detected in 55% of the cluster's cells, more than in the others (logfc 0.47)."], "seconds": 56.7}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-62ef0fd4ba"} +{"attempts": [{"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'basophil' is not the name of CL:0000171 ('pancreatic A cell'). 'basophil' is the name of CL:0000767 (basophil).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000767 (basophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HPGD", "stance": "supports"}], "rationale": "TPSB2, TPSAB1, and CPA3 are highly specific mast cell markers encoding granule proteases with logfc >3. MS4A2 (FcεRI-β) is the high-affinity IgE receptor characteristic of mast cells. LTC4S, HPGDS, and HPGD reflect mast cell involvement in eicosanoid metabolism. GATA2 supports mast cell identity through developmental transcription factor expression. All top-ranked markers align with a pure mast cell phenotype with no evidence of contamination or mixed populations."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.9}, {"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}], "rationale": "The absence of CCR3 expression (0% of cells) excludes mast cells, which require this chemokine receptor by Cell Ontology definition. The top markers—TPSB2, TPSAB1, and CPA3 with high logfc—encode granule proteases shared between basophils and mast cells. MS4A2 (FcεRI-β), LTC4S (leukotriene C4 synthase), and GATA2 support IgE-dependent effector function characteristic of basophils. Basophils are circulating and tissue-resident cells that express these markers without requiring CCR3, making basophil the correct identity for this cluster."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 16.2}, {"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}], "rationale": "Top markers TPSB2, TPSAB1, and CPA3 are serine proteases enriched in basophil and mast cell granules. MS4A2 (FcεRI-β), LTC4S (leukotriene C4 synthase), and GATA2 support IgE-dependent effector function and transcriptional regulation of basophils. The strong expression pattern with high logfc and pct_in values identifies this as basophil rather than mast cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'basophil' is not the name of CL:0000171 ('pancreatic A cell'). 'basophil' is the name of CL:0000767 (basophil)."], "seconds": 7.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-68351aaa63"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}], "rationale": "The combination of high expression of C1Q complement components (C1QA, C1QB, C1QC), canonical macrophage markers (AIF1, CST3), monocyte/macrophage-specific genes (MS4A7), elevated MHC class II molecules (HLA-DR complex, CD74), chemokines (CCL3, CCL4), and myeloid markers (TYROBP) is pathognomonic for macrophages. These markers show high pct_in and strong logfc with low pct_out, indicating a pure, well-defined cluster without contamination from other cell types."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.2}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-6dacd7effa"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}], "rationale": "The cluster is dominated by T cell-specific markers. CD3D/E/G (TCR complex) and TRAC/TRBC2 (TCR chains) are definitive T cell markers with high expression within the cluster and very low expression outside (pct_out 0.12-0.43 for TCR genes). Supporting markers include IL7R (T cell development), CD2 (T cell adhesion), IL32 (T cell cytokine), and CD40LG (helper T cell marker). BCL11B and RORA indicate T cell differentiation and development. The high within-cluster expression and low between-cluster expression of TCR components confirm this is a homogeneous T cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.2}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-72757d8950"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CBLB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "IL7R is a canonical T cell marker with high cluster specificity (96.9% in-cluster vs 13.9% out-cluster expression). The cluster exhibits a strong T cell signature across multiple functional categories: T cell receptor signaling (FYN, CAMK4), activation (CD69, CD96), differentiation (STAT4, ETS1), and T cell-associated chemokine production (CCL5, CCL4). The high expression uniformity across these markers and their low expression outside the cluster indicates a well-defined T cell population without evidence of contamination or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-72dfb189c0"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "H1-0", "stance": "supports"}, {"gene": "MSI2", "stance": "supports"}], "rationale": "This cluster is characterized by co-expression of CD34 and PROM1 (CD133), the hallmark immunophenotype of hematopoietic stem and progenitor cells. CD34 shows strong enrichment (logfc 3.363, pct_in 0.977 vs pct_out 0.043), establishing this cluster definitively as CD34+ HSPCs. Supporting markers include cell-cycle regulators (CDK6, STMN1) and progenitor-associated genes (MSI2: Musashi 2, a known regulator of HSC self-renewal; H1-0, a histone variant enriched in stem cell states). The cluster exhibits the expected phenotype and marker gene profile of bone marrow or mobilized hematopoietic stem/progenitor cells in a blood specimen."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.7}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-75adde23f7"} +{"attempts": [{"codes": ["BEV004"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "TRBC1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "KRT81", "stance": "contradicts"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "The cluster is identified as T cells based on dominant expression of T cell receptor and lymphoid markers. TRBC1 (TCR beta chain) is definitive; LTB, LST1, IL7R, and CD52 are characteristic T cell markers. KLRB1, TNFRSF18, and TNFRSF4 indicate activated or effector T cells. Keratin genes (KRT81, KRT86) contradict T cell identity and suggest either doublets with epithelial cells or ambient epithelial RNA contamination in this endometrial tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-76fa626271"} +{"attempts": [{"codes": ["BEV004"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "EGFL7", "stance": "contradicts"}], "rationale": "The cluster is identified as hematopoietic stem cells based on the prominent expression of CD34 (logfc 3.217, 98.7% of cells) and PROM1/CD133 (logfc 2.184, 88.5% of cells), which are canonical HSC markers. The strong proliferation signature (TYMS, CDK6, STMN1, MCM2, PCNA) indicates active cell cycling consistent with bone marrow progenitors. IGLL1 expression is consistent with lymphoid-primed HSCs or early B-cell progenitor potential. EGFL7 (an endothelial marker) is unusual in an HSC cluster and may indicate minor contamination or a specialized HSC population with endothelial interaction."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.7}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-7a81a9a19f"} +{"attempts": [{"codes": ["BEV017"], "evidence": 19, "findings": [{"message": "The label 'CD8-positive, alpha-beta T cell' is not the name of CL:0000630 ('supporting cell'). 'CD8-positive, alpha-beta T cell' is the name of CL:0000625 (CD8-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 19, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000630", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LIME1", "stance": "supports"}], "rationale": "This cluster exhibits the canonical CD8+ T cell transcriptomic signature: complete T cell identity markers (CD3 complex, CD2, CD52), alpha-beta T cell receptor components (TRAC, TRBC2), CD8 lineage markers (CD8A, CD8B), and a full complement of cytotoxic granule proteins (granzymes K, M, H and CST7). The high expression of IL32, CCL5, and CD69 indicates these are activated effector T cells. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.9}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LIME1", "stance": "supports"}], "rationale": "This cluster exhibits the canonical CD8+ T cell transcriptomic signature: complete T cell identity markers (CD3 complex, CD2, CD52), alpha-beta T cell receptor components (TRAC, TRBC2), CD8 lineage markers (CD8A, CD8B), and a full complement of cytotoxic granule proteins (granzymes K, M, H and CST7). The high expression of IL32, CCL5, and CD69 indicates these are activated effector T cells. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD8-positive, alpha-beta T cell' is not the name of CL:0000630 ('supporting cell'). 'CD8-positive, alpha-beta T cell' is the name of CL:0000625 (CD8-positive, alpha-beta T cell)."], "seconds": 10.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-7c21a7ad85"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'effector gamma-delta T cell' is not the name of CL:0000911 ('effector T cell'). Closest names: CL:0000800 (mature gamma-delta T cell); CL:0000798 (gamma-delta T cell); CL:0020001 (V1delta gamma-delta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000911", "cell_type_label": "effector gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}], "rationale": "TRDC (TCR delta constant) is the defining marker for gamma-delta T cells. The cluster shows strong expression of cytotoxic molecules (CTSW, GNLY), NK cell receptors (KLRB1, KLRC1), and cytotoxic signaling components (FCER1G, TYROBP), along with chemokines (XCL1/XCL2) characteristic of effector lymphocytes. T cell markers (IL7R, CD7, TNFRSF18) and AREG confirm the activated effector phenotype. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.7}, {"answer": {"cell_type_id": "CL:0000800", "cell_type_label": "mature gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}], "rationale": "TRDC (TCR delta constant) is the defining marker for gamma-delta T cells. The cluster shows strong expression of cytotoxic molecules (CTSW, GNLY), NK cell receptors (KLRB1, KLRC1), and cytotoxic signaling components (FCER1G, TYROBP), along with chemokines (XCL1/XCL2) characteristic of mature effector gamma-delta lymphocytes. T cell markers (IL7R, CD7, TNFRSF18) and AREG confirm the activated mature phenotype. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'effector gamma-delta T cell' is not the name of CL:0000911 ('effector T cell'). Closest names: CL:0000800 (mature gamma-delta T cell); CL:0000798 (gamma-delta T cell); CL:0020001 (V1delta gamma-delta T cell)."], "seconds": 11.7}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-7ec8cd3664"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The cluster is characterized by a dominant C1Q signature (complement components C1QA, C1QB, C1QC), which is a hallmark of tissue-resident macrophages. This is combined with robust MHC class II expression (HLA-DR, HLA-DP, HLA-DQ genes) and CD74, consistent with antigen-presenting macrophages. CD14, AIF1, TYROBP, FCER1G, and MS4A6A confirm myeloid/monocyte lineage. In the kidney cortex context, macrophages with this transcriptional profile represent resident kidney macrophages. No contradictory markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-819cfbd986"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "LINC02446", "stance": "supports"}], "rationale": "CD8A and CD8B are definitive CD8+ T cell markers. SELL, CCR7, and KLF2 together indicate a naive T cell phenotype (these genes are upregulated in naive T cells and downregulated in activated/effector cells). LEF1 and CD7 are general T cell markers. LINC02446 is a T cell-associated lncRNA. The combination of strong CD8 markers with naive-associated genes clearly identifies this cluster as naive CD8+ T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-81b1e8f8f5"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}], "rationale": "Plasma cells are professional antibody-secreting cells characterized by high expression of immunoglobulin heavy and light chains, JCHAIN (for IgA/IgM), and XBP1 (ER unfolded protein response enabling massive immunoglobulin synthesis). All major markers in this cluster are consistent with plasma cell identity. The context of human endometrial tissue suggests these are likely plasma cells producing immunoglobulins as part of mucosal immune responses."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-879d085000"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "PSAP", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "MARCKS", "stance": "supports"}], "rationale": "This cluster is a macrophage population. The signature is dominated by HLA class II genes (HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DQB1) combined with CD74, which together indicate antigen-presenting capability characteristic of myeloid lineage cells. The co-expression of classical macrophage markers—LYZ (lysozyme), AIF1, CD14, CTSB/CTSS (cathepsins), C1QA (complement), and MARCKS—confirms macrophage identity. PSAP and CST3 reflect the lysosomal and immune functions of macrophages. All top markers consistently support macrophage annotation with no contradicting cell-type-specific markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-89c1241fbf"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "This cluster is definitively a T lymphocyte population. TRAC and TRBC2 encode the constant regions of T cell receptor alpha and beta chains—hallmark markers of T cells. CD3D and CD3E are core components of the T cell receptor complex. IL7R (IL-7 receptor), CD2, and CD52 are all well-established T cell surface markers. IL32 and LTB are cytokines characteristically produced by T cells. The combination of TCR constant region genes alongside CD3 complex components and IL-7 receptor makes this unambiguously a T cell cluster. Ribosomal proteins (RPS4Y1, RPS27, RPS29, RPL34) are housekeeping genes and do not inform cell-type identity. KLRB1 (CD161) is found on certain T cell subsets and supports rather than contradicts this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-8ab1b5fbd8"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}, {"gene": "PSAP", "stance": "supports"}, {"gene": "CD86", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}], "rationale": "The cluster shows a comprehensive monocyte signature with FCGR3A as the top marker, alongside classical monocyte markers (CST3, AIF1, CTSS) and myeloid-specific genes (FCER1G, TYROBP, MPEG1). The combination of high FCGR3A expression and broad monocyte marker representation is highly consistent with the monocyte lineage. No contradicting lineage markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-8c07cf76ca"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "The cluster is identified as gamma-delta T cells based on TRDC expression (T cell receptor delta chain constant region), the defining marker for this lineage. The strong cytotoxic signature (GNLY, NKG7, CTSW, GZMB) indicates activated/effector gamma-delta T cells. CD7 confirms T cell lineage, while KLRD1/KLRC1/KLRF1 (NK-type receptors) are characteristically expressed by gamma-delta T cells. Chemokines (XCL1, XCL2, CCL5) and cytotoxic molecules are consistent with activated cytotoxic lymphocytes. This profile is typical of gamma-delta T cells in secondary lymphoid tissue (tonsil)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-8d82b1a772"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "DUSP2", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}], "rationale": "Strong CD8+ T cell signature with canonical markers: CD8A/B (lineage-defining), TCR complex components (CD3E/G, TRAC, TRGC2), and cytotoxic effector molecules (NKG7, GZMA, CTSW, KLRK1). All high logfc, high expression in cluster, low expression outside. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.2}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-95367720e6"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'mature B cell' is not the name of CL:0000818 ('transitional stage B cell'). 'mature B cell' is the name of CL:0000785 (mature B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000818", "cell_type_label": "mature B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "BACH2", "stance": "supports"}], "rationale": "This cluster is clearly defined by canonical B cell markers (MS4A1/CD20, CD79A, IGKC, BANK1) with strong HLA class II expression (HLA-DRA/DRB1/DQA1/DPA1) and CD74, indicating a mature, activated B cell population. The high prevalence of these markers across 80-97% of cells, combined with low expression in other clusters (pct_out 0.013-0.551 for B-specific genes), strongly supports B cell identity. No contradictory markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.6}, {"answer": {"cell_type_id": "CL:0000785", "cell_type_label": "mature B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "BACH2", "stance": "supports"}], "rationale": "This cluster is defined by canonical B cell markers (MS4A1/CD20, CD79A, IGKC, BANK1) with exceptionally strong HLA class II expression (HLA-DRA/DRB1/DQA1/DPA1) and CD74, indicating a mature, activated B cell population capable of antigen presentation. The prominence of IGKC (antibody expression) at logfc 1.932 and the robust HLA class II signature support mature rather than transitional B cell identity. All markers show high prevalence (80-97% of cells) with low expression outside the cluster, strongly supporting mature B cell identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'mature B cell' is not the name of CL:0000818 ('transitional stage B cell'). 'mature B cell' is the name of CL:0000785 (mature B cell)."], "seconds": 22.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-9814423bdc"} +{"attempts": [{"codes": ["BEV004"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "contradicts"}], "rationale": "This cluster is clearly natural killer cells based on the combined expression of canonical NK cell markers and cytotoxic machinery. NKG7 (NK cell granule protein 7) with extremely high logfc (2.954) and near-universal expression (pct_in 0.991) is one of the most reliable NK cell identifiers. NK-specific receptors KLRD1, KLRF1, and KLRB1 are all prominently expressed. FCGR3A (CD16) is a classic NK marker. The cytotoxic granule proteins (GNLY, GZMB, PRF1, GZMA, CST7, CTSW) are consistent with NK cell function. CD247 (CD3 zeta chain), which is part of the T cell receptor complex, is unexpected in this population and suggests either minor T cell contamination, technical artifact, or an atypical NK cell state, making it contradictory to the primary NK cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-98402e60db"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CTSD", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "This cluster is a macrophage population. The marker signature is dominated by HLA class II genes (HLA-DR, HLA-DP, HLA-DQ) with CD74 (MHC class II invariant chain), indicating professional antigen-presenting cells. The defining feature is the strong co-expression of complement component 1q subunits (C1QA, C1QB, C1QC), which is a hallmark of tissue macrophages. Additional supporting markers include APOE and LYZ (lysozyme), both characteristic of macrophages, along with lysosomal enzymes (CTSD, CST3) and myeloid signaling molecules (TYROBP). This phenotype is consistent with tissue-resident macrophages in the bladder mucosa. No contradicting markers indicating alternative cell types (e.g., lymphocytes, epithelial cells) are prominent."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-9d243229e7"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "MPO and AZU1 are neutrophil-specific granule proteins. RNASE2 and RNASE3 are neutrophil serine proteases. LYZ (lysozyme), S100A8 (calprotectin), and SRGN (serglycin) are all characteristic of neutrophil granules and cytoplasm. The high pct_in values (0.83–1.0) for these markers and their high logfc values confirm this is a neutrophil cluster. The elevated cell cycle genes (TYMS, PCNA, CDC20) suggest proliferating or immature neutrophils, but the core identity is unambiguous."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-9d2a6afe3f"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'conventional dendritic cell, type 2, CD1c+' is not the name of CL:0000622 ('acinar cell'). Closest names: CL:0000990 (conventional dendritic cell); CL:0002010 (pre-conventional dendritic cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000622", "cell_type_label": "conventional dendritic cell, type 2, CD1c+", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The cluster shows a classic cDC2 signature: FCER1A is the strongest marker and is characteristic of dendritic cells; CD1C is the defining marker for the CD1c+ conventional dendritic cell subset; strong HLA class II expression (DRA/DRB1/DRB5/DPA1/DPB1/CD74) reflects their role as professional antigen-presenting cells; ITGAX (CD11c) and myeloid markers (LYZ, CST3) confirm myeloid dendritic cell lineage. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.1}, {"answer": {"cell_type_id": "CL:0000990", "cell_type_label": "conventional dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "Classic conventional dendritic cell signature: FCER1A and CD1C as strongest markers define the cDC lineage; comprehensive HLA class II expression (DRA/DRB1/DRB5/DPA1/DPB1/CD74) reflects professional antigen-presenting function; ITGAX (CD11c) and myeloid markers (LYZ, CST3) confirm myeloid dendritic cell identity. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'conventional dendritic cell, type 2, CD1c+' is not the name of CL:0000622 ('acinar cell'). Closest names: CL:0000990 (conventional dendritic cell); CL:0002010 (pre-conventional dendritic cell)."], "seconds": 18.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-9e8b98aab5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'intestinal crypt stem cell' is not the name of CL:0002241 ('pulmonary interstitial fibroblast'). 'intestinal crypt stem cell' is the name of CL:0002250 (intestinal crypt stem cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002241", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "This cluster exhibits a robust proliferation signature characteristic of intestinal stem cells and transit-amplifying cells in colon crypts. The markers encompass all phases of active cell cycle regulation (MKI67, CDK1, CENPF), DNA replication (TOP2A, TYMS, PCLAF), mitotic machinery (NUSAP1, ASPM, TUBA1B, TUBB, STMN1), and cell cycle checkpoint control (UBE2C). The high logfc values and near-universal expression (pct_in 0.7-1.0) combined with low pct_out (<0.1 for most cell cycle markers) strongly indicate a distinct proliferative compartment, consistent with the highly dynamic crypt epithelial stem cell niche of the colon."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.3}, {"answer": {"cell_type_id": "CL:0002250", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "This cluster exhibits a robust proliferation signature characteristic of intestinal stem cells and transit-amplifying cells in colon crypts. The markers encompass all phases of active cell cycle regulation (MKI67, CDK1, CENPF), DNA replication (TOP2A, TYMS, PCLAF), mitotic machinery (NUSAP1, ASPM, TUBA1B, TUBB, STMN1), and cell cycle checkpoint control (UBE2C). The high logfc values and near-universal expression (pct_in 0.7-1.0) combined with low pct_out (<0.1 for most cell cycle markers) strongly indicate a distinct proliferative compartment, consistent with the highly dynamic crypt epithelial stem cell niche of the colon."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'intestinal crypt stem cell' is not the name of CL:0002241 ('pulmonary interstitial fibroblast'). 'intestinal crypt stem cell' is the name of CL:0002250 (intestinal crypt stem cell)."], "seconds": 9.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-a321096724"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79B", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "RCSD1", "stance": "supports"}], "rationale": "The marker profile is characteristic of B lymphocytes. CD79A and CD79B are core components of the B cell receptor complex with high logfc (1.49 and 2.91). IGHM, IGLL1, VPREB3, and VPREB1 are immunoglobulin and pre-BCR components essential to B cell identity. Classic B cell markers CD24, CD37, and MZB1 are highly expressed. IGKC (immunoglobulin kappa chain) supports B cell lineage. TCF4 and RCSD1 are B cell-enriched transcription factors. The coherent expression of BCR components alongside developmental markers definitively identifies this cluster as B cells with no contradictory markers indicating contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-a33f382e85"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 18, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000817 ('precursor B cell'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000817 (precursor B cell) is defined as having neprilysin (MME) on the membrane, but MME is detected in only 3% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000817", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "LY9", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "All markers are B cell-specific or B cell-associated genes. The combination of immunoglobulin heavy chains (IGHM, IGHD), light chains (IGKC, IGLC2, IGLC3), and B cell surface markers (MS4A1/CD20, CD79A/B) with very high pct_in values indicates a homogeneous, mature naive B cell population. The presence of both IgM and IgD (IGHM, IGHD) without plasma cell differentiation markers confirms naive/mature B cell status rather than plasma cells or germinal center B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.5}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "LY9", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "This cluster represents naive B cells (CL:0000788), not precursor B cells. The markers establish a mature, resting B cell population: CD20+ (MS4A1) and CD79A/B+ cells express both IgM (IGHM) and IgD (IGHD) without class switching, indicating cells in the naive/follicular compartment that have not encountered antigen. High expression of B cell markers (CD37, BANK1, SPIB, LY9/CD229, TNFRSF13C/BAFFR) with very high pct_in values (0.988–1.0) confirms a homogeneous B cell population. The presence of VPREB3 reflects surrogate light chain persistence occasionally seen in naive B cells. Crucially, this cluster lacks MME (neprilysin), disqualifying precursor B cell assignment—precursor B cells require MME+ phenotype and are CD20-negative, neither of which applies here."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000817 ('precursor B cell'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "object id: CL:0000817 (precursor B cell) is defined as having neprilysin (MME) on the membrane, but MME is detected in only 3% of the cluster's cells."], "seconds": 16.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ac7ec2b016"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004", "BEV017"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'plasmablast' is not the name of CL:0000815 ('regulatory T cell'). 'plasmablast' is the name of CL:0000980 (plasmablast).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV026"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000980 (plasmablast) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}, {"gene": "MT-ATP6", "stance": "supports"}, {"gene": "MT-CO2", "stance": "supports"}, {"gene": "MT-ND2", "stance": "supports"}, {"gene": "MT-ND5", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "Immunoglobulin genes (IGKC, IGHG1, IGHG3) combined with ELL2 (plasma cell-specific elongation factor) and high mitochondrial content (reflecting active antibody synthesis and secretion) are canonical markers of plasma cells. HDC (histidine decarboxylase) typically marks mast cells/basophils and is incongruent with plasma cell identity, suggesting possible minor contamination or a mixed population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.6}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "plasmablast", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}, {"gene": "MT-ATP6", "stance": "supports"}, {"gene": "MT-CO2", "stance": "supports"}, {"gene": "MT-ND2", "stance": "supports"}, {"gene": "MT-ND5", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "Immunoglobulin genes (IGKC, IGHG1, IGHG3) combined with ELL2 (elongation factor upregulated during antibody synthesis) are canonical markers of antibody-secreting cells. High mitochondrial gene expression reflects the metabolic demands of active protein synthesis. Plasmablasts are differentiated from mature plasma cells (CL:0000786) by lower syndecan-1 (SDC1) expression; only 8% of this cluster expresses SDC1, typical of plasmablasts rather than terminally differentiated plasma cells. HDC expression is incongruent with plasmablast identity and suggests minor contamination or mixed populations."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells."], "seconds": 25.6}, {"answer": {"cell_type_id": "CL:0000980", "cell_type_label": "plasmablast", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}, {"gene": "MT-ATP6", "stance": "supports"}, {"gene": "MT-CO2", "stance": "supports"}, {"gene": "MT-ND2", "stance": "supports"}, {"gene": "MT-ND5", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "Immunoglobulin genes (IGKC, IGHG1, IGHG3) combined with ELL2 (elongation factor upregulated during antibody synthesis) are canonical markers of antibody-secreting cells. High mitochondrial gene expression reflects the metabolic demands of active protein synthesis. The marker profile is consistent with plasmablasts, differentiated but not terminally differentiated B cells. HDC (histidine decarboxylase) expression is incongruent with plasmablast identity and suggests minor contamination or heterogeneity in the cluster."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'plasmablast' is not the name of CL:0000815 ('regulatory T cell'). 'plasmablast' is the name of CL:0000980 (plasmablast)."], "seconds": 23.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ad2d591627"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "Natural Killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "TRDC", "stance": "contradicts"}, {"gene": "CD247", "stance": "contradicts"}], "rationale": "Strong consensus of NK cell-specific markers (NKG7, KLRC1, KLRD1, HOPX, KLRB1) and cytotoxic effector molecules (GNLY, GZMA, GZMB, PRF1) indicate Natural Killer cells. TCR genes (TRDC, CD247) present at substantial levels suggest possible contamination with γδ T cells or technical doublets, warranting classification as contradicting markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.4}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "Gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "KLRC1", "stance": "contradicts"}, {"gene": "KLRD1", "stance": "contradicts"}, {"gene": "KLRB1", "stance": "contradicts"}], "rationale": "The detection of CD3E in 65% of cells (logfc 0.59) by validation definitively excludes Natural Killer cells, which are CD3E-negative by definition. The high expression of TRDC (TCR delta chain, logfc 2.107, pct_in 0.894) is the defining feature of gamma-delta T cells, together with CD247 (CD3 zeta) and CD7 (pan-T cell marker). Strong cytotoxic molecule expression (GNLY, GZMA, GZMB, PRF1, CST7) indicates activated effector gamma-delta T cells. NK cell receptors (KLRC1, KLRD1, KLRB1) are typically NK-associated and contradict gamma-delta T cell identity, though they can rarely be expressed on minor populations."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59)."], "seconds": 31.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ae89c1380f"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "THBS1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}], "rationale": "The cluster is defined by a characteristic macrophage signature dominated by LYZ (lysozyme M), a canonical macrophage marker with near-universal expression (95% in-cluster, 34% out-cluster). Supporting markers include complement receptor C5AR1, AIF1 (IBA1), the myeloid signaling adapter TYROBP, and S100A8/A9 (inflammatory myeloid proteins). ECM remodeling genes (THBS1, VCAN, TIMP1) and the urokinase receptor PLAUR indicate tissue-resident macrophage function. No contradicting markers detected."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b269766ee9"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "EMP3", "stance": "supports"}], "rationale": "This cluster exhibits the canonical naive T cell signature. SELL (CD62L) and CCR7 encode lymph node-homing receptors expressed on naive T cells. KLF2 is a master regulator of naive T cell development and quiescence. LEF1 (TCF/LEF family) participates in TCF signaling pathways active in naive lymphocytes. IL7R (CD127) is the IL-7 receptor expressed on T cells. EMP3 marks cells in the naive state. The remaining top markers (ribosomal proteins, TMSB10, LDHB, TXNIP) are general housekeeping/metabolic genes present across cell types and do not contradict naive T cell identity. The tonsil tissue context is consistent with naive T cell enrichment in lymphoid tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.7}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b322bece33"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 77% of the cluster's cells, more than in the others (logfc 0.70).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'cytotoxic T lymphocyte' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CD3D", "stance": "contradicts"}, {"gene": "CD3G", "stance": "contradicts"}, {"gene": "TRGC2", "stance": "contradicts"}], "rationale": "This cluster is dominated by NK cell-specific markers, particularly NKG7 (99.6%), GNLY (93%), and KLRD1/KLRG1 (NK receptors). The complete cytotoxic machinery (granzymes A/B/H, perforin) is uniformly expressed. CD3D/CD3G/TRGC2 suggest minor T cell contamination or admixture in an otherwise pure NK population, but the overwhelming frequency and concordance of canonical NK markers leaves no ambiguity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.6}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "cytotoxic T lymphocyte", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The cluster expresses CD3E at 77% (logfc 0.70), which is incompatible with NK cell definition. This indicates a T cell population. The very high expression of cytotoxic machinery (NKG7 99.6%, GNLY 93%, granzymes A/B/H, perforin) combined with robust CD3 markers (CD3D, CD3G, and especially CD3E) identifies this as a cytotoxic T lymphocyte population. Both CTLs and NK cells share cytotoxic granule genes, but the presence of CD3E at 77% definitively indicates T cell lineage. KLRD1/KLRG1 reflect NK receptors that can be expressed on activated or memory CTLs."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 77% of the cluster's cells, more than in the others (logfc 0.70)."], "seconds": 23.9}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The cluster expresses CD3D and CD3G at high frequencies (85.7% and 62.9%), establishing T cell lineage. Very high expression of cytotoxic granule genes (NKG7 99.6%, GNLY 93%, granzymes A/B/H, perforin PRF1) combined with robust CD3 markers identifies this as a CD8+ T cell population. KLRD1 and KLRG1 reflect NK receptors expressed on activated or memory CD8+ T cells. The co-expression of chemokines (CCL5, CCL4) and IL32 is consistent with activated cytotoxic T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cytotoxic T lymphocyte' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell)."], "seconds": 10.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b51a9f2d53"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV026"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'regulatory T cell' is not the name of CL:0000819 ('B-1 B cell'). 'regulatory T cell' is the name of CL:0000815 (regulatory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000819 (B-1 B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000819 (B-1 B cell) is defined as having membrane-spanning 4-domains subfamily A member 1 (MS4A1) on the membrane, but MS4A1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000819", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "CTLA4", "stance": "supports"}, {"gene": "IL10", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "KLRB1", "stance": "contradicts"}], "rationale": "The co-expression of CTLA4 and IL10 is highly specific for regulatory T cells. CTLA4 is a defining marker of Tregs (especially activated Tregs), and IL10 is their signature immunosuppressive cytokine. IKZF3 and RGS1 support Treg identity through their roles in Treg differentiation and function. KLRB1 (NKR-P1B) is atypical for Tregs and more commonly associated with NK cells, suggesting either an activated/effector Treg subset with NK-associated marker expression, or minimal contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.4}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "CTLA4", "stance": "supports"}, {"gene": "IL10", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "KLRB1", "stance": "contradicts"}], "rationale": "CTLA4 and IL10 are defining markers of regulatory T cells. CTLA4 is the canonical Treg checkpoint molecule expressed on the cell surface, and IL10 is the signature immunosuppressive cytokine. IKZF3 (IKAROS) and RGS1 are key transcriptional and functional regulators of Treg differentiation and suppressive function. MAF is a transcription factor that promotes IL-10 production in Tregs. KLRB1 (NKR-P1B), a marker typically associated with NK cells, is atypical for conventional Tregs but may indicate an activated or specialized Treg subset, or trace contamination. The dominant marker profile unambiguously indicates regulatory T cell identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'regulatory T cell' is not the name of CL:0000819 ('B-1 B cell'). 'regulatory T cell' is the name of CL:0000815 (regulatory T cell).", "object id: CL:0000819 (B-1 B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 2% of the cluster's cells.", "object id: CL:0000819 (B-1 B cell) is defined as having membrane-spanning 4-domains subfamily A member 1 (MS4A1) on the membrane, but MS4A1 is detected in only 8% of the cluster's cells."], "seconds": 16.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b5ea73db74"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'neutrophil' is not the name of CL:0000738 ('leukocyte'). 'neutrophil' is the name of CL:0000775 (neutrophil).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000738", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE6", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}, {"gene": "FOS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CD14", "stance": "contradicts"}, {"gene": "FCN1", "stance": "contradicts"}, {"gene": "VCAN", "stance": "contradicts"}, {"gene": "CSTA", "stance": "contradicts"}, {"gene": "CST3", "stance": "contradicts"}], "rationale": "S100A8 and S100A9 are the canonical neutrophil markers—they form calprotectin, the S100A8/A9 heterodimer that is diagnostic for neutrophils. Both have exceptionally high logfc (~3.19) and are expressed in ~99.4% of cluster cells, which is definitive. CSF3R (G-CSF receptor) marks neutrophil lineage differentiation. LYZ and the neutrophil-specific ribonucleases (RNASE2, RNASE6) are core neutrophil granule proteins. ITGAM (CD11b), FCER1G, and TYROBP support immune function. However, the presence of monocyte markers (CD14, FCN1, VCAN, CSTA, CST3) indicates this cluster likely contains some doublets or monocyte contamination, which is not uncommon in blood samples."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 57.4}, {"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE6", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}, {"gene": "FOS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CD14", "stance": "contradicts"}, {"gene": "FCN1", "stance": "contradicts"}, {"gene": "VCAN", "stance": "contradicts"}, {"gene": "CSTA", "stance": "contradicts"}, {"gene": "CST3", "stance": "contradicts"}], "rationale": "S100A8 and S100A9 are canonical neutrophil markers—they form calprotectin (S100A8/A9 heterodimer), diagnostic for neutrophils. Both have exceptionally high logfc (~3.19) and are expressed in ~99.4% of cluster cells. CSF3R (G-CSF receptor) marks neutrophil lineage differentiation. LYZ and neutrophil-specific ribonucleases (RNASE2, RNASE6) are core neutrophil granule proteins. ITGAM (CD11b), FCER1G, and TYROBP support immune function typical of neutrophils. The presence of monocyte markers (CD14, FCN1, VCAN, CSTA, CST3) suggests doublet contamination or minor monocyte presence, not uncommon in blood samples."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'neutrophil' is not the name of CL:0000738 ('leukocyte'). 'neutrophil' is the name of CL:0000775 (neutrophil)."], "seconds": 9.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b7c75983d8"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}], "rationale": "MHC class II genes (HLA-DR/DP/DQ) and CD74 indicate antigen-presenting cell function. Myeloid lineage markers LYZ (lysozyme), AIF1 (allograft inflammatory factor 1), and TYROBP (myeloid signaling) are characteristic of macrophages. Additional immune cell markers CST3, MS4A6A, and RGS1 support myeloid identity. This expression signature is consistent with tissue-resident macrophages in kidney cortex."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b864a5744b"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'gamma-delta T cell' is not the name of CL:0000794 ('CD8-positive, alpha-beta cytotoxic T cell'). 'gamma-delta T cell' is the name of CL:0000798 (gamma-delta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000794", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "ITGAX", "stance": "contradicts"}], "rationale": "The cluster is identified as gamma-delta T cells based on the defining markers TRDC (TCR delta) and TRGC2 (TCR gamma constant) both present with high logfc values. This indicates T cells expressing gamma-delta T cell receptors rather than conventional alpha-beta TCRs. The high expression of cytotoxic markers (NKG7, GNLY, CTSW, CST7, GZMA) and multiple killer cell immunoglobulin-like receptors (KLRK1, KLRF1, KLRB1, KLRD1) identifies these as cytotoxic, likely activated gamma-delta T cells. Pan-T cell markers CD2 and CD7 further support T cell identity. SELL (L-selectin) is consistent with some gamma-delta T cell subsets. ITGAX (CD11c) is atypical for gamma-delta T cells, being primarily a dendritic cell and myeloid marker, and may indicate either a minor doublet population or an unusual activated subset."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.6}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "ITGAX", "stance": "contradicts"}], "rationale": "The cluster is identified as gamma-delta T cells based on the defining markers TRDC (TCR delta chain) and TRGC2 (TCR gamma constant region) both present with high logfc values, indicating T cells expressing gamma-delta T cell receptors. High expression of cytotoxic markers (NKG7, GNLY, CTSW, CST7, GZMA) and multiple killer cell immunoglobulin-like receptors (KLRK1, KLRF1, KLRB1, KLRD1) identifies these as cytotoxic gamma-delta T cells. Pan-T cell markers CD2 and CD7 further support T cell identity. SELL (L-selectin) is consistent with gamma-delta T cell subsets. ITGAX (CD11c) is atypical for gamma-delta T cells, being primarily a dendritic cell and myeloid marker, and may indicate a minor doublet population or contamination."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'gamma-delta T cell' is not the name of CL:0000794 ('CD8-positive, alpha-beta cytotoxic T cell'). 'gamma-delta T cell' is the name of CL:0000798 (gamma-delta T cell)."], "seconds": 10.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-b95794dcf3"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHGP", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "SPCS1", "stance": "supports"}, {"gene": "TXNDC5", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "PRDX4", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "CYTOR", "stance": "supports"}, {"gene": "ANKRD28", "stance": "supports"}], "rationale": "This cluster is clearly a plasma cell population. The abundance of immunoglobulin genes (IGKC, IGHA1, IGLC1/2/3, IGHG1/3/P) and joining chain (JCHAIN) are definitive markers of antibody-secreting cells. The high expression of ER protein processing genes (SSR4, SEC11C, SPCS1), unfolded protein response regulator (XBP1), and protein quality control genes (TXNDC5, FKBP11, PRDX4, DERL3) reflects the enormous protein synthesis and secretory burden characteristic of plasma cells. MZB1 further supports this identity. The mix of different immunoglobulin isotypes (IgA, IgG) and light chains indicates a diverse antibody-secreting population, consistent with a polyclonal plasma cell compartment in bladder tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ba5f0288e7"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "This cluster is clearly T lymphocytes. The top markers are dominated by T cell-specific genes: the CD3 complex components (CD3D, CD3E, CD3G) with high logfc and pct_in, and T cell receptor constant regions (TRAC, TRBC2), which are absolutely specific to T cells. CD7 is a pan-T cell marker, and the high expression of CD69 (logfc 1.391, pct_in 0.888) indicates activated T cells. IL7R and IL32 are additional supporting markers for T cell identity. The high pct_in values (>78% for CD3D, CD3E, TRAC, TRBC2) confirm these are T cell-specific genes highly expressed in this cluster. No markers suggest doublets or mixed identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-be2c0ee626"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "PSAP", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}], "rationale": "This cluster is clearly composed of monocytes based on the classical monocyte/myeloid marker signature. FCN1 (ficolin-1) is a particularly strong indicator of monocytes, especially classical monocytes, with high expression across 91.7% of the cluster. The cluster also expresses characteristic monocyte markers including AIF1 (IBA1), CST3 (cystatin C), CTSS (cathepsin S), FCER1G, TYROBP (DAP12), and MS4A7, which are all involved in immune function and antigen presentation. HLA-DRA indicates antigen-presenting capability consistent with monocytes. The high prevalence of lysosomal proteins (CTSS, PSAP) and the overall gene expression pattern are consistent with the metabolically active, phagocytic nature of monocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-c5e3a0ec1f"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 12, "findings": [{"message": "The label 'regulatory T cell' is not the name of CL:0000785 ('mature B cell'). 'regulatory T cell' is the name of CL:0000815 (regulatory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000785 (mature B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000785 (mature B cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 79% of the cluster's cells, more than in the others (logfc 0.89).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000785", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "FOXP3 is the master transcription factor defining regulatory T cells and shows the lowest pct_out (0.002) indicating highly selective expression. IL2RA (CD25) and CTLA4 are canonical Treg markers, with CTLA4 having very low expression outside the cluster (pct_out: 0.032). TIGIT is a coinhibitory receptor enriched in Tregs. TNFRSF4 and TNFRSF18 are involved in Treg biology. CD3D, CD3G, TRAC, and T cell receptor genes confirm T cell lineage. The high pct_in for most markers and strong logfc values across the panel unambiguously support Treg identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.7}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "FOXP3 is the master transcription factor defining regulatory T cells, with extremely restricted expression outside the cluster (pct_out: 0.002). IL2RA (CD25) and CTLA4 are canonical Treg markers with low external expression (pct_out: 0.102 and 0.032 respectively). TIGIT and TNFRSF4/TNFRSF18 are coinhibitory receptors enriched in Tregs. CD3D, CD3G, TRAC, TRBC1, and TRBC2 confirm T cell lineage and TCR expression. CD27 is a marker of activated/memory T cells. The high logfc values and pct_in frequencies across the marker panel unambiguously support Treg identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'regulatory T cell' is not the name of CL:0000785 ('mature B cell'). 'regulatory T cell' is the name of CL:0000815 (regulatory T cell).", "object id: CL:0000785 (mature B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 0% of the cluster's cells.", "object id: CL:0000785 (mature B cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 79% of the cluster's cells, more than in the others (logfc 0.89)."], "seconds": 11.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-c99aec2a45"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD82", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}], "rationale": "This cluster is characterized by canonical B cell markers including CD79A/B (B cell receptor complex), MS4A1/CD20, and CD19, all with very high expression (logfc 1.6–3.8) and specificity. The high expression of HLA class II genes and CD74 (invariant chain) indicates mature, antigen-presenting B cells. IGKC confirms immunoglobulin production. The markers are largely consistent, though VPREB3 (pre-B cell marker) and JCHAIN (plasma cell marker) suggest the cluster may contain some developmental variants or activated cells, but these do not contradict the overall B cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ccd8ad8cc1"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}], "rationale": "The cluster is unambiguously mast cells based on highly specific marker genes. TPSAB1, TPSB2, and CPA3 are mast cell-restricted serine proteases stored in secretory granules. HDC catalyzes histamine synthesis—mast cells are the primary histamine source in tissue. HPGDS produces prostaglandin D2, a cardinal mast cell mediator. GATA2 is a master transcription factor for mast cell development. SLC18A2 (VMAT2) packages histamine into granules. IL33R and RHEX support mast cell function in cytokine response and degranulation. No markers contradict this identification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.9}, {"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [], "rationale": "The marker profile strongly indicates mast cells: TPSAB1, TPSB2, and CPA3 are mast cell-restricted serine proteases; HDC catalyzes histamine synthesis; HPGDS produces prostaglandin D2; GATA2 is a master transcription factor for mast cell development; SLC18A2 packages histamine into granules. However, the Cell Ontology definition of CL:0000097 (mast cell) requires CCR3 expression, which is absent in this cluster (0% of cells). This fundamental discrepancy between the marker profile (which is unambiguously mast cell) and the required CCR3 surface marker cannot be resolved without access to alternative mast cell terms in Cell Ontology or clarification on whether this represents a mast cell variant lacking CCR3 in this tissue context."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 23.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ceffe8616a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000019 ('sperm'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000019", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "Simultaneous high expression of IGHM and IGHD with TCL1A, CD79A/B, MS4A1, CD19, and VPREB3 is the canonical signature of naive mature B cells before antigen encounter. The near-universal expression within the cluster (pct_in 0.75–1.0) and low contamination (pct_out <0.4 for most markers) confirm homogeneity. Supporting markers include IGKC (B cell immunoglobulin), CD37 and CD72 (B cell co-receptors), and CXCR4 (lymphoid homing). MHC class II genes reflect their antigen-presenting capacity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.6}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "Simultaneous high expression of IGHM and IGHD with TCL1A, CD79A/B, MS4A1, CD19, and VPREB3 is the canonical signature of naive mature B cells before antigen encounter. The near-universal expression within the cluster (pct_in 0.75–1.0) and low contamination (pct_out <0.4 for most markers) confirm homogeneity. Supporting markers include IGKC (B cell immunoglobulin), CD37 and CD72 (B cell co-receptors), FCMR (Fc receptor for IgM), and CXCR4 (lymphoid homing). MHC class II genes reflect their antigen-presenting capacity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000019 ('sperm'). 'naive B cell' is the name of CL:0000788 (naive B cell)."], "seconds": 10.2}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-d44564d7f6"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}], "rationale": "This cluster exhibits a classic monocyte expression signature. LYZ is a canonical monocyte/macrophage marker with very high logfc (3.952) and prevalence (98% within cluster). The S100A8/A9 pair (calprotectin) are hallmark markers of classical monocytes, with both showing high logfc (3.770, 3.540) and ~98% expression in the cluster. FCN1 (Ficolin-1) is a well-established monocyte marker (logfc 2.571). Supporting myeloid lineage are TYROBP (DAP12, 2.448), AIF1/Iba1 (2.421), and FCER1G (1.954). CTSS and HLA-DRA indicate antigen-processing capacity typical of monocytes. The S100 family members (A6, A11, A12) and CSTA further support the monocytic phenotype. No markers contradict this assignment (no T cell, B cell, or DC-specific markers are prominent). The cluster represents classical or intermediate monocytes in kidney cortex tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.3}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-d7d3163b78"} +{"attempts": [{"codes": ["BEV004"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "ACTA2", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "PPP1R14A", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}, {"gene": "TPSAB1", "stance": "contradicts"}], "rationale": "The cluster is clearly smooth muscle cells based on a dominant signature of well-established smooth muscle markers: ACTA2 (alpha-smooth muscle actin, the canonical smooth muscle marker), TAGLN (transgelin), contractile proteins (TPM1, TPM2, MYL9), and smooth muscle-associated regulatory proteins (CALD1, PPP1R14A). This is consistent with the myometrium of the endometrium. The presence of TPSB2 and TPSAB1 (tryptase genes; mast cell markers) is atypical for smooth muscle and likely indicates some contamination from mast cell doublets, but the overwhelming evidence supports the primary cell type identity as smooth muscle."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.4}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-d929ec7963"} +{"attempts": [{"codes": ["BEV004"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "FCMR", "stance": "contradicts"}], "rationale": "Strong expression of T cell receptor (TRAC), pan-T cell markers (CD3E, CD2), and a definitive naive T cell signature (IL7R, CCR7, CD27, SELL/CD62L). CD4 expression identifies these as helper T cells. FCMR expression is atypical for T cells and suggests minor B cell contamination or doublets, but does not override the dominant naive CD4+ T cell phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.6}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-e1bfaa2341"} +{"attempts": [{"codes": ["BEV017"], "evidence": 15, "findings": [{"message": "The label 'cytotoxic T lymphocyte' is not the name of CL:0000911 ('effector T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000911", "cell_type_label": "cytotoxic T lymphocyte", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "This cluster exhibits a strong cytotoxic T lymphocyte (CTL) profile. Key supporting evidence: (1) CD247 and CD7 establish T cell lineage; (2) granzymes (GZMA, GZMK, GZMM) and NKG7 indicate cytotoxic effector function; (3) killer cell lectin-like receptors (KLRD1, KLRB1, KLRC1), while typically NK-associated, are also expressed on activated CTLs; (4) chemokines XCL1/XCL2 and CCL4/CCL5 are characteristic of effector T cells; (5) CD69 marks T cell activation. CST7 (cystatin) is a marker of cytotoxic cells. All top markers cohesively support CTL identity with no conflicting cell-type markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.0}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "This cluster exhibits a strong cytotoxic T cell profile. Key supporting evidence: (1) CD247 and CD7 establish T cell lineage; (2) granzymes (GZMA, GZMK, GZMM) and NKG7 indicate cytotoxic effector function; (3) killer cell lectin-like receptors (KLRD1, KLRB1, KLRC1) are expressed on cytotoxic T cells; (4) chemokines XCL1/XCL2 and CCL4/CCL5 are characteristic of effector T cells; (5) CD69 marks T cell activation. CST7 is a marker of cytotoxic cells. All top markers cohesively support cytotoxic T cell identity with no conflicting cell-type markers."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cytotoxic T lymphocyte' is not the name of CL:0000911 ('effector T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell)."], "seconds": 10.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-e712a5eb84"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "CD82", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}], "rationale": "Cluster shows high expression of immunoglobulin genes (IGHM, IGHD, IGKC), B cell receptor complex components (CD79A, CD79B), and canonical B cell surface markers (MS4A1/CD20, CD19, CD24, CD37, CD82). MHC class II genes (HLA-DRA, HLA-DRB1, etc.) support B cell identity as B cells are professional antigen-presenting cells. VPREB3 and FCMR further confirm B cell lineage. No contradicting markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-e7ae6683c5"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}], "rationale": "This cluster is clearly a CD8+ T cell population based on high expression of CD8A and CD8B (the defining markers of cytotoxic T lymphocytes). The top-ranked markers include multiple genes encoding cytotoxic granule proteins (GZMA, GZMK, CST7, CTSW) and effector chemokines (CCL5, CCL4), indicating these are activated effector CD8+ T cells. NKG7 and KLRG1 are consistent with effector T cell function. CXCR3 supports T cell identity, particularly Th1-like CD8+ populations. No markers clearly contradict this identification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.8}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ec5325a064"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'cytotoxic T lymphocyte' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "cytotoxic T lymphocyte", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}], "rationale": "The marker signature is dominated by genes encoding cytotoxic granule proteins (GNLY, GZMB, GZMA, PRF1, CST7, CTSW), which are hallmarks of cytotoxic lymphocytes. The presence of CD247 (CD3-zeta component of the TCR) indicates these are T cells rather than NK cells. NKG7, KLRD1 (CD94), and CCL5 are consistent with activated CTLs. FYN and ETS1 are involved in T cell signaling and transcriptional regulation. FGFBP2 is characteristic of highly activated cytotoxic cells. This profile strongly indicates mature cytotoxic T lymphocytes (CD8+ T cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.7}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}], "rationale": "The marker signature is dominated by genes encoding cytotoxic granule proteins (GNLY, GZMB, GZMA, PRF1, CST7, CTSW), which are hallmarks of cytotoxic lymphocytes. CD247 (CD3-zeta component of the TCR) indicates these are T cells, and specifically alpha-beta T cells. KLRD1 (CD94) and NKG7 are consistent with CD8+ T cells. CCL5, FYN, and ETS1 are involved in T cell signaling and transcriptional regulation. FGFBP2 is characteristic of highly activated cytotoxic cells. This profile strongly indicates CD8-positive, alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cytotoxic T lymphocyte' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell)."], "seconds": 12.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ed05c45d83"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'intermediate monocyte' is not the name of CL:0000857 ('slow muscle myoblast'). 'intermediate monocyte' is the name of CL:0002393 (intermediate monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "GCA", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}], "rationale": "This cluster shows a classic neutrophil marker signature. S100A8 and S100A9 (calprotectin complex) are hallmark neutrophil markers, consistently showing high expression (logfc 5.1 and 4.9, expressed in 100% and 97.8% of cluster cells). FCGR3B (CD16b) is a neutrophil-specific Fc receptor absent from monocytes and other immune lineages (logfc 2.3, absent outside cluster). CSF3R (G-CSF receptor), S100A12, and GCA (grancalicin, a neutrophil granule protein) are additional neutrophil-specific markers. The S100A8/A9/A11/A12 protein set, combined with myeloid markers like MNDA and immune markers like CXCL8 and LST1, confirms myeloid lineage with neutrophil-specific identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.1}, {"answer": {"cell_type_id": "CL:0000857", "cell_type_label": "intermediate monocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "RGS2", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}], "rationale": "Intermediate monocytes are defined by CD14++CD16+ phenotype and express the calprotectin complex (S100A8/A9) as a hallmark feature. This cluster shows maximal S100A8/A9 expression (logfc >4.9), with FCGR3B (CD16b) as a defining differentiator expressed almost exclusively in this cluster (pct_out 0.015). The inflammatory myeloid signature (CXCL8, RGS2, G0S2, MNDA, LST1) is consistent with intermediate monocyte biology. The absence of neutrophil-specific markers (CEACAM8, ITGAM, SPN) rules out the neutrophil classification, and the CD16+ phenotype with calprotectin signature specifically identifies intermediate monocytes rather than classical monocytes.\""}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells."], "seconds": 61.7}, {"answer": {"cell_type_id": "CL:0002393", "cell_type_label": "intermediate monocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "RGS2", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}], "rationale": "Intermediate monocytes are defined by CD14++CD16+ phenotype and express the calprotectin complex (S100A8/A9) as a hallmark feature. This cluster shows maximal S100A8/A9 expression (logfc >4.9), with FCGR3B (CD16b) as a defining differentiator expressed almost exclusively in this cluster (pct_out 0.015). The inflammatory myeloid signature (CXCL8, RGS2, G0S2, MNDA, LST1) is consistent with intermediate monocyte biology. The absence of neutrophil-specific markers (CEACAM8, ITGAM, SPN) rules out the neutrophil classification, and the CD16+ phenotype with calprotectin signature specifically identifies intermediate monocytes rather than classical monocytes."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'intermediate monocyte' is not the name of CL:0000857 ('slow muscle myoblast'). 'intermediate monocyte' is the name of CL:0002393 (intermediate monocyte)."], "seconds": 9.9}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-f2e4fa20cc"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "FOS", "stance": "supports"}, {"gene": "JUNB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "TSC22D3", "stance": "supports"}, {"gene": "ZFP36", "stance": "supports"}, {"gene": "ZFP36L2", "stance": "supports"}], "rationale": "IL7R, GPR183, and FYB1 are definitive T cell markers. GPR183 is particularly enriched in lymphocytes within secondary lymphoid organs. The high expression of immediate early genes FOS and JUNB indicates recent TCR signaling and T cell activation. KLRB1 is present in a subset, consistent with activated T cells or specific T cell lineages (e.g., MAIT cells). CXCR4 supports T cell identity. Stress-response and mRNA stability genes (ZFP36, ZFP36L2, TSC22D3) are typical of activated lymphocytes. No contradicting markers for other cell types are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-f5551fdf21"} +{"attempts": [{"codes": ["BEV004"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000765", "cell_type_label": "erythroblast", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "MCM5", "stance": "supports"}, {"gene": "CKS2", "stance": "supports"}, {"gene": "ITGA2B", "stance": "contradicts"}], "rationale": "This cluster shows a strong erythroid signature with hemoglobin genes (HBB, HBD) as top markers, combined with erythroid-specific markers including transferrin receptor (TFRC) for iron uptake, carbonic anhydrase 1 (CA1), ferroportin (SLC40A1), biliverdin reductase (BLVRB) for heme metabolism, and NFE2 (master erythroid transcription factor). The exceptionally high expression of cell cycle markers (STMN1, CDK6, TYMS, PCNA, MCM2/5, CKS2) is consistent with actively proliferating early erythroid progenitors/erythroblasts. ITGA2B (integrin alpha-2b, CD41) is a megakaryocyte marker and suggests either minor megakaryocyte contamination or represents doublet cells, as it is not typically co-expressed with this level of hemoglobin."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.5}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-f5e849f6ff"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "PDCD1", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "CORO1B", "stance": "supports"}, {"gene": "CORO1A-AS1", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "ITM2A", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of T cell-specific checkpoint molecules (PDCD1, TIGIT), T cell transcription factor (TOX2), and lymphocyte markers (CORO1B, SRGN, COTL1). This coherent marker profile robustly identifies the cluster as T cells from an active immune response in tonsil tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.0}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-f6eff45a55"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 8, "findings": [{"message": "The label 'natural killer cell' is not the name of CL:0000950 ('IgE plasmablast'). 'natural killer cell' is the name of CL:0000623 (natural killer cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000950 (IgE plasmablast) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000950 (IgE plasmablast) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'cytotoxic T lymphocyte' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000950", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}], "rationale": "This cluster is a proliferating natural killer cell population. GNLY and GZMA are cytotoxic granule proteins and the strongest indicators of NK cells (or cytotoxic lymphocytes). The remaining supporting markers (MKI67, TYMS, TOP2A, CENPF, PCLAF, NUSAP1) indicate active cell cycle progression and DNA replication, consistent with a proliferating state. The histone and tubulin genes (H4C3, TUBA1B, TUBB, H1-5, H1-3) further support this cycling phenotype. No markers clearly contradict NK cell identity; the dominant signal is proliferating cytotoxic lymphocytes in an active cell cycle phase."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.7}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "cytotoxic T lymphocyte", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}], "rationale": "This cluster is a proliferating cytotoxic T lymphocyte (CTL) population. GNLY and GZMA are hallmark markers of cytotoxic granule proteins expressed by CD8+ T cells and NK cells. The strong expression of cell cycle markers (MKI67, TYMS, TOP2A, CENPF, PCLAF, NUSAP1) indicates active proliferation. The validator's detection of CD3E in 78% of cells confirms T cell identity, distinguishing this from NK cells. The absence of CD19 (0%) rules out B cell lineage. The dominant signal is proliferating cytotoxic T lymphocytes with active DNA replication and cytotoxic granule gene expression."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'natural killer cell' is not the name of CL:0000950 ('IgE plasmablast'). 'natural killer cell' is the name of CL:0000623 (natural killer cell).", "object id: CL:0000950 (IgE plasmablast) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 0% of the cluster's cells.", "object id: CL:0000950 (IgE plasmablast) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 19.8}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}], "rationale": "This cluster is a proliferating cytotoxic T cell population. GNLY and GZMA are hallmark markers of cytotoxic granule proteins expressed by CD8+ T cells. The strong expression of cell cycle markers (MKI67, TYMS, TOP2A, CENPF, PCLAF, NUSAP1) indicates active proliferation. The dominant signal is proliferating cytotoxic T cells with active DNA replication and cytotoxic granule gene expression."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cytotoxic T lymphocyte' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell)."], "seconds": 12.2}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-f7efaf4b7a"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 8, "findings": [{"message": "The label 'Mature CD4-positive, alpha-beta T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). Closest names: CL:0000624 (CD4-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as lacking C-C chemokine receptor type 7 (CCR7), but CCR7 is detected in 57% of the cluster's cells, more than in the others (logfc 1.54).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "Mature CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}], "rationale": "This cluster expresses a comprehensive CD4+ T cell signature with high expression of T cell lineage markers (TRAC, CD3E, CD2) and CD4. The elevated IL7R (highest marker, 3.513 logfc), combined with CCR7 and CD27 expression, indicates either naive or central memory CD4+ T cells in peripheral blood. The consistent, high-specificity expression of these markers (low pct_out) with no contradicting lineage markers supports confident annotation as mature CD4-positive, alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.5}, {"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}], "rationale": "This cluster expresses a comprehensive CD4+ T cell signature with high specificity. Core T cell lineage markers are strongly expressed: TRAC (3.414 logfc, 97% cells), CD3E (2.368 logfc), and CD2 (2.230 logfc). CD4 expression (1.312 logfc, 86% cells) identifies the CD4+ subset. The markedly elevated IL7R (3.513 logfc, highest marker) supports T cell identity. Expression of CCR7 (1.541 logfc, 57% cells) and CD27 (1.817 logfc) are consistent with CD4+ T cells, particularly naive or central memory subsets. All key markers show high specificity (low pct_out), supporting confident annotation as CD4-positive, alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'Mature CD4-positive, alpha-beta T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). Closest names: CL:0000624 (CD4-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell).", "object id: CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as lacking C-C chemokine receptor type 7 (CCR7), but CCR7 is detected in 57% of the cluster's cells, more than in the others (logfc 1.54)."], "seconds": 19.1}], "model": "claude-haiku", "protocol": 3, "task_id": "ct-ff19304f5c"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "TGFBI", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "CD14 is expressed in nearly every cell of the cluster (pct_in 0.994) and in few cells elsewhere (pct_out 0.205). This comes with high FCN1, VCAN, S100A8/9, LYZ, CSTA and TGFBI, which together are the classical CD14+ monocyte signature. CST3, AIF1, CTSS, MPEG1, FCER1G and TYROBP confirm the myeloid/monocyte identity. HLA-DRA expression rules out neutrophils, even though CSF3R is high. FCGR3A and other non-classical monocyte markers are not among the top markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-0094010baa"} +{"attempts": [{"codes": ["BEV026"], "evidence": 15, "findings": [{"message": "CL:0002028 (basophil mast progenitor cell) is defined as lacking high affinity immunoglobulin epsilon receptor subunit alpha (FCER1A), but FCER1A is detected in 94% of the cluster's cells, more than in the others (logfc 3.37).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000613 (basophil progenitor cell) is defined as lacking mast/stem cell growth factor receptor (KIT), but KIT is detected in 64% of the cluster's cells, more than in the others (logfc 1.49).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002028", "cell_type_label": "basophil mast progenitor cell", "decision": "annotate", "markers": [{"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "LMO4", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "ITGA2B", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}], "rationale": "HDC, CPA3, FCER1A, CLC, PRG2, LMO4 and SRGN together point to the basophil/mast cell lineage (PRG2 and RNASE2 also hint at eosinophil-basophil granule genes). Mature blood basophils would not express this progenitor and proliferation program: PRSS57, SOX4, CDK6, STMN1, TYMS, ITGA2B/NFE2 (shared with the MEP-like stage) and HMGB1. That fits a circulating basophil/mast cell progenitor rather than a mature basophil. If the reference does not separate progenitors, the fallback label is basophil (CL:0000767)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}, {"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "PRG2", "stance": "supports"}, {"gene": "LMO4", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "CD82", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}], "rationale": "HDC (97% of cells against 0.3% outside), CPA3, FCER1A, CLC, PRG2, LMO4 and SRGN together are the basophil granule and receptor signature. The 94% FCER1A detection rules out the FCER1A-negative basophil/mast progenitor term (CL:0002028), so the cluster is annotated as basophil. Some cells also express immature or proliferation genes: PRSS57, SOX4, CDK6, STMN1, TYMS, ITGA2B and NFE2. This suggests the cluster contains some immature or cycling basophil-lineage cells, but these genes do not point to a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0002028 (basophil mast progenitor cell) is defined as lacking high affinity immunoglobulin epsilon receptor subunit alpha (FCER1A), but FCER1A is detected in 94% of the cluster's cells, more than in the others (logfc 3.37)."], "seconds": 11.6}, {"answer": {"cell_type_id": "CL:0000613", "cell_type_label": "basophil progenitor cell", "decision": "annotate", "markers": [{"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "PRG2", "stance": "supports"}, {"gene": "LMO4", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "ITGA2B", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "HDC, CPA3, FCER1A, CLC, PRG2 and LMO4 are expressed in almost all cells of the cluster, which puts it in the basophil lineage. The cluster also expresses progenitor and proliferation genes (PRSS57, SOX4, CDK6, STMN1, TYMS, ITGA2B, NFE2). CD40LG, which the ontology requires for a mature basophil, is not detected. Together these point to an immature or committed basophil progenitor rather than a mature basophil. The CL:0000613 term was chosen from memory and was not checked against the pinned ontology."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells."], "seconds": 18.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-0224ef5d63"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [{"gene": "TAGLN", "stance": "contradicts"}, {"gene": "TPM2", "stance": "contradicts"}, {"gene": "TPSB2", "stance": "contradicts"}], "rationale": "Top markers are immediate-early/stress-response genes (FOS, FOSB, JUN, ZFP36, NFKBIA, PPP1R15A, KLF2/6, HSP90AA1) plus nuclear lncRNAs (NEAT1, MALAT1, MIR23AHG), which mark dissociation stress, not a cell type. Lineage signals are weak and conflict: smooth-muscle/perivascular genes (TAGLN, TPM2, C11orf96) are in about 28-36% of cells and the mast cell tryptase TPSB2 in 25%. Strong markers for any single lineage are missing. This suggests a mixed, stressed or low-quality cluster that cannot be confidently annotated."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-027de551e6"} +{"attempts": [{"codes": ["BEV004"], "evidence": 16, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "PLAC8", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "C12orf75", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "PLP2", "stance": "supports"}, {"gene": "CD99", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}, {"gene": "IGLC2", "stance": "contradicts"}], "rationale": "The cluster has the standard pDC signature: IL3RA (CD123), IRF7, GZMB, TCF4 (E2-2), BCL11A, CCDC50, PLAC8, ITM2C, C12orf75 and SOX4. JCHAIN and MZB1 are also known to be highly expressed in human pDCs. IGKC and IGLC2 are immunoglobulin light chains and point to plasma cells. In colon data they most likely come from ambient RNA released by the many IgA plasma cells, or from a small number of plasma-cell doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-0460394dc8"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "LINC01781", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "This cluster expresses several B-cell-specific genes: MS4A1 (CD20), CD79A, CD79B, BANK1 and LINC01781. These genes are found in fewer than 2.5% of cells outside the cluster, except CD79B (about 10%). The cluster also has high levels of MHC class II genes (CD74, HLA-DR/DQ/DP), which fits antigen-presenting B cells, along with CD37, IRF8 and LTB. Immunoglobulin transcripts (IGKC, IGHA1, IGHG1, IGLC2) are present at moderate levels. The cells do not look like plasma cells, because MS4A1 and the MHC class II genes are high and JCHAIN, XBP1 and MZB1 are absent from the top markers. Some class-switched memory B cells or ambient plasma-cell RNA could explain the immunoglobulin signal. Overall, the cluster is best annotated as B cell."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-04f3e6a976"} +{"attempts": [{"codes": ["BEV004"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "MYH11", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "DSTN", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "contradicts"}], "rationale": "The cluster has a strong contractile smooth muscle profile: MYH11, ACTA2, TAGLN, MYL9, CALD1, TPM1 and TPM2 are all specific to it. It also expresses ADIRF, C11orf96, MGP, SPARCL1 and IGFBP7, which are typical of uterine and vascular smooth muscle. MYH11 is enriched (53% of cluster cells vs 5% of other cells), and pericyte markers like RGS5 are missing. Together, these point to smooth muscle cells (myometrial or vascular) rather than pericytes or stromal fibroblasts. HSPA1A, ATF3 and GADD45B suggest a stress response to tissue dissociation. HLA-DRA is fairly high (76% of cluster cells vs 37% of other cells), which may mean some antigen-presenting or immune cells are mixed in, or there are doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.3}], "model": "claude-opus", "protocol": 3, "task_id": "ct-0919bb7151"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000909", "cell_type_label": "CD8-positive, alpha-beta memory T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "CD8A and CD8B are strongly enriched, and together with TRAC, CD3E and CD2 they mark CD8 alpha-beta T cells. IL7R and CD27 indicate a memory phenotype. GZMA, NKG7, CST7, CTSW and KLRK1 are moderately enriched, suggesting a partly cytotoxic, effector-memory-leaning population. The markers can't tell central from effector memory, so the broader CD8 alpha-beta memory T cell term is used. TRGC2 is often detected in alpha-beta CD8 T cells and is not taken as contradictory."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.0}], "model": "claude-opus", "protocol": 3, "task_id": "ct-15649bcc33"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CLEC10A", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}], "rationale": "MHC class II genes dominate the top markers, with HLA-DQ especially high. CST3 is a typical dendritic cell marker, and CLEC10A is a cDC2-specific marker (70% of cells in the cluster vs 18.5% outside). CD83 and GPR183 indicate activated or migrating dendritic cells. Macrophage markers (C1Q genes, CD163, APOE) are not among the top markers. Together these point to colonic CD1c+ cDC2."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-18bf2c5651"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "T-cell receptor/CD3 genes (TRAC, TRBC1/2, CD3D/E, CD2) with specific CD8A/CD8B enrichment and a GZMK+ cytotoxic program (GZMK, CCL5, GZMA, CST7, CCL4) indicate GZMK+ effector-memory-like CD8 alpha-beta T cells; CD69/RGS1/CXCR4 suggest tissue-resident/activated state in kidney. Partial CD8 detection may reflect dropout or minor CD4/NK admixture."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-1c3cf91fbc"} +{"attempts": [{"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}, {"gene": "VWA5A", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "CD9", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "LAPTM4A", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}], "rationale": "The cluster's top markers are the mast cell tryptases TPSAB1 and TPSB2, along with CPA3, MS4A2 (FcεRIβ), HPGDS, GATA2 and RGS13. All of these are highly specific, with pct_out below 2%. Lysosomal and granule genes (CD63, LAPTM4A, CD9) and activation genes (AREG, CD69, RGS1/2) fit tissue-resident mast cells. No markers point to a different lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.8}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}, {"gene": "VWA5A", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "CD9", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "LAPTM4A", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}], "rationale": "The cluster's top markers are the mast-cell tryptases TPSAB1 (all cells) and TPSB2, along with CPA3, MS4A2 (FcεRIβ), HPGDS, GATA2 and RGS13. All of these are highly specific, with pct_out below 2%, so the cluster is clearly mast cells. The validator objected that CCR3 is undetected, but that doesn't argue against the call. The ontology's text mentions CCR3, yet resting human tissue mast cells express little CCR3 mRNA, and 10x 3' v2 often misses lowly expressed receptors. Mast-cell clusters in scRNA-seq atlases routinely lack CCR3. CMA1 (chymase) isn't in the marker list, so assigning a connective-tissue or mucosal subtype would be speculative. The parent term 'mast cell' is therefore the most accurate annotation. No markers point to another lineage."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 19.1}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}, {"gene": "VWA5A", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "CD9", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}], "rationale": "The cluster's top markers are the mast-cell tryptases TPSAB1 (in all cells) and TPSB2, together with CPA3, MS4A2 (FcεRIβ), HPGDS, GATA2 and RGS13. Each is detected in under 2% of other cells. Together they clearly identify mast cells, and no marker points to another lineage. The validator objected that CCR3 is undetected, but that doesn't argue against the call. Resting human tissue mast cells express little CCR3 mRNA, and 10x 3' v2 data often misses weakly expressed receptors, so mast-cell clusters in scRNA-seq atlases routinely lack CCR3. The connective-tissue and mucosal mast-cell subtypes would likely inherit the same CCR3 requirement, and with no chymase (CMA1) signal there is no basis for picking one. The parent term 'mast cell' is therefore the most accurate annotation."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 13.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-1cdfab3be0"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TSPO", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "ANXA1", "stance": "supports"}, {"gene": "LGALS1", "stance": "supports"}, {"gene": "EMP3", "stance": "supports"}], "rationale": "The cluster's top markers include S100A8, S100A9, LYZ, FCN1, VCAN and MNDA, and they are very specific to it (FCN1 is in 87% of cluster cells vs 1.4% elsewhere; VCAN 66% vs 3.7%). That is the classic CD14+ classical monocyte signature, here probably monocytes newly recruited into the colon tissue. CST3 is expressed in 99% of cells, while macrophage genes (C1Q, APOE) and dendritic-cell genes are missing. That fits monocytes rather than mature macrophages or DCs. RETN and G0S2 can also be expressed by neutrophils. However, FCN1, VCAN, CST3 and LYZ all point to monocytes, and the strongest neutrophil-specific genes (CSF3R, FCGR3B, CXCR2) are not in the list. So this does not look like a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-1dc66b7bae"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}], "rationale": "The B-cell identity is clear from CD79A, CD79B, MS4A1, CD19, CD72, IGKC and MHC-II genes. The cells co-express IGHM and IGHD (both unswitched antibody classes), and they have high TCL1A, FCMR and VPREB3. That pattern is typical of naive mature B cells rather than memory B cells or plasma cells. High CD24 and VPREB3 could mean some transitional B cells are mixed in, but naive B cell fits best. No markers from other lineages stand out."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-1fdfebb69c"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "Strong cytotoxic program (NKG7, GNLY, GZMA, CST7, CTSW) with NK receptors KLRF1 (NKp80), KLRD1, KLRK1 and CD16 (FCGR3A) plus ADGRG1, consistent with CD56dim NK cells. No CD3 genes among top markers. TRDC/TRGC2 expression is compatible with germline transcripts in NK cells, though some gamma-delta T cell admixture can't be excluded."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.9}], "model": "claude-opus", "protocol": 3, "task_id": "ct-21afd5c734"} +{"attempts": [{"codes": ["BEV026"], "evidence": 13, "findings": [{"message": "CL:0001071 (group 3 innate lymphoid cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 68% of the cluster's cells, more than in the others (logfc 0.78).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KRT86", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "PRR5", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The cluster expresses IL7R, KLRB1, ID2, RORA and LTB together with a set of genes that mark human ILC3s: KRT86, IL4I1, LST1, AQP3, TMIGD2 and PRR5. KRT86 is almost entirely limited to this cluster (pct_out 0.015). ILCs often express germline TRDC and TRBC transcripts. T-cell markers such as CD3D/E, CD4 and CD8A, and MAIT-cell markers such as SLC4A10, are not among the top genes. High CD69 fits tissue-resident colonic ILC3s. Expression of TRBC1 in 88% of cells leaves a small chance of RORγt+ T-cell contamination, but ILC3 is the best fit overall."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.3}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "KRT86", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "TRBC1", "stance": "contradicts"}], "rationale": "CD3E is detected in 68% of the cluster's cells, so these are T cells, not ILCs. TRDC is the most specific T-lineage gene in the list: it is found in 78% of cells in the cluster but only 7% outside it. This points to γδ T cells. KRT86 is almost exclusive to this cluster, and together with KLRB1, IL7R, RORA, IL4I1, AQP3 and TMIGD2 it fits the innate-like, type-3/IL-17-type γδ T cells that live in the gut mucosa. High CD69 fits tissue-resident colonic lymphocytes. TRBC1 is expressed in 88% of cells. Gut γδ T cells can carry non-productive TRB transcripts, but this level of TRBC1 could also mean some RORγt+ αβ T cells (MAIT or Th17-like) are mixed in. For that reason TRBC1 is listed as contradicting."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0001071 (group 3 innate lymphoid cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 68% of the cluster's cells, more than in the others (logfc 0.78)."], "seconds": 13.0}], "model": "claude-opus", "protocol": 3, "task_id": "ct-227cbde019"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "PLD4", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "UGCG", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "RNASE6", "stance": "supports"}, {"gene": "C12orf75", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}], "rationale": "IL3RA (CD123) and TCF4 (E2-2) are the defining pDC markers. IRF8, IRF7, PLD4, ITM2C, CCDC50, UGCG, JCHAIN, RNASE6 and C12orf75 are typical of human pDCs. MZB1, DERL3 and SEC61B fit the secretory machinery of pDCs, and CXCR3, STMN1 and FCER1A are also seen in blood pDCs. IGKC and IGHM likely reflect ambient immunoglobulin signal; with no other B or plasma cell markers, they don't indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-26fda93c9c"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "ITGA6", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}], "rationale": "CD8A, CD8B, TRAC and CD3E define an alpha-beta CD8 T-cell cluster. CCR7, SELL, IL7R and CD27 point to a naive or central-memory state rather than an effector state. ITGA6, FCMR, and high ribosomal and translation genes (RPLP2, EEF1A1, NPM1, GAS5) favour naive cells. Effector markers (GZMB, PRF1, NKG7) are absent from the top genes. Moderate IL32, CTSW and KLRK1 could mean some central-memory cells are mixed in, but the overall profile best fits naive CD8 T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-28eb7ea379"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "MRC1", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "F13A1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "STAB1", "stance": "supports"}, {"gene": "MERTK", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "SLCO2B1", "stance": "supports"}, {"gene": "COLEC12", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "RAB31", "stance": "supports"}], "rationale": "MRC1, CD163, C1QA/B, MERTK and STAB1 together mark macrophages. LYVE1, F13A1, SELENOP, RNASE1, FOLR2-like SLCO2B1 and COLEC12 indicate the LYVE1+ perivascular, tissue-resident M2-like subset in the bladder stroma. No markers clearly point to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-302af8ae13"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000553", "cell_type_label": "megakaryocyte progenitor cell", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "GUCY1B1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "PDLIM1", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "FERMT3", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "TSC22D1", "stance": "supports"}, {"gene": "RSU1", "stance": "supports"}], "rationale": "CD34 together with proliferation genes (STMN1, TYMS, CDK6) marks a cycling progenitor. ITGA2B (CD41) is the top marker, and with TAL1, NFE2 and platelet genes (PPBP, GUCY1B1, SPARC, NPR3, PDLIM1, PLEK) it shows megakaryocyte commitment. FCER1A and SLC40A1 fit the megakaryocyte-erythroid progenitor stage. The best overall match is megakaryocyte progenitor; megakaryocyte-erythroid progenitor (CL:0000050) is a close alternative."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-3775a26491"} +{"attempts": [{"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000484 (connective tissue type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "SLC24A3", "stance": "supports"}, {"gene": "IL18R1", "stance": "supports"}, {"gene": "LINC02147", "stance": "supports"}, {"gene": "NTM", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The cluster specifically expresses tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), KIT, HPGDS and IL1RL1 (listed as IL33R), with very low expression outside the cluster. This is the canonical signature of tissue mast cells. SLC24A3, LINC02147 and NTM are also commonly enriched in mast cells in tissue atlases. None of the markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.1}, {"answer": {"cell_type_id": "CL:0000484", "cell_type_label": "connective tissue type mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "SLC24A3", "stance": "supports"}, {"gene": "LINC02147", "stance": "supports"}, {"gene": "NTM", "stance": "supports"}], "rationale": "This cluster has the full tissue mast-cell signature, and these genes are rarely detected in other cells: the tryptases TPSB2 and TPSAB1, CPA3, KIT (CD117), HPGDS and IL1RL1 (listed as IL33R). SLC24A3, LINC02147 and NTM are also commonly enriched in tissue mast cells. The generic term CL:0000097 was rejected because its ontology definition requires CCR3 (CD193), which this cluster does not express. That fits mature human tissue mast cells, which usually don't express CCR3. I chose the connective tissue subtype instead because of the strong CPA3 signal, which is typical of tryptase/chymase-type (MC_TC) mast cells, and because the bladder dome wall is mostly connective tissue and smooth muscle. Caveat: CMA1 (chymase) is not in the top markers, so this subtype assignment is less certain than the overall mast-cell identity. None of the markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 16.0}, {"answer": {"cell_type_id": "CL:0000766", "cell_type_label": "myeloid leukocyte", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "SLC24A3", "stance": "supports"}], "rationale": "The cluster is clearly a tissue mast cell. It has the full signature, and these genes are almost absent from other cells: TPSB2, TPSAB1, CPA3, KIT, HPGDS, IL1RL1 (listed as IL33R) and SLC24A3. The pinned ontology defines mast cell (CL:0000097) and its subtypes as expressing CCR3. This cluster expresses no CCR3, which fits mature human tissue mast cells, so those terms cannot be used. I therefore annotate with the nearest parent term that has no CCR3 requirement: myeloid leukocyte. Biologically, these cells are mast cells. None of the markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000484 (connective tissue type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 15.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-3959f97db0"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000837", "cell_type_label": "hematopoietic multipotent progenitor cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "DEPTOR", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "NPM1", "stance": "supports"}, {"gene": "FAM117A", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TSC22D1", "stance": "supports"}], "rationale": "CD34, CRHBP, NPR3, DEPTOR and CDK6 are expressed in nearly all cells of this cluster and rarely outside it. That pattern marks circulating CD34+ hematopoietic stem and progenitor cells. STMN1 and NPM1 point to proliferating, ribosome-active progenitors. FCER1A, CPA3, SLC40A1 and NFE2 suggest these cells lean toward the megakaryocyte, erythroid and mast/basophil lineages (MEP/BMCP priming), which is typical of HSPCs in peripheral blood. These genes fit progenitors rather than mature basophils or dendritic cells, because mature cells would not express CD34 or CRHBP. So I annotated the cluster at the broader level: hematopoietic multipotent progenitor cell."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-3b8c7f5246"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "S100A10", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}, {"gene": "PMAIP1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "FABP5", "stance": "supports"}], "rationale": "Genes for cell division (STMN1, TYMS, HMGB2, TUBA1B, TUBB, H4C3) mark this as a dividing cluster. GZMK, combined with effector/memory genes (S100A4, S100A10, S100A6, VIM, ANXA2) and activation genes (CD74 as HLA class II invariant chain, PMAIP1, FABP5), points to activated, dividing GZMK+ CD8 T cells in the tonsil. No CD8A or CD3 genes appear in the top markers, so the CD8 call is moderately confident."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-3daee1395a"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "effector memory CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}], "rationale": "CD3E/CD3G/TRAC/CD2 with CD8A and CD8B mark alpha-beta CD8 T cells. CD8B in particular argues against NK cells. Strong cytotoxic genes (NKG7, CST7, GZMA, CTSW, GNLY, KLRK1) show an effector-memory state. ADGRG1, FCGR3A and KLRF1 suggest a late or terminally differentiated (TEMRA-like) subset, for which CL:0001062 would be the more specific term. TRGC2 transcripts are common in alpha-beta CD8 cells, but some gamma-delta T or NK cells may be mixed in."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-4b8439fcc9"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0008001", "cell_type_label": "hematopoietic precursor cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CDCA7", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "NPM1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}], "rationale": "The cluster expresses CD34 and other stem/progenitor genes: SPINK2, PRSS57, IGLL1, CDK6, SOX4 and CDCA7. STMN1 and NPM1 point to cells that are actively dividing. It also expresses early lineage-priming genes, including MPO, AZU1 and RNASE2 (granulocyte/monocyte), CPA3 (mast cell/basophil) and NFE2 (megakaryocyte/red cell). This mix fits circulating CD34+ hematopoietic stem and progenitor cells (HSPCs) rather than one committed lineage. None of the markers clearly points to a different, mature cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-4e9d71ecad"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "FCER1G", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "CTSL", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "SLC16A10", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "AQP9", "stance": "supports"}, {"gene": "PLIN2", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "CCL20", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "EREG", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}], "rationale": "FCER1G, IFI30, CTSL, PLAUR and AQP9 indicate myeloid cells. KYNU, SLC16A10, PLIN2 and TIMP1 suggest a macrophage that has differentiated from a monocyte. CCL20, CXCL8, EREG, SOD2 and MT2A show NF-κB-driven inflammatory activation. Some genes overlap with inflammatory monocytes and neutrophils, so the cluster may lie on the monocyte-to-macrophage path, but the macrophage signal is stronger. Best match: an activated macrophage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-5169234be6"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}], "rationale": "The top two markers are TRDC and TRGC2, the constant regions of the TCR delta and gamma chains. Almost every cell in the cluster expresses them (97% and 96%), and they are rare outside it. CD3E and CD2 confirm these are T cells. The cytotoxic and NK-like program (NKG7, GZMA, CST7, CTSW, KLRK1, KLRD1, GNLY) fits circulating gamma-delta T cells. The KLRB1, IL7R and DUSP2 pattern fits the Vgamma9Vdelta2 subset, which is the most common gamma-delta T cell type in blood. None of the markers point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-56d8f3ebbf"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000980", "cell_type_label": "plasmablast", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "SEL1L3", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC61B", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}], "rationale": "Strong JCHAIN, IGKC and MZB1, plus an ER/secretory programme (DERL3, FKBP11, SEC11C, SSR4, SEC61B, HSP90B1, HERPUD1) and XBP1, define antibody-secreting cells. CD27 and CD38 support this. In blood, the retained CD19 and CD79A favour circulating plasmablasts over mature plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-62995bbc69"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "effector memory CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "LAG3", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "PRDM1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "MIR4435-2HG", "stance": "supports"}, {"gene": "CYTOR", "stance": "supports"}], "rationale": "Activated memory T cell genes (S100A4, IL32, CD2, MIR4435-2HG, CYTOR, RGS1, TNFRSF1B) together with KLRB1/RORA (Th17-like effector) and activation/checkpoint genes (LAG3, CTLA4, TNFRSF4, TNFRSF18, PRDM1, MAF) indicate effector memory CD4 T cells in tonsil, possibly Tr1-like. FOXP3 is absent from the top markers, so this is not labelled as Treg."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-62ef0fd4ba"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000484 (connective tissue type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}, {"gene": "HPGD", "stance": "supports"}, {"gene": "CD9", "stance": "supports"}], "rationale": "Tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the high-affinity IgE receptor beta chain (MS4A2), GATA2, HPGDS and LTC4S together form the classic mast cell signature. They are highly specific to this cluster (pct_out ≤0.03 for the core genes). None of the markers points to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 7.6}, {"answer": {"cell_type_id": "CL:0000484", "cell_type_label": "connective tissue type mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}, {"gene": "HPGD", "stance": "supports"}, {"gene": "CD9", "stance": "supports"}], "rationale": "The cluster is clearly mast cells. The tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the IgE receptor beta chain (MS4A2), GATA2, HPGDS and LTC4S are expressed in 77–97% of the cluster. The most specific of these (TPSB2, TPSAB1, CPA3, MS4A2, GATA2) are in at most 3% of other cells. CCR3, which the generic mast cell term's definition mentions, is usually not detected in mature tissue mast cells in scRNA-seq, so its absence is not evidence against this identity. The strong CPA3 expression together with the tryptases is typical of connective-tissue-type (tryptase/chymase) mast cells, so the more specific term CL:0000484 is used. CMA1 is not among the top markers, so the subtype call depends mostly on CPA3. If the subtype cannot be confirmed, CL:0000097 (mast cell) is still the correct broader identity. No markers point to another lineage."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 18.8}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}, {"gene": "HPGD", "stance": "supports"}, {"gene": "CD9", "stance": "supports"}], "rationale": "The cluster is clearly mast cells. The tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the IgE receptor beta chain (MS4A2) and GATA2 are each expressed in 77–97% of the cluster and in at most 3% of other cells. HPGDS, LTC4S and HPGD add support. The earlier subtype term, CL:0000484 (connective tissue type mast cell), was dropped for two reasons. Its definition requires CCR3, which this cluster does not express at all. Chymase (CMA1) is also not among the top markers, so there is no direct evidence for that subtype. The broader term CL:0000097 (mast cell) is therefore used. No markers point to another lineage."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000484 (connective tissue type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 14.9}], "model": "claude-opus", "protocol": 3, "task_id": "ct-68351aaa63"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "FCGRT", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}], "rationale": "The cluster has strong, specific expression of the complement genes C1QA, C1QB and C1QC, along with SELENOP and MS4A7. This profile is typical of tissue-resident macrophages in the colon lamina propria. Other myeloid genes (TYROBP, AIF1, CST3, FCGRT, NPC2) and MHC class II genes (HLA-DRA, HLA-DRB1, HLA-DPA1, CD74) back this up. CCL3 and CCL4 suggest the cells are somewhat activated. I didn't find any markers of another lineage, so I see no sign of a mixed cluster or doublets. HES1 and HSPA1A are probably a stress response from tissue dissociation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.0}], "model": "claude-opus", "protocol": 3, "task_id": "ct-6dacd7effa"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "SPOCK2", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}], "rationale": "The T-cell receptor and CD3 complex genes (TRAC, TRBC2, CD3D/E/G) are expressed together with CD2 and BCL11B, which marks this as an alpha-beta T-cell cluster. CD40LG is expressed in 54% of cluster cells versus 3% of all other cells. Together with high IL7R and LTB, this points to CD4 helper T cells. There are no cytotoxic or CD8 markers (CD8A, GZMs, NKG7) among the top markers. KLRB1, RORA, GPR183 and S100A4 suggest a memory or effector-memory phenotype, possibly Th17-like, which is common in tissue-resident T cells in the endometrium."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.3}], "model": "claude-opus", "protocol": 3, "task_id": "ct-72757d8950"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CBLB", "stance": "supports"}, {"gene": "NIBAN1", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "IL7R (97% in vs 14% out), CD96, CAMK4 (83% vs 6%), FYN, CBLB, ETS1 and NIBAN1 together point to T cells. CD69 suggests tissue-resident or recently activated cells, and CCL5, CCL4, STAT4 and SYTL3 suggest a memory or effector state. High IL7R and CAMK4, with no NK markers in the list, argue against NK cells. CD4 and CD8 genes don't appear in the list, so the broad T cell term is used."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-72dfb189c0"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "MSI2", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "H1-0", "stance": "supports"}, {"gene": "NRIP1", "stance": "supports"}, {"gene": "TSC22D1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "Nearly all cells in this cluster express CD34, SPINK2, CRHBP, PROM1 (CD133), NPR3 and HOPX, and very few cells outside it do. Together these define the most primitive CD34+ hematopoietic stem and progenitor cells (HSC/MPP) found circulating in blood. CRHBP, HOPX, MSI2 and EGFL7 point to the stem-cell end of that compartment rather than to committed progenitors. STMN1, CDK6, NPM1 and the snoRNA host genes (GAS5, SNHG8, ZFAS1) fit an immature, biosynthetically active progenitor state. No lineage-commitment markers stand out (for example MPO, GATA1, CD79A or IL7R). I chose hematopoietic stem cell (CL:0000037). The cluster probably also contains multipotent progenitors, so 'hematopoietic multipotent progenitor cell' (CL:0000837) would also be a reasonable label."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-75adde23f7"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "KRT81", "stance": "supports"}, {"gene": "KRT86", "stance": "supports"}, {"gene": "ALDOC", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "KIT+ IL7R+ LTB+ lymphocytes expressing the human ILC3 signature (LST1, IL4I1, KRT81, KRT86, ALDOC, TMIGD2, AHR, TNFRSF4/18, KLRB1). No CD3 genes or cytotoxic NK genes appear among the top markers. TRBC1 is consistent with the germline TRBC transcripts often found in ILCs."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.0}], "model": "claude-opus", "protocol": 3, "task_id": "ct-76fa626271"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0008001", "cell_type_label": "hematopoietic precursor cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "NUCB2", "stance": "supports"}, {"gene": "CDCA7", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}], "rationale": "Nearly every cell expresses CD34, and almost none outside the cluster do. Most cells also express PROM1 (CD133), SPINK2, NPR3, EGFL7, CDK6, CDCA7 and NUCB2. This is the classic signature of CD34+ hematopoietic stem and progenitor cells (HSPCs) found in circulating blood. IGLL1 suggests some early lymphoid priming. Proliferation genes (STMN1, TYMS, MCM2, PCNA, TUBB) are also high, which points to cycling progenitors rather than quiescent stem cells. That is why the broader term \"hematopoietic precursor cell\" was chosen over \"hematopoietic stem cell\". None of the markers clearly indicates a different lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-7a81a9a19f"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "LIME1", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "T-cell receptor complex genes (CD3D/G/E, TRAC, TRBC2), CD2 and BCL11B show this is an alpha-beta T-cell cluster. CD8A plus the highly specific CD8B mark the CD8 lineage. CCL5, GZMK, GZMM, GZMH and CST7 show a cytotoxic effector-memory program, and CD69 and CXCR4 fit tissue-resident T cells in the endometrium. No markers point to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.3}], "model": "claude-opus", "protocol": 3, "task_id": "ct-7c21a7ad85"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001065", "cell_type_label": "innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "This cluster expresses innate lymphoid genes. TYROBP and FCER1G are strongly specific to it (pct_out about 0.01–0.02), and CD7 is also expressed, but the T cell receptor genes and CD3 are not among the top markers. The signals are mixed. XCL1/XCL2, GNLY, CTSW and KLRC1 point to CD56bright-like NK cells. IL7R, KLRB1, LST1, AREG, SPINK2 and TNFRSF18 (GITR) point to helper-like ILCs, especially ILC3 and ILC precursors, which are common in tonsil. TRDC transcripts are often detected in human NK cells and ILCs. Because the cluster seems to mix NK-like and ILC3-like cells, I chose the broader term, innate lymphoid cell."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-7ec8cd3664"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}], "rationale": "The cluster expresses the complement genes C1QA, C1QB and C1QC very specifically (pct_out at most 0.06). It also has high MHC class II genes (HLA-DR, HLA-DP, HLA-DQ and CD74) and myeloid genes (AIF1, TYROBP, FCER1G, CD14, MS4A6A). Expression of SELENOP, RNASE1 and NPC2 fits tissue-resident macrophages. Together these point to resident macrophages in the kidney interstitium, not monocytes or dendritic cells. None of the markers clearly points to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-819cfbd986"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "LINC02446", "stance": "supports"}, {"gene": "NELL2", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "TXNIP", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}, {"gene": "LDHB", "stance": "supports"}, {"gene": "FLT3LG", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "CD8B and CD8A are highly specific top markers, together with the CD8 T cell-associated LINC02446 and NELL2. The naive or recirculating markers CCR7, SELL, LEF1 and KLF2, plus quiescence-associated TXNIP, NOSIP and LDHB and high ribosomal genes, point to a naive state. Cytotoxic or effector genes are absent. AIF1 is commonly seen at low levels in naive CD8 T cells and does not suggest contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-81b1e8f8f5"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "PRDX4", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}], "rationale": "Many immunoglobulin heavy- and light-chain genes are strongly enriched (IGKC, IGHG1-4, IGHA1, IGHM, IGLC1-3). JCHAIN, MZB1, DERL3 and FKBP11 are also enriched, together with genes for the expanded protein-secretion machinery (XBP1, HERPUD1, SSR4, SEC11C, PRDX4). CD79A confirms B-cell lineage. Together these markers define antibody-secreting plasma cells. No marker clearly points to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-879d085000"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "PSAP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}], "rationale": "The cluster has a strong myeloid antigen-presenting signature: high MHC class II genes (HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DQB1, CD74) together with AIF1, CST3 and IFI30. CD14 and LYZ point to the monocyte/macrophage lineage. Complement C1QA and lysosomal/phagocytic genes (CTSB, CTSS, PSAP, NPC2) point to tissue-resident macrophages rather than circulating monocytes. Some monocytes or dendritic cells may be mixed in, since C1QA is found in only 64% of the cluster's cells, but the overall profile fits endometrial macrophages best."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-89c1241fbf"} +{"attempts": [{"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "GPR171", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "TRAC, TRBC2, CD3D, CD3E and CD2 show these are alpha-beta T cells. The strongest marker is IL7R, and LTB, IL32, GPR171 and KLRB1 are also high, while CD8 cytotoxic genes are absent. This pattern fits CD4 helper or memory T cells. CD4 itself is not listed, so the CD4 assignment is likely but not certain. HSPA1B and JUN reflect dissociation stress, RPS4Y1 reflects a male donor, and the ribosomal genes are not informative."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.2}, {"answer": {"cell_type_id": "CL:0000789", "cell_type_label": "alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "GPR171", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "TRAC, TRBC2, CD3D, CD3E and CD2 identify these cells as alpha-beta T cells. IL7R, LTB, IL32 and GPR171 are high, and CD8 cytotoxic genes are absent. Together these suggest a CD4-like helper or memory T-cell population. However, CD4 is detected in only 8% of the cells, so the evidence does not support the narrower CD4-positive term. Some of this may be dropout in 10x v2 data, but I have chosen the broader term alpha-beta T cell. HSPA1B and JUN reflect dissociation stress, RPS4Y1 reflects a male donor, and the ribosomal genes are not informative."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 8% of the cluster's cells."], "seconds": 9.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-8ab1b5fbd8"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002396", "cell_type_label": "CD14-low, CD16-positive monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "NR4A1", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CD86", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "SAT1", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}], "rationale": "The strongest marker is FCGR3A (CD16), with a log fold change near 4 and expression in essentially every cell. It comes with the myeloid and monocyte genes MS4A7, LST1, AIF1, CST3, FCER1G, TYROBP, CTSS and CD86. NR4A1 is a transcription factor that non-classical monocytes depend on, and its enrichment here, along with ITGAX, COTL1 and MPEG1, fits the CD16+ non-classical monocyte profile. Classical monocyte genes such as CD14, S100A8/9 and LYZ are not among the top markers. No marker clearly points to a different lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-8c07cf76ca"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}], "rationale": "Strong NK signature: GNLY, NKG7, KLRD1, KLRF1 (NKp80, near-NK-specific), TYROBP and FCER1G (adaptors for activating receptors), IL2RB, and cytotoxic genes (CTSW, CST7, GZMB, CMC1). High XCL1/XCL2 and KLRC1 (NKG2A), with modest GZMB and no FCGR3A, suggest CD56-bright-like tonsillar NK cells; the general NK term is used because CD56 is not in the list. NK cells commonly express TRDC transcripts. γδ T cells are not fully ruled out, but no T-cell genes (CD3E, TRGC) are among the top markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-8d82b1a772"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "These cells express the T-cell receptor and CD3 complex (TRAC, CD3E, CD3G), along with CD2. They are strongly and specifically positive for both CD8A and CD8B: pct_out is 0.145 for CD8A and 0.076 for CD8B. They also have a cytotoxic program (NKG7, GZMA, CST7, CTSW, KLRK1). Taken together, this is a cytotoxic CD8+ alpha-beta T cell. TRGC2 is often detected in CD8 alpha-beta T cells, and TRAC is high, so a gamma-delta T-cell identity is unlikely. Partial CD27 expression and the lack of strong GZMB/GZMH markers suggest a mix of memory and effector cells, so I used the broader CD8+ alpha-beta T cell term rather than a more specific subset."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.9}], "model": "claude-opus", "protocol": 3, "task_id": "ct-95367720e6"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "BACH2", "stance": "supports"}, {"gene": "AFF3", "stance": "supports"}, {"gene": "RALGPS2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "ST6GAL1", "stance": "supports"}, {"gene": "MEF2C", "stance": "supports"}], "rationale": "MS4A1, CD79A and BANK1 are highly specific (pct_out <5%) and define mature B cells. MHC class II genes and CD74 fit antigen-presenting B cells. BACH2, AFF3, RALGPS2 and MEF2C are B-lineage genes. IGKC is present, but plasma-cell markers (JCHAIN, MZB1, XBP1) are missing from the top list and MS4A1 is retained, so these are B cells, not plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.9}], "model": "claude-opus", "protocol": 3, "task_id": "ct-9814423bdc"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}], "rationale": "Strong cytotoxic program (GNLY, NKG7, GZMB, GZMA, PRF1) plus NK-specific receptors KLRF1 (NKp80, highly specific: 85% vs 5%) and KLRD1 (CD94). FCGR3A (CD16), FGFBP2, SPON2 and CLIC3 indicate mature CD56dim CD16+ NK cells. TYROBP and FCER1G are NK activating-receptor adaptors. No T-cell markers (CD3D/E, CD8A, TRAC) appear among the top genes; CD247 is also expressed by NK cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.0}], "model": "claude-opus", "protocol": 3, "task_id": "ct-98402e60db"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CTSD", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "PLXDC2", "stance": "supports"}], "rationale": "Strong complement C1Q (C1QA/B/C) together with APOE, high MHC class II (HLA-DR/DP/DQ, CD74), TYROBP, LYZ and lysosomal genes (CTSD, NPC2) define tissue-resident macrophages in the bladder wall. No markers clearly point to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-9d243229e7"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000836", "cell_type_label": "promyelocyte", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "CDC20", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "MGST1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "SPNS3", "stance": "supports"}], "rationale": "Strong, highly specific expression of azurophil-granule genes (MPO, AZU1, RNASE2, RNASE3) together with cell-cycle genes (STMN1, TYMS, PCNA, CDC20, tubulins) and myeloid genes (LYZ, S100A8, CSTA, SRGN) indicates dividing early neutrophil-lineage cells, i.e. promyelocytes, in circulation. IGFBP7 and SPNS3 suggest an early progenitor-like stage; GMP/myeloblast is the main alternative."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-9d2a6afe3f"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "CD33", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "RNASE6", "stance": "supports"}], "rationale": "FCER1A is strongly specific to this cluster (90% in vs 6% out), and CD1C is enriched (64% vs 7%). Together with high MHC class II genes (HLA-DR/DP/DQ, CD74), CST3, ITGAX (CD11c) and myeloid genes (CD33, LYZ), this is the classic profile of blood cDC2. No CD14/FCGR3A dominance suggests monocytes, and there are no basophil markers apart from FCER1A, which fits the DC call."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 8.8}], "model": "claude-opus", "protocol": 3, "task_id": "ct-9e8b98aab5"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "CL:0009011", "cell_type_label": "transit amplifying cell of colon", "decision": "uncertain", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}], "rationale": "Every top marker is a cell-cycle or proliferation gene: G2/M genes (MKI67, TOP2A, CENPF, UBE2C, CDK1, ASPM, NUSAP1), S-phase genes (PCLAF, TYMS, H4C3), and chromatin or microtubule genes (HMGB2, STMN1, TUBB). No lineage markers appear (no epithelial EPCAM/KRT/LGR5/OLFM4, no immune PTPRC/CD3, no stromal genes). So the cluster is clearly cycling cells, but its lineage cannot be determined from these markers. In colon, the largest group of proliferating cells is usually transit-amplifying epithelium, so I give that as the best guess. Cycling T, B or plasma cells, or a mix of lineages, cannot be ruled out. Checking EPCAM or PTPRC expression in this cluster would settle it."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-a321096724"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000817", "cell_type_label": "precursor B cell", "decision": "annotate", "markers": [{"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "ARPP21", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "AKAP12", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "NEIL1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "These are B-lineage cells: CD79A, CD79B, IGHM and CD37 are all expressed. The surrogate light chain genes IGLL1 and VPREB1 are highly specific here (pct_out 0.024 for both), and VPREB3 is also strong. Together these point to the pre-BCR stage. ARPP21, CD24, SOX4, TCF4, AKAP12 and NEIL1 are typical of immature pro-B/pre-B cells. IGHM is present while IGKC is only partly expressed, which fits a precursor B cell (likely pre-B) that has not yet finished light-chain rearrangement. Cells like this are most likely found in fetal colon/gut tissue. None of the markers clearly point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-a33f382e85"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "LY9", "stance": "supports"}], "rationale": "Pan-B-cell markers are present: MS4A1, CD79A, CD79B, BANK1, SPIB and BAFF-R (TNFRSF13C). IGHM and IGHD are both expressed, along with TCL1A and VPREB3, which together point to a naive B cell that has not switched class. There are no plasma-cell markers (such as JCHAIN or XBP1, or high IGHA), and no germinal-centre or memory markers (such as CD27). The cluster is therefore naive B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ac7ec2b016"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}, {"gene": "COBLL1", "stance": "supports"}, {"gene": "MIR29B2CHG", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "The cluster-specific signal points to antibody-secreting cells. It is enriched for the immunoglobulin transcripts IGKC, IGHG1 and IGHG3, which are rarely expressed outside the cluster (pct_out 0.04–0.17). It is also enriched for ELL2, which plasma cells use to process immunoglobulin transcripts, and for COBLL1. However, the evidence is weak. The immunoglobulin genes reach only 39–65% of cells with modest fold changes, and the cluster lacks the classic plasma-cell markers JCHAIN, MZB1 and XBP1. The top of the list is mostly nuclear lncRNAs (NEAT1, MALAT1, XIST), mitochondrial genes and stress-response genes (FOSB, TSC22D3, CCNL1). That suggests a small or low-quality cluster. HDC, found in a third of cells, hints that some mast cells or basophils may be mixed in. So this is a tentative call: a low-quality cluster of plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.1}, {"answer": {"cell_type_id": "CL:0000946", "cell_type_label": "antibody secreting cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}, {"gene": "COBLL1", "stance": "supports"}, {"gene": "MIR29B2CHG", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "The signal specific to this cluster comes from immunoglobulin transcripts. IGKC, IGHG1 and IGHG3 are expressed in 39–65% of the cluster's cells but rarely outside it (pct_out 0.04–0.17). ELL2, which handles immunoglobulin transcripts in antibody-secreting cells, is also enriched, along with COBLL1 and MIR29B2CHG. That points to IgG-class antibody-secreting B-lineage cells. However, only 8% of cells express SDC1 (CD138), and the classic markers JCHAIN, MZB1 and XBP1 are not among the top genes. That does not support the term 'plasma cell', which is defined as SDC1-positive. I therefore use the broader term 'antibody secreting cell' instead. Most of the top of the list is nuclear lncRNAs (NEAT1, MALAT1, XIST), mitochondrial genes and immediate-early or stress genes (FOSB, TSC22D3, CCNL1). This suggests a small, low-quality cluster. HDC, expressed in a third of the cells, hints that some mast cells or basophils are mixed in. This is a tentative call."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells."], "seconds": 13.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ad2d591627"} +{"attempts": [{"codes": ["BEV026"], "evidence": 16, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The top markers are a cytotoxic lymphocyte program: GNLY, NKG7, GZMA, GZMB, PRF1, CTSW and CST7. Alongside these are NK receptors and signalling genes: KLRD1, KLRC1 (NKG2A), IL2RB and CD247. No CD3D, CD3E or TCR alpha/beta genes appear among the top markers. High KLRC1, XCL1/XCL2 and HOPX fit uterine (endometrial) NK cells, which are CD56bright-like. NK cells commonly express TRDC transcripts, so TRDC does not argue against NK cells here. Some gamma-delta or CD8 T cells could still be mixed in, but the cluster as a whole is best called natural killer cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.3}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The top markers are a cytotoxic lymphocyte program: GNLY, NKG7, GZMA, GZMB, PRF1, CTSW and CST7. Alongside these are NK receptors KLRD1, KLRC1 and IL2RB. CD3E is detected in 65% of the cluster's cells and is enriched (logfc 0.59), which rules out the NK cell term because CL:0000623 is defined as lacking CD3E. TRDC is strongly specific: 89% inside the cluster vs 14% outside. CD247 is also present, and neither CD8A nor CD4 appears among the top markers. Together this points to gamma-delta T cells, which in the endometrium and mucosa (often Vdelta1) express NK receptors such as KLRC1/NKG2A, along with XCL1/XCL2, HOPX and cytotoxic granule genes. Some conventional NK cells may still be mixed in."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59)."], "seconds": 16.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ae89c1380f"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "THBS1", "stance": "supports"}, {"gene": "EREG", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}], "rationale": "The cluster's markers fit classical (CD14+) monocytes. VCAN, S100A8, S100A9 and LYZ are characteristic of this cell type, and VCAN is highly specific here (pct_in 0.93 vs pct_out 0.08). Inflammatory monocyte genes also point the same way: THBS1, EREG, IL1R2, C5AR1, PLAUR, NAMPT and KYNU. General myeloid genes support this (AIF1, TYROBP, IFI30). The high VCAN, S100A8/9 and THBS1, together with no macrophage genes such as C1Q, APOE or CD163 among the top markers, suggest these are recently recruited monocytes rather than tissue-resident macrophages. The S100A8/9 signal could also come from neutrophils, but VCAN, LYZ and AIF1 argue against that. None of the markers points to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.0}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b269766ee9"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "TXNIP", "stance": "supports"}, {"gene": "FLT3LG", "stance": "supports"}, {"gene": "LINC00861", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}, {"gene": "LDHB", "stance": "supports"}, {"gene": "PLAC8", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}], "rationale": "CCR7, SELL, LEF1, KLF2, IL7R and TXNIP mark naive/resting T cells that circulate back to lymph nodes. FLT3LG, LINC00861, NOSIP, LDHB and PLAC8 are typical of naive CD4 T cells, and IL7R is higher than in naive CD8 cells, so this leans towards naive CD4 T cells. CD4 and CD8 are not among the top genes, so the CD4 call is inferred. No B-cell, germinal-centre or myeloid markers suggest contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.3}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b322bece33"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "CD3D/CD3G show these are T cells, and GNLY, NKG7, GZMH, GZMB, GZMA, PRF1 and CST7 show they are cytotoxic. FGFBP2, KLRG1 and KLRD1 suggest effector-memory/TEMRA-like CD8 T cells. CD8A/B are absent from the top markers and TRGC2 hints at some gamma-delta T cells (possibly NK cells too), so the general cytotoxic T cell term is used. HBB is likely ambient contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b51a9f2d53"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "DUSP4", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "STAT3", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "MAP3K8", "stance": "supports"}, {"gene": "MIR4435-2HG", "stance": "supports"}], "rationale": "IL10 is the most specific marker (34% in the cluster vs 2.5% elsewhere). Together with MAF, CTLA4, IKZF3, TNFRSF1B, DUSP4, RGS1 and STAT3 signalling, this points to activated, IL-10-producing regulatory CD4 T cells. FOXP3 is not among the top markers, so these look like Tr1-like cells (the IL-10 Treg / Tr1 population seen in tonsil atlases), not classical FOXP3+ Tregs. KLRB1 and IL32 fit a memory or effector CD4 phenotype. I used the parent term, regulatory T cell, because I'm not sure of the CL ID for a more specific Tr1 term."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b5ea73db74"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002057", "cell_type_label": "CD14-positive, CD16-negative classical monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "MGST1", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "RNASE6", "stance": "supports"}], "rationale": "The cluster has high CD14, VCAN, FCN1, S100A8/9, LYZ, CSTA and CST3, which is the standard profile of classical monocytes. VCAN and FCN1 together with strong CD14 point to classical CD14+ monocytes, not CD16+ non-classical monocytes. They also argue against neutrophils, because CST3 and VCAN are monocyte-specific in blood. CSF3R and ITGAM are also expressed in monocytes. No marker clearly points to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b7c75983d8"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000113", "cell_type_label": "mononuclear phagocyte", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}, {"gene": "HLA-DMB", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}], "rationale": "Nearly every cell in the cluster expresses MHC-II genes and CD74 at high levels, together with CST3, LYZ, MS4A6A, AIF1, TYROBP and NPC2. This marks antigen-presenting myeloid cells (mononuclear phagocytes) in kidney cortex. Classic macrophage genes (C1QA/C1QB/APOE) are missing from the top markers, and high CST3/HLA-DQ hints at dendritic cells, but MS4A6A and LYZ also fit monocyte-derived cells. The broader mononuclear phagocyte term is therefore used."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b864a5744b"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "TRDC (96% in vs 12% out) and TRGC2 (81% in) strongly indicate gamma-delta T cells. A cytotoxic NK-like programme (NKG7, GNLY, CTSW, GZMA, CST7, KLRK1/KLRF1/KLRD1/KLRB1, HOPX) fits peripheral Vd2 gamma-delta T cells. CD2 and CD7 confirm the T/NK lineage. NK cells are the main alternative, given FCER1G and KLRF1, but strong expression of both TCR constant genes and the lack of FCGR3A/GZMB/PRF1 among the top markers favour gamma-delta T. CD3 expression was not available to confirm this."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-b95794dcf3"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "TXNDC5", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "PRDX4", "stance": "supports"}], "rationale": "The cluster has very high, specific expression of antibody genes (JCHAIN, IGHA1, IGKC, IGLC genes, IGHG genes) and plasma-cell markers (MZB1, DERL3, TXNDC5). It also shows raised protein-secretion genes (XBP1, SSR4, SEC11C, FKBP11, PRDX4). Most cells look IgA-secreting, as expected in mucosa, but some IgG expression means the general plasma cell term fits best."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ba5f0288e7"} +{"attempts": [{"codes": ["BEV026"], "evidence": 13, "findings": [{"message": "CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 9% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "ITM2A", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "ANXA1", "stance": "supports"}], "rationale": "CD3D/E/G, TRAC and TRBC2 mark alpha-beta T cells. IL7R, LTB, ICOS and ITM2A are high, and there are no cytotoxic or CD8 markers (CD8A, GZMK, NKG7) in the list. Together that suggests CD4 helper or memory T cells. CD69, ANXA1, RGCC and TNFAIP3 point to tissue-resident or activated memory cells in the colon mucosa. CD4 itself isn't among the top markers, so the CD4 call is inferred and not directly shown."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.2}, {"answer": {"cell_type_id": "CL:0000789", "cell_type_label": "alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}, {"gene": "ITM2A", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "CD3D/E/G mark T cells, and TRAC and TRBC2 place them in the alpha-beta lineage. IL7R, LTB, ICOS, ITM2A and IL32 suggest helper or memory-like T cells. CD69, ANXA1, RGCC and TNFAIP3 suggest activated or tissue-resident cells in the colon mucosa. CD4 is detected in only 9% of cells and CD8 or cytotoxic markers are not among the top markers, so the call stays at the alpha-beta T cell level and does not assert CD4 or CD8 status."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 9% of the cluster's cells."], "seconds": 13.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-be2c0ee626"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000875", "cell_type_label": "non-classical monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "IFITM3", "stance": "supports"}, {"gene": "PELATON", "stance": "supports"}], "rationale": "The cluster expresses general myeloid genes (AIF1, TYROBP, FCER1G, CTSS, CST3, HLA-DRA). FCN1 and SERPINA1 indicate circulating monocytes. FCGR3A (CD16, 92.5% of cells in the cluster) together with LST1, MS4A7, COTL1, IFITM3 and PELATON matches the CD16-positive non-classical monocyte signature. The classical monocyte markers CD14, S100A8/9 and LYZ are not among the top genes. No markers point clearly to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.9}], "model": "claude-opus", "protocol": 3, "task_id": "ct-c5e3a0ec1f"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TBC1D4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}], "rationale": "These are T cells: they express TRAC, TRBC1, TRBC2, CD3D, CD3G, CD2 and BCL11B. They also show a clear regulatory T-cell profile. FOXP3 is in 63.5% of cluster cells and 0.2% of other cells. The cluster also expresses IL2RA (CD25), CTLA4, TIGIT, TNFRSF4 (OX40), TNFRSF18 (GITR), TBC1D4 and CD27. No markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-c99aec2a45"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "SEL1L3", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}], "rationale": "CD79A, MS4A1 (CD20), CD79B, CD19 and immunoglobulin kappa light chain (IGKC) are expressed almost uniformly, the canonical B-cell signature. Strong MHC class II (HLA-DR/DP, CD74) and B-cell-associated genes (FCMR, SEL1L3, CD37, CD24, VPREB3, IRF8) fit circulating B cells. High CD24/VPREB3 hints at naive/transitional cells and some JCHAIN expression may reflect a few activated/memory cells, but with MS4A1 at ~99% this is not a plasmablast cluster, so the general B cell term is assigned."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ccd8ad8cc1"} +{"attempts": [{"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "LMO4", "stance": "supports"}, {"gene": "CNRIP1", "stance": "supports"}], "rationale": "This cluster expresses the mast cell tryptases TPSAB1 and TPSB2, along with carboxypeptidase CPA3, histidine decarboxylase (HDC), the transcription factor GATA2, the vesicular monoamine transporter SLC18A2, HPGDS and the IL-33 receptor IL1RL1 (listed here as IL33R). Almost no cells outside the cluster express these genes. Taken together, this is the classic signature of mucosal mast cells in the colon. None of the markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 7.7}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "LMO4", "stance": "supports"}, {"gene": "CNRIP1", "stance": "supports"}], "rationale": "The cluster carries the full mast cell program. It expresses the tryptases TPSAB1 and TPSB2, carboxypeptidase CPA3, histidine decarboxylase (HDC), the transcription factor GATA2, the vesicular monoamine transporter SLC18A2, HPGDS, the IL-33 receptor (IL33R, official symbol IL1RL1) and RHEX. These genes are found in 75-100% of the cluster's cells and in almost no other cells (at most 1.4%, except HPGDS). The validator rejected the term because its ontology definition mentions CCR3, but that is not good evidence against mast cell identity. In single-cell RNA-seq, CCR3 mRNA is low or undetected in human tissue-resident mast cells, including those in the gut lining, so its absence in 10x 3' data is expected. The more specific term \"mucosal type mast cell\" inherits the same CCR3 statement, so switching would not help, and without CMA1 the mast cell subtype can't be resolved. No markers point to basophils, eosinophils or any other cell type, so CL:0000097 (mast cell) is kept."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 20.4}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "LMO4", "stance": "supports"}, {"gene": "CNRIP1", "stance": "supports"}], "rationale": "This cluster has the full mast cell program. It expresses the tryptases TPSAB1 and TPSB2, CPA3 (carboxypeptidase A3), HDC (histidine decarboxylase), the transcription factor GATA2, SLC18A2 (vesicular monoamine transporter), HPGDS, IL33R (official symbol IL1RL1, the IL-33 receptor) and RHEX. These genes are found in 75-100% of the cluster's cells and in at most 1.4% of other cells, except HPGDS. The CCR3 statement in the ontology definition comes from protein-level studies. CCR3 mRNA is low or undetected in human tissue-resident mast cells, including those in the gut lining, so 0% detection in 10x 3' data is expected and does not count against mast cell identity. The more specific term \"mucosal type mast cell\" inherits the same CCR3 statement, and without CMA1 (chymase) the subtype can't be resolved. No markers point to basophils, eosinophils or any other cell type, so CL:0000097 (mast cell) is kept."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 17.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ceffe8616a"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IL4R", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "B-cell identity: CD79A, CD79B, MS4A1, CD19, VPREB3, CD72 and immunoglobulin genes. The cells are IgM+ IgD+, with high TCL1A (97% in vs 3% out) and high IL4R and FCMR, which points to naive rather than memory B cells. No markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.3}], "model": "claude-opus", "protocol": 3, "task_id": "ct-d44564d7f6"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001054", "cell_type_label": "CD14-positive monocyte", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "The cluster strongly expresses the classical monocyte genes LYZ, S100A8, S100A9, S100A12, FCN1, VCAN, CSTA and MNDA. It also expresses general myeloid genes: TYROBP, AIF1, CTSS, FCER1G, LST1 and CST3. HLA-DRA is present but only moderately, so these are not dendritic cells. FCGR3A is missing, which argues against non-classical monocytes. C1Q and APOE are also missing, which argues against tissue-resident macrophages. In kidney cortex, this most likely reflects monocytes that circulate in the blood."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 8.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-d7d3163b78"} +{"attempts": [{"codes": ["BEV004"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "PPP1R14A", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}, {"gene": "TPSAB1", "stance": "contradicts"}], "rationale": "Strong contractile signature (TAGLN, ACTA2, MYL9, TPM1/2, CALD1, PPP1R14A) with ADIRF, C11orf96, SPARCL1 and IGFBP7 indicates smooth muscle / perivascular myofibroblast-like cells of the endometrium. Pericyte markers such as RGS5 and PDGFRB are not among the top genes, so smooth muscle is preferred over pericyte. TPSB2/TPSAB1 (mast cell tryptases) are expressed in most cells, suggesting mast-cell contamination or doublets. MT genes, FOS and GADD45B likely reflect dissociation stress."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.5}], "model": "claude-opus", "protocol": 3, "task_id": "ct-d929ec7963"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "ITGA6", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "GAS5", "stance": "supports"}, {"gene": "SNHG32", "stance": "supports"}], "rationale": "The cells express αβ T-cell genes (TRAC, CD3E, CD2) and CD4. They also have a lymph-node homing pattern (high CCR7 and SELL) with IL7R and CD27. ITGA6 (CD49f), FCMR and TESPA1 are enriched, and ribosomal and quiescence-associated transcripts (GAS5, SNHG32, RPLP1/2, EEF1A1) are high. Together these point to naive CD4 T cells rather than central memory cells. Effector or cytotoxic genes such as GZMs, NKG7 and CCL5 are absent, and IL32 is only modest. No markers point to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-e1bfaa2341"} +{"attempts": [{"codes": ["BEV026"], "evidence": 17, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "MATK", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "KLRD1 and KLRC1 are highly specific to this cluster (in 80-90% of its cells vs under 4% elsewhere). Together with NKG7, the granzymes GZMA/GZMK/GZMM, CST7 and CMC1, the signalling genes CD247 and MATK, and the chemokines XCL1/XCL2/CCL4/CCL5, this indicates cytotoxic NK cells. XCL1/2, GZMK and NKG2A (KLRC1) point to a CD56-bright, tissue-resident NK type, and CD69 fits colon residency. No CD3 genes are among the top markers, which argues against T cells. ILC1s and CD8 T cells cannot be fully excluded, so the broader NK cell term is used."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.0}, {"answer": {"cell_type_id": "CL:0000814", "cell_type_label": "mature NK T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "MATK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The cluster has a strong NK-receptor and cytotoxic program. KLRD1 (CD94) and KLRC1 (NKG2A) are each detected in 80-90% of cluster cells but in under 4% of other cells. NKG7, KLRB1 (CD161), the granzymes GZMA/GZMK/GZMM, CST7 and CMC1 are also high. However, CD3E is detected in about half of the cells and is enriched compared with other cells (logfc 0.35), so the cluster cannot be called a strictly CD3-negative NK cell. Taken together, CD3 expression plus NK receptors (CD94/NKG2A, CD161) and cytotoxic genes fit NK-like T cells (CL:0000814, mature NK T cell). CD247, XCL1/XCL2, CCL4/CCL5 and CD69 fit tissue-resident innate-like cytotoxic lymphocytes in the colon. Because CD3E is detected in only about 50% of cells, the cluster may also contain true NK cells or ILC1s mixed with NKT-like and CD8 T cells. This annotation is a best fit, not a definitive one."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35)."], "seconds": 18.9}], "model": "claude-opus", "protocol": 3, "task_id": "ct-e712a5eb84"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}], "rationale": "These are B cells: CD79A, CD79B, MS4A1 (CD20) and CD19 are all strongly expressed, along with high MHC class II. Several markers point to naive B cells in particular. IGHM and IGHD are both high, so the cells still carry IgM and IgD and have not class-switched. FCMR, CD24, VPREB3 and CXCR5 are also expressed, which fits resting naive or transitional B cells. There is no sign of the memory B cell markers CD27 or switched isotypes such as IGHG/IGHA, and no plasmablast markers. No markers clearly point to a different lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 8.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-e7ae6683c5"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "effector memory CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}, {"gene": "DUSP2", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "CD8A and CD8B are expressed alongside cytotoxic and effector genes: CCL5, NKG7, GZMK, GZMA, CST7, CTSW and CCL4. High GZMK with little GZMB/PRF1 among the top markers, together with CXCR3 and KLRG1, is typical of GZMK+ CD8 effector memory T cells, which are common in tonsil. CD8 expression argues against NK cells. CD74 and HLA-C are expressed in most cells inside and outside the cluster, so they don't identify a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 8.4}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ec5325a064"} +{"attempts": [{"codes": ["BEV026"], "evidence": 16, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "SAMD3", "stance": "supports"}, {"gene": "PYHIN1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "PRKCH", "stance": "supports"}], "rationale": "Strong cytotoxic program (GNLY, NKG7, GZMB, GZMA, PRF1, CST7) with KLRD1, HCST and CD247, plus near-exclusive FGFBP2, fits mature CD56dim-like NK cells. No CD3, TCR or CD8 genes among the top markers, which argues against cytotoxic T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}, {"gene": "SAMD3", "stance": "supports"}, {"gene": "PYHIN1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "PRKCH", "stance": "supports"}], "rationale": "CD3E is detected in 73% of the cluster's cells and is enriched here (logfc 0.60). That points to T cells, not NK cells. The cluster has a strong cytotoxic program (GNLY, NKG7, GZMB, GZMA, PRF1, CST7, CTSW, KLRD1, CCL5) and expresses the TCR-signalling genes CD247 and FYN. FGFBP2 is almost exclusive to this cluster. Together these fit terminally differentiated effector cytotoxic T cells with NK-like features. CD8 genes are not among the top markers and some NK cells may be mixed in, so the general term cytotoxic T cell is used."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60)."], "seconds": 16.1}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ed05c45d83"} +{"attempts": [{"codes": ["BEV026"], "evidence": 13, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 13, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "GCA", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}, {"gene": "IFITM2", "stance": "supports"}], "rationale": "This marker profile is a strong match for neutrophils. FCGR3B (CD16b) is close to specific to neutrophils, and its pct_out is only 0.015. CSF3R, S100P, S100A12, G0S2, CXCL8, GCA and MNDA are also typical of neutrophils. The high S100A8 and S100A9 levels fit myeloid granulocytes. Classical monocyte markers such as CD14, LYZ and HLA-DR are not among the top genes. No marker clearly points to another cell type. The kidney setting fits blood-derived neutrophils."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 8.9}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "GCA", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}, {"gene": "IFITM2", "stance": "supports"}], "rationale": "This cluster is a myeloid granulocyte population and is most likely neutrophils. FCGR3B is found in 67% of the cluster's cells but only 1.5% of other cells. CSF3R, S100P, S100A12, G0S2, CXCL8, GCA, MNDA and high S100A8/S100A9 also fit neutrophil-like granulocytes. Classical monocyte markers are not among the top genes. The neutrophil term (CL:0000775) is defined by CEACAM8, ITGAM and SPN on the membrane, but none of them is detected in this cluster. These genes often go undetected in 10x 3' neutrophil data, but their absence here means the neutrophil definition can't be confirmed. I am therefore assigning the parent term granulocyte, which the markers fully support. The neutrophil-specific genes FCGR3B, CSF3R and S100P make neutrophil the most likely specific identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells."], "seconds": 16.1}, {"answer": {"cell_type_id": "CL:0000766", "cell_type_label": "myeloid leukocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "GCA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}, {"gene": "IFITM2", "stance": "supports"}], "rationale": "This cluster is clearly a myeloid leukocyte population, and its pattern looks like neutrophils. S100A8, S100A9, S100A12 and MNDA point to myeloid cells. FCGR3B is found in 67% of the cluster's cells but only 1.5% of other cells. CSF3R, S100P, G0S2, CXCL8 and GCA are typical of neutrophils. The granulocyte and neutrophil terms both require CEACAM8 and ITGAM on the membrane, but neither gene is detected in this cluster. This is probably because these genes are often missed in 10x 3' data. Since those definitions can't be confirmed, I am assigning the broader parent term, myeloid leukocyte. The markers fully support this term. The most likely specific identity is neutrophil."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells."], "seconds": 12.3}], "model": "claude-opus", "protocol": 3, "task_id": "ct-f2e4fa20cc"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000897", "cell_type_label": "CD4-positive, alpha-beta memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "PASK", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}, {"gene": "KLF6", "stance": "supports"}, {"gene": "ZFP36L2", "stance": "supports"}, {"gene": "TSC22D3", "stance": "supports"}, {"gene": "CITED2", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "TXNIP", "stance": "supports"}], "rationale": "IL7R, GPR183, KLRB1, PASK and FYB1 point to resting memory T cells. Quiescence genes (KLF6, ZFP36L2, BTG1, TSC22D3, TXNIP, CITED2) and immediate-early genes are also present. There is no CD8 or cytotoxic signal, so this most likely is a CD4 memory (likely central memory) T-cell population in tonsil."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.2}], "model": "claude-opus", "protocol": 3, "task_id": "ct-f5551fdf21"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000050", "cell_type_label": "megakaryocyte-erythroid progenitor cell", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "PRDX2", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "ITGA2B", "stance": "supports"}, {"gene": "CD82", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "MCM5", "stance": "supports"}, {"gene": "CKS2", "stance": "supports"}], "rationale": "This cluster expresses early erythroid genes (HBB, HBD, CA1, BLVRB, PRDX2, TFRC, SLC40A1) together with megakaryocytic genes (ITGA2B/CD41 in 87% of cells vs 4% elsewhere, plus NFE2). The progenitor gene CDK6 is also high, as are many proliferation genes (STMN1, TYMS, PCNA, MCM2/5, CKS2, TUBB). A cycling progenitor that carries both erythroid and megakaryocyte programmes fits a megakaryocyte-erythroid progenitor (MEP). It is unlikely to be a later erythroblast because mature erythroid markers such as GYPA and ALAS2 are not among the top genes and ITGA2B is high. The other possibility is an early erythroid progenitor (CL:0000038, erythroid progenitor cell)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.6}], "model": "claude-opus", "protocol": 3, "task_id": "ct-f5e849f6ff"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002038", "cell_type_label": "T follicular helper cell", "decision": "annotate", "markers": [{"gene": "TOX2", "stance": "supports"}, {"gene": "PDCD1", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "GNG4", "stance": "supports"}, {"gene": "MAGEH1", "stance": "supports"}, {"gene": "CORO1A-AS1", "stance": "supports"}, {"gene": "ITM2A", "stance": "supports"}, {"gene": "NR3C1", "stance": "supports"}, {"gene": "FKBP5", "stance": "supports"}, {"gene": "PASK", "stance": "supports"}], "rationale": "TOX2, PDCD1, TIGIT, MAF and the GC-Tfh-specific GNG4 are enriched, along with MAGEH1, CORO1A-AS1, ITM2A and PASK. Together these define tonsillar germinal-center T follicular helper cells. No markers point to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-f6eff45a55"} +{"attempts": [{"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}], "rationale": "Strong cell-cycle signature: MKI67, TOP2A, TYMS, CENPF, PCLAF and NUSAP1 are in most cells of the cluster but rare elsewhere. Alongside it, the cytotoxic granule genes GNLY and GZMA are clearly expressed. In endometrium, GNLY- and GZMA-high lymphocytes are mostly uterine NK cells, which proliferate, especially in the secretory phase. This points to proliferating (uterine) NK cells, so the cluster is mapped to the parent term natural killer cell. Proliferating cytotoxic T cells can't be fully ruled out without CD3, NCAM1 and KLRD1 data."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.9}, {"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}], "rationale": "This cluster has a strong cell-cycle signature: MKI67, TOP2A, TYMS, CENPF, PCLAF and NUSAP1 are expressed in most of its cells but are rare elsewhere. These proliferating cells are cytotoxic lymphocytes, since they express the granule genes GNLY and GZMA. CD3E is found in 78% of the cluster's cells and is enriched compared with the rest of the dataset. That makes most of these cells T cells, not NK cells, which lack CD3. So the cluster is mapped to the general term T cell. The cytotoxic profile suggests proliferating effector T cells, likely CD8+. A smaller share of proliferating uterine NK cells may also be mixed in."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 10.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-f7efaf4b7a"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "ITGA6", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}], "rationale": "The T-cell identity is clear: TRAC, CD3E and CD2 are all high. CD4 is enriched, and no CD8 or cytotoxic genes appear among the top markers. High IL7R, CD27 and CCR7, with no effector genes (GZMB, NKG7 and so on), point to resting naive or central-memory CD4 T cells. ITGA6 and TESPA1 lean naive, while IL32 leans memory, so the cluster probably mixes both. I therefore chose the broader CD4-positive alpha-beta T cell term."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.7}], "model": "claude-opus", "protocol": 3, "task_id": "ct-ff19304f5c"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "TGFBI", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical markers of classical monocytes (CD14+ monocytes), including CD14, FCN1, VCAN, S100A8, S100A9, and LYZ, alongside other characteristic myeloid/monocyte markers (CST3, CSF3R, MPEG1, CTSS, TYROBP, and HLA-DRA). No contradicting lineage-specific markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-0094010baa"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}], "rationale": "The cluster shows high, specific enrichment for canonical basophil marker genes, including HDC (histidine decarboxylase, critical for histamine synthesis), CLC (Charcot-Leyden crystal protein), PRG2 (proteoglycan 2), FCER1A (high-affinity IgE receptor subunit alpha), CPA3 (carboxypeptidase A3), and RNASE2. Because mast cells do not typically circulate in human peripheral blood, this profile unambiguously identifies the cluster as basophils (CL:0000767)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.0}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "The cluster exhibits strong, specific expression of canonical mast cell markers, notably HDC (histidine decarboxylase, essential for histamine synthesis), CPA3 (carboxypeptidase A3, a key mast cell secretory granule protease), FCER1A (high-affinity IgE receptor subunit alpha), PRG2 (proteoglycan 2), CLC (Charcot-Leyden crystal protein), RNASE2, and SRGN (serglycin). Because CL:0000767 (basophil) was rejected due to its formal Cell Ontology definition requiring CD40LG, the profile aligns directly with mast cell (CL:0000097), which shares these hallmark granule and IgE-receptor components and is supported by membrane FCER1A expression."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells."], "seconds": 55.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-0224ef5d63"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [], "rationale": "The top marker genes for this cluster are predominantly immediate-early genes (FOS, FOSB, JUN), heat shock response genes (HSP90AA1, DNAJA1), stress/NF-kB pathway-related factors (NFKBIA, PPP1R15A, ZFP36, KLF2, KLF6), and nuclear non-coding RNAs (NEAT1, MALAT1, MIR23AHG). These genes reflect a cellular stress response or dissociation-induced artifact rather than defining a specific physiological cell type. Furthermore, canonical lineage-defining markers for major endometrial populations (epithelial, stromal fibroblast, endothelial, immune) are absent, and the weakly enriched markers (e.g., TAGLN/TPM2 for smooth muscle and TPSB2 for mast cells) are expressed at low fractions (25–35%) and are mutually contradictory. Therefore, the markers do not identify a distinct cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-027de551e6"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "PLAC8", "stance": "supports"}], "rationale": "The marker gene profile is characteristic of plasmacytoid dendritic cells (pDCs). Key lineage-defining transcription factors and markers include TCF4 (E2-2, the master regulator of pDC development), BCL11A, IRF7 (regulator of high type I interferon production), and IL3RA (CD123). Additionally, GZMB (granzyme B), CCDC50, ITM2C, PLAC8, MZB1, and JCHAIN are canonical markers highly expressed by human plasmacytoid dendritic cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.8}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-0460394dc8"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}], "rationale": "The cluster exhibits strong, specific expression of canonical B cell lineage markers, including MS4A1 (CD20), CD79A, CD79B, and BANK1, alongside high expression of antigen presentation molecules (CD74 and MHC class II genes HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DQB1) and CD37. This expression profile conclusively identifies the cluster as B cells (CL:0000236)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-04f3e6a976"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000359", "cell_type_label": "vascular associated smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}], "rationale": "The cluster exhibits high and specific expression of canonical vascular smooth muscle cell (VSMC) contractile and structural markers, including TAGLN (transgelin), ACTA2 (alpha-smooth muscle actin), MYH11 (smooth muscle myosin heavy chain), TPM1/TPM2 (tropomyosins), MYL9 (myosin light chain 9), and CALD1 (caldesmon 1). In particular, MYH11 robustly distinguishes mature vascular smooth muscle cells from other perivascular mural cells such as pericytes. In addition, the cluster expresses well-established VSMC and mural-associated genes including MGP (matrix Gla protein), ADIRF, SPARCL1, IGFBP7, and C11orf96. Together, this expression profile definitively identifies the cluster as vascular associated smooth muscle cells (CL:0000359)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-0919bb7151"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "This cluster shows strong expression of canonical T cell lineage markers (CD3E, CD2) and the alpha-beta T cell receptor constant chain (TRAC), alongside high expression of both CD8 co-receptor chains (CD8A, CD8B). It also expresses cytotoxic and effector/activation molecules typical of CD8+ alpha-beta T cells, such as KLRK1, CTSW, NKG7, CST7, and GZMA."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-15649bcc33"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "CLEC10A", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}], "rationale": "This cluster is characterized by extremely high expression of MHC class II molecules (HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQA1, HLA-DQB1, CD74, HLA-DMA) and dendritic/myeloid markers (CST3, COTL1, AIF1, CD83, GPR183). Crucially, it specifically expresses CLEC10A (CD301a), which is the canonical marker distinguishing type 2 conventional dendritic cells (cDC2; Cell Ontology: CD1c-positive myeloid dendritic cell, CL:0002399) from cDC1 (CLEC9A/XCR1), pDCs, and other myeloid lineages (such as monocytes or macrophages, whose key lineage markers like CD14, FCGR3A, CD163, CD68, C1Q are absent)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-18bf2c5651"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The cluster demonstrates high expression of classic T-cell lineage markers (CD3D, CD3E, CD2) and T-cell receptor alpha and beta chains (TRAC, TRBC1, TRBC2). Expression of both CD8A and CD8B clearly distinguishes these as CD8-positive, alpha-beta T cells. Furthermore, high expression of cytotoxic and effector markers such as GZMK, GZMA, CCL5, CCL4, CST7, along with the tissue residency/activation marker CD69, indicates an effector/tissue-resident memory CD8+ T cell phenotype. No conflicting lineage markers are observed."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-1c3cf91fbc"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "The cluster strongly and specifically expresses classical mast cell marker genes, including the mast cell-specific proteases TPSAB1, TPSB2, and CPA3, the high-affinity IgE receptor subunit MS4A2 (FcεRIβ), hematopoietic prostaglandin D synthase (HPGDS), the mast cell transcription factor GATA2, and RGS13. This profile conclusively identifies the cluster as mast cells (CL:0000097)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.6}, {"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [], "rationale": "Although the cluster expresses canonical mast cell markers such as TPSAB1, TPSB2, CPA3, HPGDS, and MS4A2, the pinned Cell Ontology definition for mast cell (CL:0000097) strictly requires plasma membrane presence of CCR3. Because CCR3 is detected in 0% of the cells in this cluster, it fails the formal criteria of CL:0000097, and no alternative specific Cell Ontology term accurately captures this marker profile without contradiction. Consequently, the markers do not definitively identify an ontology-compliant cell type, leading to an uncertain decision."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 43.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-1cdfab3be0"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "RETN", "stance": "supports"}], "rationale": "The marker gene expression profile is characteristic of monocytes (CL:0000576) recruited into the human colon mucosa. High expression of the alarmins S100A9 and S100A8 together with FCN1 and VCAN represents the canonical signature of infiltrating classical monocytes before they differentiate into mature tissue macrophages. Other enriched markers such as LYZ (lysozyme), MNDA, CST3, and RETN further support a monocyte identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-1dc66b7bae"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}], "rationale": "The cluster shows high and specific expression of canonical B-cell lineage markers (CD19, MS4A1/CD20, CD79A, CD79B, CD72, CD37) along with defining hallmarks of naive B cells, including strong co-expression of surface immunoglobulins IGHD and IGHM, together with TCL1A, VPREB3, and CD24. There are no contradicting marker genes from other lineages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-1fdfebb69c"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}], "rationale": "The cluster expresses the hallmark T cell receptor constant chains of the gamma-delta lineage, TRDC and TRGC2, along with cytotoxic and NK-like receptors characteristic of circulating gamma-delta T cells (such as NKG7, GNLY, GZMA, CST7, KLRB1, KLRK1, KLRD1, and FCGR3A)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-21afd5c734"} +{"attempts": [{"codes": ["BEV004"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "TRBC1", "stance": "contradicts"}], "rationale": "The cluster is characterized by high expression of TRDC (T cell receptor delta constant), which specifically defines gamma-delta T cells. Additionally, it expresses key mucosal gamma-delta T cell markers including KLRB1 (CD161), IL7R (CD127), CD69 (tissue residency/activation), TMIGD2 (CD28H), LTB, and RORA. High expression of TRBC1 (T cell receptor beta constant 1) contradicts a pure gamma-delta T cell identity and likely indicates contamination from ambient RNA or doublets with alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-227cbde019"} +{"attempts": [{"codes": ["BEV004"], "evidence": 12, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "PLD4", "stance": "supports"}, {"gene": "UGCG", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "FCER1A", "stance": "contradicts"}], "rationale": "The cluster strongly expresses hallmark markers of human plasmacytoid dendritic cells (pDCs), including IL3RA (CD123), the master transcription factors TCF4 (E2-2), IRF8, and IRF7, as well as canonical pDC-associated transcripts such as ITM2C, CCDC50, PLD4, UGCG, MZB1, JCHAIN, and CXCR3. In contrast, FCER1A is a canonical marker of conventional dendritic cells (specifically cDC2s) and basophils, which pDCs typically lack, likely reflecting minor doublet/ambient RNA contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-26fda93c9c"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). Closest names: CL:0000906 (activated CD8-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The cluster strongly and specifically expresses canonical markers of CD8+ T cells (CD8A, CD8B, CD3E, TRAC, CD2) together with key markers of naive T cell state, including CCR7, SELL (CD62L), CD27, and IL7R (CD127), while lacking mature effector/cytotoxic gene expression programs. This profile precisely identifies naive CD8-positive, alpha-beta T cells (CL:0000900)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.9}, {"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The cluster strongly expresses CD8+ alpha-beta T cell markers (CD8A, CD8B, CD3E, TRAC, CD2) alongside canonical naive T cell markers (CCR7, SELL, CD27, IL7R). In Cell Ontology, the exact term name for CL:0000900 is 'naive thymus-derived CD8-positive, alpha-beta T cell'."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). Closest names: CL:0000906 (activated CD8-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell)."], "seconds": 10.0}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-28eb7ea379"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "MRC1", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "MERTK", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "STAB1", "stance": "supports"}, {"gene": "F13A1", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical macrophage markers, including scavenger receptors (MRC1/CD206, CD163, STAB1, MERTK, LYVE1), complement components (C1QA, C1QB), and resident macrophage-associated genes (F13A1, SELENOP, RNASE1). This profile unambiguously identifies the cluster as macrophages (CL:0000235)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-302af8ae13"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV026"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'megakaryocyte progenitor cell' is not the name of CL:0002048 ('late pro-B cell'). 'megakaryocyte progenitor cell' is the name of CL:0000553 (megakaryocyte progenitor cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0002048 (late pro-B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0002048 (late pro-B cell) is defined as having neprilysin (MME) on the membrane, but MME is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0002048", "cell_type_label": "megakaryocyte progenitor cell", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "GUCY1B1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "PDLIM1", "stance": "supports"}, {"gene": "FERMT3", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "FCER1A", "stance": "contradicts"}], "rationale": "The cluster exhibits high expression of the hematopoietic stem and progenitor marker CD34 alongside cell cycle/proliferation markers (STMN1, CDK6, TYMS), indicating an active progenitor population. Concurrently, it strongly expresses ITGA2B (CD41), the cardinal marker of megakaryocytic commitment among CD34+ progenitors, together with megakaryocyte lineage-specific transcription factors (TAL1, NFE2) and megakaryocyte/platelet-associated genes (PPBP, PLEK, GUCY1B1, SPARC, FERMT3, PDLIM1). This combination definitively identifies the cells as megakaryocyte progenitor cells (CL:0002048). FCER1A, which is primarily a marker of basophils, mast cells, and conventional dendritic cells, is listed as contradicting."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.2}, {"answer": {"cell_type_id": "CL:0000553", "cell_type_label": "megakaryocyte progenitor cell", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "GUCY1B1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "PDLIM1", "stance": "supports"}, {"gene": "FERMT3", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "FCER1A", "stance": "contradicts"}], "rationale": "The cluster shows high expression of CD34 along with proliferation markers (STMN1, CDK6, TYMS), characteristic of progenitor cells. Concurrently, it expresses ITGA2B (CD41), the cardinal marker of megakaryocytic commitment among CD34+ progenitors, together with megakaryocytic transcription factors (TAL1, NFE2) and megakaryocyte/platelet-lineage genes (PPBP, PLEK, GUCY1B1, SPARC, FERMT3, PDLIM1). This identifies the population as megakaryocyte progenitor cells (CL:0000553). FCER1A expression is noted as contradicting."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'megakaryocyte progenitor cell' is not the name of CL:0002048 ('late pro-B cell'). 'megakaryocyte progenitor cell' is the name of CL:0000553 (megakaryocyte progenitor cell).", "object id: CL:0002048 (late pro-B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 4% of the cluster's cells.", "object id: CL:0002048 (late pro-B cell) is defined as having neprilysin (MME) on the membrane, but MME is detected in only 0% of the cluster's cells."], "seconds": 9.0}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-3775a26491"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster exhibits high and specific expression of canonical mast cell marker genes, including tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), KIT (CD117), hematopoietic prostaglandin D synthase (HPGDS), and the IL-33 receptor (IL33R/IL1RL1). These genes strongly support the identification of this cluster as mast cells (CL:0000097)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.3}, {"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "Although the cluster strongly expresses canonical marker genes of mast cells—including tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), KIT (CD117), hematopoietic prostaglandin D synthase (HPGDS), and the IL-33 receptor (IL33R/IL1RL1)—the formal Cell Ontology definition for mast cell (CL:0000097) requires the presence of C-C chemokine receptor type 3 (CCR3) on the plasma membrane. Because CCR3 is detected in 0% of the cells in this cluster, it fails the formal ontological criteria for CL:0000097, and no alternative cell type term uniquely and consistently fits this expression profile. Therefore, following the guideline, the decision is set to uncertain."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 101.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-3959f97db0"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 4, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004"], "evidence": 4, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "CD34", "stance": "contradicts"}], "rationale": "This cluster expresses key hallmark markers of basophils in human peripheral blood, most notably FCER1A, CPA3 (carboxypeptidase A3), and SLC40A1 (ferroportin). While CD34 is present and typically marks hematopoietic stem/progenitor cells (contradicts mature basophil identity), the combination of high FCER1A and CPA3 expression with high SLC40A1 strongly defines the basophil cluster in targeted mRNA blood profiling."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 84.9}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "CD34", "stance": "contradicts"}], "rationale": "This cluster is characterized by high, specific expression of FCER1A (high-affinity IgE receptor subunit alpha) and CPA3 (carboxypeptidase A3), along with SLC40A1, which are canonical hallmark markers of mast cells (CL:0000097). Although basophil (CL:0000767) shares these markers, its formal Cell Ontology definition requires CD40LG, which is undetected (0%) in this cluster. Consequently, the cluster corresponds to mast cell (CL:0000097). CD34 is present and typically associated with immature progenitor cells, thus contradicting mature mast cell status."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells."], "seconds": 53.5}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-3b8c7f5246"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "MT2A", "stance": "supports"}, {"gene": "S100A10", "stance": "supports"}, {"gene": "FABP5", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "H4C3", "stance": "supports"}, {"gene": "PMAIP1", "stance": "supports"}, {"gene": "CD99", "stance": "supports"}, {"gene": "ACTG1", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "CLIC1", "stance": "supports"}, {"gene": "PPIA", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}], "rationale": "This cluster represents proliferating/cycling T cells from the human tonsil dataset. It is characterized by high expression of canonical cell cycle and mitosis-associated genes (STMN1, TUBA1B, TUBB, HMGB2, H4C3, TYMS) alongside markers of T lymphocytes and T-cell activation/effector function, including GZMK (Granzyme K, characteristic of effector/memory cytotoxic T cells), CD99 (involved in T-cell adhesion and transendothelial migration), CD74 (upregulated on activated human T cells), and members of the S100 family (S100A4, S100A6, S100A10) and FABP5. In standard Cell Ontology mappings for single-cell atlases, proliferating T-cell clusters map to 'T cell' (CL:0000084). None of the marker genes clearly indicate doublets or a contradicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 63.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-3daee1395a"} +{"attempts": [{"codes": ["BEV004"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TRGC2", "stance": "contradicts"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CD99", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}], "rationale": "This cluster displays high expression of pan-T cell markers (CD3E, CD3G, CD2) along with TCR alpha constant (TRAC) and CD8 co-receptors (both CD8A and CD8B), definitively identifying it as a CD8-positive, alpha-beta T cell (CL:0000625). It also expresses a strong cytotoxic effector/TEMRA profile (NKG7, CST7, GZMA, GNLY, CTSW, KLRK1, KLRD1, ADGRG1, FCGR3A, HCST). TRGC2 (TCR gamma constant 2) typically characterizes gamma-delta T cells and is thus listed as contradicting the alpha-beta lineage, although sterile or rearranged TCRG transcripts can occasionally be detected in cytotoxic alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.0}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-4b8439fcc9"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0008001", "cell_type_label": "hematopoietic precursor cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "MPO", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}], "rationale": "This cluster represents hematopoietic stem and progenitor cells (HSPCs), annotated in the Cell Ontology as hematopoietic precursor cell (CL:0008001). It is characterized by high, specific expression of canonical stem/progenitor markers CD34, SPINK2, and PRSS57, along with proliferation markers such as STMN1 and CDK6. In single-cell RNA-seq of blood/PBMCs, HSPCs characteristically exhibit multilineage transcriptional priming, displaying early markers of myeloid differentiation (MPO, AZU1, CSF3R), lymphoid/B-lineage differentiation (IGLL1, SOX4), and erythroid/mast cell differentiation (CPA3, NFE2) rather than marking contaminating mature cell types."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.8}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-4e9d71ecad"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "TIMP1", "stance": "supports"}, {"gene": "CTSL", "stance": "supports"}, {"gene": "FTH1", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "AQP9", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "CCL20", "stance": "supports"}, {"gene": "PLIN2", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}], "rationale": "The cluster expresses characteristic markers of tissue macrophages, including lysosomal enzymes and antigen processing machinery (CTSL, IFI30), high levels of iron storage proteins (FTH1, FTL), Fc receptor signaling components (FCER1G), and tissue remodeling/activation markers (TIMP1, PLAUR, KYNU, CXCL8, CCL20, PLIN2). Lack of monocyte markers (such as S100A8, S100A9, VCAN) and lineage markers for epithelial, stromal, or other immune compartments confirms this cluster is macrophage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-5169234be6"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The cluster shows strong and specific expression of T cell receptor gamma and delta chain constant regions (TRDC and TRGC2), together with the pan-T cell marker CD3E and CD2. It also displays a characteristic cytotoxic and NK-like gene expression profile typical of gamma-delta T cells in peripheral blood, including NKG7, CST7, GZMA, CTSW, KLRB1 (CD161), KLRK1 (NKG2D), KLRD1 (CD94), and GNLY. There are no contradictory markers from other lineages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-56d8f3ebbf"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000980", "cell_type_label": "plasmablast", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "SEL1L3", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC61B", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}], "rationale": "This cluster exhibits the hallmark transcriptomic profile of plasmablasts (CL:0000980), which are circulating antibody-secreting B-lineage cells found in peripheral blood. The top marker genes prominently feature immunoglobulin production (JCHAIN, IGKC), plasma cell/plasmablast differentiation and master transcription factors (MZB1, XBP1), components of the expanded endoplasmic reticulum and secretory/ER-associated degradation machinery (DERL3, FKBP11, SEC11C, SEC61B, SSR4, HSP90B1, HERPUD1), and canonical surface phenotypes including CD27, CD38, ITM2C, and retained expression of B-cell lineage markers CD19 and CD79A characteristic of plasmablasts. None of the listed markers contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-62995bbc69"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'T-helper 17 cell' is not the name of CL:0001077 ('ILC1, human'). 'T-helper 17 cell' is the name of CL:0000899 (T-helper 17 cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001077", "cell_type_label": "T-helper 17 cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "PRDM1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "This cluster represents T-helper 17 (Th17) cells (CL:0001077). In human tonsil and peripheral lymphoid tissues, Th17 cells are uniquely characterized by high expression of KLRB1 (CD161), which marks human IL-17-producing CD4+ T cells, together with the Th17 lineage-specifying transcription factor RORA and MAF (c-Maf). The cluster also displays characteristic memory and activation markers associated with tonsillar effector CD4+ T helper subsets, including CD2, S100A4, TNFRSF4 (OX40), TNFRSF18 (GITR), CTLA4, PRDM1 (BLIMP1), and IL32, with no expression of confounding lineage markers for B cells, myeloid cells, or cytotoxic/NK cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.2}, {"answer": {"cell_type_id": "CL:0000899", "cell_type_label": "T-helper 17 cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "PRDM1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "This cluster represents T-helper 17 (Th17) cells (CL:0000899). In human tonsil and peripheral lymphoid tissues, Th17 cells are characterized by expression of KLRB1 (CD161), along with the lineage-associated transcription factor RORA and MAF (c-Maf). The cluster also displays activation, costimulatory, and effector markers characteristic of CD4+ memory/effector helper T cells, including CD2, S100A4, TNFRSF4 (OX40), TNFRSF18 (GITR), CTLA4, PRDM1, and IL32."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'T-helper 17 cell' is not the name of CL:0001077 ('ILC1, human'). 'T-helper 17 cell' is the name of CL:0000899 (T-helper 17 cell)."], "seconds": 9.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-62ef0fd4ba"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster specifically expresses canonical mast cell markers at high levels and high specificity, including tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the high-affinity IgE receptor subunit beta (MS4A2), hematopoietic prostaglandin D synthase (HPGDS), the essential mast cell lineage transcription factor GATA2, and leukotriene C4 synthase (LTC4S)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.9}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "uncertain", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical mast cell markers at high levels and specificity, including tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the high-affinity IgE receptor beta subunit (MS4A2), hematopoietic prostaglandin D synthase (HPGDS), GATA2, and leukotriene C4 synthase (LTC4S). However, the Cell Ontology definition for mast cell (CL:0000097) requires C-C chemokine receptor type 3 (CCR3) on the plasma membrane. Because CCR3 is detected in 0% of the cluster's cells, the cluster fails to satisfy the formal ontology definition of CL:0000097. Consequently, the markers do not definitively identify an ontology-conformant cell type, and the decision is set to uncertain."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 113.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-68351aaa63"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "CST3", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "FCGRT", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}], "rationale": "The cluster exhibits high expression of classic macrophage marker genes, including complement C1q components (C1QA, C1QB, C1QC), tissue-resident intestinal macrophage markers (SELENOP, CST3, AIF1/IBA1, MS4A7, TYROBP), antigen presentation molecules (HLA-DRA, HLA-DRB1, HLA-DPA1, CD74), and inflammatory chemokines (CCL3, CCL4), which unequivocally identify this cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-6dacd7effa"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}], "rationale": "The cluster demonstrates high and specific expression of canonical T cell lineage markers (CD3D, CD3E, CD3G, CD2, BCL11B) and T cell receptor alpha and beta constant chains (TRAC, TRBC2), establishing it as an alpha-beta T cell. Furthermore, the strong enrichment of IL7R (CD127) and CD40LG (CD154), alongside cytokine/effector-associated genes like LTB and IL32, and the lack of CD8A/CD8B or cytotoxic granules, specifically identifies this cluster as CD4-positive, alpha-beta T cells (CL:0000624)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.8}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-72757d8950"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CBLB", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}], "rationale": "The cluster is characterized by high, specific expression of key T cell markers including IL7R (CD127), FYN (Src family kinase involved in TCR signaling), CD96 (T/NK cell receptor), CAMK4 (calcium/calmodulin-dependent protein kinase IV involved in T cell development/activation), ETS1 (transcription factor essential for T cell survival and differentiation), and activation/tissue-resident marker CD69, along with effector/chemokine genes like CCL5. This expression profile conclusively identifies the cluster as a T cell (CL:0000084)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-72dfb189c0"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "SPINK2", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "MSI2", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}], "rationale": "The marker profile is defined by canonical human hematopoietic stem and progenitor cell (HSPC) markers, particularly CD34 and PROM1 (CD133), alongside genes characteristic of primitive hematopoietic stem cells (HSCs) such as SPINK2, CRHBP, HOPX, EGFL7, and MSI2. In particular, CRHBP and SPINK2 are well-established specific markers for human hematopoietic stem cells and multipotent progenitors."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-75adde23f7"} +{"attempts": [{"codes": ["BEV004"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "TRBC1", "stance": "contradicts"}], "rationale": "This cluster is identified as group 3 innate lymphoid cells (ILC3; CL:0001071). The cluster strongly expresses hallmark markers of human ILC3s, including IL7R (CD127), KIT (CD117), KLRB1 (CD161), the key lineage-specifying transcription factor AHR, the functional cytokine LTB (lymphotoxin beta), IL4I1, and costimulatory members of the TNF receptor superfamily (TNFRSF18/GITR, TNFRSF4/OX40). In contrast, the expression of TRBC1 (T cell receptor beta constant 1) contradicts an innate lymphoid cell classification, as ILCs by definition lack rearranged antigen receptors; this indicates the presence of contaminating T cells or T-cell doublets in the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 61.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-76fa626271"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "SPINK2", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}], "rationale": "The cluster expresses classic hematopoietic stem and progenitor cell markers, notably CD34, SPINK2, and PROM1 (CD133), along with proliferation/progenitor-associated genes such as STMN1, CDK6, and EGFL7. In blood scRNA-seq datasets, these cells correspond to circulating CD34+ hematopoietic stem cells (CL:0000037)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.5}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-7a81a9a19f"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}], "rationale": "The cluster specifically expresses pan-T cell markers (CD3D, CD3E, CD3G, CD2, BCL11B) alongside alpha-beta T-cell receptor constant regions (TRAC, TRBC2). It shows high and specific expression of both CD8 co-receptor chains (CD8A and CD8B) as well as effector/cytotoxic molecules (GZMK, GZMM, GZMH, CST7, CCL5, IL32), which unambiguously identifies it as a CD8-positive, alpha-beta T cell (CL:0000625)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-7c21a7ad85"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}], "rationale": "The cluster specifically and strongly expresses TRDC (T cell receptor delta constant chain), which is the definitive lineage marker for gamma-delta T cells. Furthermore, it displays characteristic cytotoxic and innate-like lymphocyte markers shared between gamma-delta T cells and NK cells, including XCL1, XCL2, CTSW, GNLY, KLRB1 (CD161), KLRC1 (NKG2A), TYROBP, and FCER1G, alongside the T-cell marker CD7."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-7ec8cd3664"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The top marker genes are canonical for kidney tissue-resident macrophages. Specifically, the strong and selective enrichment of complement C1q subunits (C1QA, C1QB, C1QC), myeloid/macrophage lineage and activation markers (CD14, AIF1/IBA1, TYROBP, FCER1G, MS4A6A, SELENOP, RNASE1), along with high expression of MHC class II antigen presentation molecules (CD74, HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1), uniquely identifies this cluster as macrophages (CL:0000235). There are no contradictory lineage markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-819cfbd986"} +{"attempts": [{"codes": ["BEV004"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "NELL2", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "LINC02446", "stance": "supports"}, {"gene": "AIF1", "stance": "contradicts"}], "rationale": "The cluster shows strong and specific expression of the CD8 co-receptors CD8A and CD8B, identifying it as a CD8-positive T cell population. Furthermore, canonical markers of naive T cells are highly enriched, including CCR7, SELL (CD62L), LEF1, NELL2, and KLF2, along with LINC02446 (a known lncRNA marker of naive CD8+ T cells). AIF1 is typically associated with myeloid cells/macrophages and may represent low-level background or minor doublet contribution, contradicting the naive T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-81b1e8f8f5"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "PRDX4", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}], "rationale": "The top differentially expressed genes are canonical markers for plasma cells. These include immunoglobulin heavy and light chains (IGKC, IGHG1, IGHG3, IGHG4, IGHG2, IGHA1, IGHM, IGLC1, IGLC2, IGLC3), joining chain (JCHAIN), plasma cell maturation and endoplasmic reticulum markers (MZB1, DERL3, FKBP11, XBP1, SEC11C, SSR4, PRDX4, HERPUD1), along with the B-lineage marker CD79A. All markers strongly and consistently support the annotation of plasma cell (CL:0000786)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-879d085000"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "AIF1", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}], "rationale": "The cluster exhibits high expression of canonical macrophage and myeloid lineage markers, including AIF1 (IBA1), C1QA (complement component C1q, characteristic of tissue-resident macrophages), CD14, and LYZ (lysozyme), along with prominent expression of MHC class II and antigen presentation machinery (HLA-DRA, HLA-DRB1, HLA-DPA1, CD74, IFI30, CTSS). This expression profile unambiguously identifies the cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-89c1241fbf"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster prominently expresses canonical T cell markers, including the CD3 complex components (CD3D, CD3E), T cell receptor constant chains (TRAC, TRBC2), T cell surface glycoprotein CD2, the IL-7 receptor subunit IL7R (CD127), and cytokines/signaling molecules characteristic of human T cells (IL32, LTB, CD52). There are no contradictory lineage markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.8}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-8ab1b5fbd8"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000875", "cell_type_label": "non-classical monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "NR4A1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "The cluster exhibits strong, specific upregulation of FCGR3A (CD16), MS4A7, LST1, AIF1, and NR4A1 alongside general myeloid/monocyte markers (CST3, FCER1G, TYROBP, ITGAX, CTSS). In human peripheral blood, this expression profile definitively identifies non-classical monocytes (CL:0000875)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.8}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-8c07cf76ca"} +{"attempts": [{"codes": ["BEV004"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "IFITM2", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "TRDC", "stance": "contradicts"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IFITM3", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}], "rationale": "The cluster is defined by high expression of canonical natural killer (NK) cell markers, including killer cell lectin-like receptors (KLRD1, KLRC1, and the NK-specific marker KLRF1/NKp80), activating signaling adapters (TYROBP/DAP12, FCER1G), cytotoxic molecules (GNLY, NKG7, GZMB, CST7, CTSW), chemokines characteristic of NK cells (XCL1, XCL2, CCL5), and typical NK surface markers (CD7, IL2RB). TRDC (T cell receptor delta constant) is expressed, which typically defines gamma-delta T cells and may represent sterile/non-productive transcripts or potential doublet/contamination, thus contradicting the NK cell assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.0}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-8d82b1a772"} +{"attempts": [{"codes": ["BEV004"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TRGC2", "stance": "contradicts"}], "rationale": "The cluster robustly expresses core T cell receptor components including CD3 (CD3E, CD3G) and the alpha-beta constant chain TRAC, along with CD8 co-receptors (CD8A, CD8B). It also highly expresses cytotoxic effector molecules and activation markers characteristic of cytotoxic CD8+ T cells (NKG7, CST7, GZMA, KLRK1, CTSW, IL32, and CD2). TRGC2 (T cell receptor gamma constant 2) is characteristic of gamma-delta T cells and thus contradicts the alpha-beta lineage assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-95367720e6"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "BACH2", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical B cell markers including MS4A1 (CD20), CD79A, BANK1, IGKC, and BACH2, along with high levels of MHC class II molecules (HLA-DRA, HLA-DRB1, HLA-DQA1, HLA-DPA1, and CD74). These markers definitively identify this cluster as a B cell (CL:0000236)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-9814423bdc"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}], "rationale": "The expression profile is characteristic of natural killer (NK) cells. It features key NK lineage and cytotoxic markers including KLRF1 (NKp80, highly specific for NK cells), KLRD1 (CD94), KLRB1 (CD161), FCGR3A (CD16), and TYROBP (DAP12), alongside classical cytotoxic effector molecules and associated genes (GNLY, NKG7, PRF1, GZMB, GZMA, FGFBP2, SPON2, CST7, and CLIC3)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-98402e60db"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The top marker genes are heavily enriched for complement component C1q genes (C1QA, C1QB, C1QC), APOE, LYZ, TYROBP, and high levels of MHC class II molecules (HLA-DRA, HLA-DRB1, HLA-DPA1, CD74). This signature is characteristic of tissue-resident macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-9d243229e7"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000836", "cell_type_label": "promyelocyte", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "CDC20", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}], "rationale": "This cluster shows high expression of primary (azurophilic) granule genes such as MPO and AZU1, combined with robust expression of cell cycle and proliferation markers (STMN1, TYMS, PCNA, CDC20, TUBA1B, TUBB). In the granulocytic lineage, azurophilic granule protein genes are maximally transcribed at the actively cycling promyelocyte stage before being downregulated in later stages (myelocytes/metamyelocytes). Together with other myeloid markers like LYZ, RNASE2, and S100A8, this profile unambiguously identifies the cluster as promyelocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-9d2a6afe3f"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "CD33", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}], "rationale": "The cluster exhibits specific and high expression of FCER1A and CD1C (BDCA-1), which are the defining canonical markers for type 2 conventional / myeloid dendritic cells (cDC2 / CD1c-positive myeloid dendritic cells) in human peripheral blood. In addition, the cluster shows strong enrichment for MHC class II antigen presentation molecules (HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DRB5, HLA-DQB1, and CD74) alongside pan-myeloid/dendritic markers such as ITGAX (CD11c), CD33, CST3, and LYZ. There are no contradicting lineage markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-9e8b98aab5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 20, "findings": [{"message": "The label 'transit amplifying cell of colon' is not the name of CL:0009010 ('transit amplifying cell'). 'transit amplifying cell of colon' is the name of CL:0009011 (transit amplifying cell of colon).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0009010", "cell_type_label": "transit amplifying cell of colon", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "H2AZ1", "stance": "supports"}, {"gene": "HMGN2", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "H4C3", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "HMGB1", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "DEK", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "NUCKS1", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}], "rationale": "The top marker genes for this cluster are canonical markers of active cell cycle, DNA replication, and mitosis, including MKI67, TOP2A, CDK1, CENPF, PCLAF, TYMS, UBE2C, NUSAP1, ASPM, STMN1, and HMGB2. In the human colon epithelium, this highly proliferative signature specifically characterizes transit-amplifying (TA) cells located within the colonic crypts. None of the top marker genes contradict this annotation or indicate doublets/lineage mixing."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.8}, {"answer": {"cell_type_id": "CL:0009011", "cell_type_label": "transit amplifying cell of colon", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "H2AZ1", "stance": "supports"}, {"gene": "HMGN2", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "H4C3", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "HMGB1", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "DEK", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "NUCKS1", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}], "rationale": "The marker profile shows high expression of proliferation, mitotic, and cell-cycle genes (TOP2A, MKI67, CDK1, CENPF, PCLAF, TYMS, UBE2C, NUSAP1, ASPM, STMN1, HMGB2), which in the human colonic crypt specifically characterizes transit amplifying cells of colon (CL:0009011). None of the marker genes contradict this cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'transit amplifying cell of colon' is not the name of CL:0009010 ('transit amplifying cell'). 'transit amplifying cell of colon' is the name of CL:0009011 (transit amplifying cell of colon)."], "seconds": 9.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-a321096724"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'pre-B cell' is not the name of CL:0000828 ('thromboblast'). Closest names: CL:0000956 (pre-B-I cell); CL:0000826 (pro-B cell); CL:0000955 (pre-B-II cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000828", "cell_type_label": "pre-B cell", "decision": "annotate", "markers": [{"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CMTM7", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "RCSD1", "stance": "supports"}], "rationale": "The cluster demonstrates characteristic expression of the pre-B cell receptor (pre-BCR) complex, defined by the immunoglobulin mu heavy chain (IGHM) paired with the surrogate light chain components IGLL1 (lambda 5) and VPREB1 (CD179a), alongside VPREB3. In addition, the cluster co-expresses the BCR signaling subunits CD79A and CD79B, the pre-BCR chaperone/regulator CMTM7, early B-cell transcription factor SOX4, and early B-lineage surface marker CD24. Together, these markers conclusively identify the cluster as pre-B cells (CL:0000828)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.5}, {"answer": {"cell_type_id": "CL:0000955", "cell_type_label": "pre-B-II cell", "decision": "annotate", "markers": [{"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CMTM7", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "RCSD1", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of the components of the pre-B cell receptor (pre-BCR) complex: the immunoglobulin mu heavy chain (IGHM) paired with the surrogate light chain elements IGLL1 (lambda 5) and VPREB1 (CD179a), as well as VPREB3. The signaling co-receptors CD79A and CD79B, pre-BCR associated regulator CMTM7, early B-cell marker CD24, and transcription factor SOX4 are also strongly expressed. The high expression of productive mu heavy chain (IGHM) alongside surrogate light chain distinguishes pre-B-II cells (CL:0000955) from pre-B-I cells (CL:0000956) and pro-B cells (CL:0000826), which lack mu heavy chain expression."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pre-B cell' is not the name of CL:0000828 ('thromboblast'). Closest names: CL:0000956 (pre-B-I cell); CL:0000826 (pro-B cell); CL:0000955 (pre-B-II cell)."], "seconds": 21.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-a33f382e85"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}], "rationale": "The cluster shows strong, specific expression of canonical B cell lineage markers, including MS4A1 (CD20), CD79A, CD79B, CD37, BANK1, SPIB, and TNFRSF13C (BAFF-R). It also highly expresses immunoglobulin heavy (IGHM, IGHD) and light chains (IGKC, IGLC2, IGLC3) in a polyclonal pattern, as well as antigen presentation molecules (CD74, HLA-DRA), firmly establishing the identity as B cells (CL:0000236). There are no contradictory markers from other lineages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.5}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ac7ec2b016"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "The cluster demonstrates high expression of immunoglobulin light and heavy constant region genes (IGKC, IGHG1, IGHG3) along with ELL2 (an elongation factor essential for the alternative polyadenylation and high-rate secretion of immunoglobulin heavy chains in plasma cells). This profile strongly supports the annotation as plasma cell (CL:0000786). HDC (histidine decarboxylase) is a canonical marker for mast cells and basophils, likely reflecting minor doublet contamination or ambient RNA, thus contradicting pure plasma cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.8}, {"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "COBLL1", "stance": "supports"}, {"gene": "HDC", "stance": "contradicts"}], "rationale": "The cluster exhibits high expression of immunoglobulin genes (IGKC, IGHG1, IGHG3) along with COBLL1, a well-established marker for B cells. Although the cluster produces immunoglobulins, the lack of substantial syndecan-1 (SDC1/CD138) expression rules out mature plasma cells, supporting its identification as a B cell (CL:0000236). HDC expression likely represents trace ambient RNA or minor mast cell doublet contamination, contradicting pure B cell identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells."], "seconds": 18.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ad2d591627"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "TRDC", "stance": "contradicts"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of classical natural killer (NK) cell markers, including cytotoxicity-associated genes (GNLY, NKG7, GZMA, GZMB, PRF1, CST7), NK cell receptors and signaling molecules (KLRC1/NKG2A, KLRD1/CD94, KLRB1/CD161, IL2RB/CD122, HCST/DAP10, CD247), as well as chemokines characteristic of endometrial/uterine NK cells (XCL1, XCL2, CCL4, CCL5). The presence of TRDC (T cell receptor delta constant) typically indicates gamma-delta T cells, contrasting with an NK cell identity, though sterile TRDC transcripts are also known to be expressed in some human NK cell populations."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.5}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The cluster strongly expresses TRDC (T cell receptor delta constant chain) and components of the CD3/TCR signaling complex (CD247/CD3-zeta, along with CD3E), identifying it as a gamma-delta T cell population rather than natural killer cells. Gamma-delta T cells, particularly in mucosal and reproductive tissues like the endometrium, exhibit a strong cytotoxic phenotype characterized by high expression of effector molecules (GNLY, NKG7, GZMA, GZMB, PRF1, CTSW, CST7), NK-associated surface receptors and signaling molecules (KLRD1, KLRC1, KLRB1, HCST, IL2RB), T-cell markers (CD7), and chemokines (CCL4, CCL5, XCL1, XCL2), all of which are consistent with this cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59)."], "seconds": 14.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ae89c1380f"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "THBS1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "EREG", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "The cluster exhibits hallmark expression of classical monocyte markers including S100A9, S100A8, VCAN, THBS1, LYZ, and C5AR1, alongside myeloid lineage genes such as AIF1, TYROBP, and IFI30. The high expression of S100A8/S100A9 (calprotectin) and VCAN, paired with the absence of mature tissue-resident macrophage markers (such as C1Q genes, CD163, MRC1), identifies this cluster as monocytes (CL:0000576)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b269766ee9"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}, {"gene": "LDHB", "stance": "supports"}, {"gene": "TXNIP", "stance": "supports"}, {"gene": "FLT3LG", "stance": "supports"}, {"gene": "LINC00861", "stance": "supports"}], "rationale": "The marker gene profile is characteristic of naive CD4+ alpha-beta T cells (naive thymus-derived CD4-positive, alpha-beta T cell, CL:0000895). Key canonical markers include lymph node homing receptors CCR7 and SELL (CD62L), key transcription factors LEF1 and KLF2 that maintain naive T cell identity and quiescence, as well as IL7R (CD127), NOSIP, LDHB, and TXNIP, which are classic signatures of quiescent naive CD4+ T lymphocytes in human lymphoid tissues such as tonsil."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b322bece33"} +{"attempts": [{"codes": ["BEV004"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "ANXA1", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}, {"gene": "HLA-C", "stance": "supports"}, {"gene": "TSC22D3", "stance": "supports"}, {"gene": "TRGC2", "stance": "contradicts"}, {"gene": "HBB", "stance": "contradicts"}], "rationale": "This cluster originates from the CD45+ immune-sorted single-cell dataset of human kidney cortex (Stewart et al., 2019). The cluster shows high and specific enrichment of T cell receptor complex components (CD3D, CD3G) alongside an extensive cytotoxic effector program including granzymes (GZMH, GZMB, GZMA), perforin (PRF1), granulysin (GNLY), NKG7, FGFBP2, chemokines (CCL5, CCL4), and killer cell lectin-like receptors (KLRD1, KLRG1). This profile uniquely identifies cytotoxic CD8-positive, alpha-beta T cells (CL:0000625). TRGC2 reflects gamma-delta T cell marker expression (likely from minor co-clustering of gd T cells), and HBB represents ambient erythrocyte hemoglobin contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 107.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b51a9f2d53"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 8, "findings": [{"message": "The label 'type 1 regulatory T cell' is not the name of CL:0000906 ('activated CD8-positive, alpha-beta T cell'). Closest names: CL:0000815 (regulatory T cell); CL:0002677 (naive regulatory T cell); CL:0002678 (memory regulatory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000906 (activated CD8-positive, alpha-beta T cell) is defined as having T cell receptor co-receptor CD8 (CD8A/CD8B) on the membrane, but CD8A/CD8B is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000906", "cell_type_label": "type 1 regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "DUSP4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "STAT3", "stance": "supports"}], "rationale": "The cluster displays the canonical expression profile of type 1 regulatory T (Tr1) cells. Specifically, it is marked by high and specific expression of IL10 (the hallmark cytokine of Tr1 cells) and MAF (c-MAF, the master transcription factor driving IL-10 expression and Tr1 cell differentiation). Additionally, it expresses coinhibitory and regulatory markers CTLA4 and TNFRSF1B, the characteristic tonsillar Tr1 surface marker KLRB1 (CD161), as well as DUSP4, IKZF3, and STAT3, all of which are key functional markers of human Tr1 cells. There are no markers pointing to other cell lineages or classic FOXP3+ regulatory T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 53.3}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "DUSP4", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "STAT3", "stance": "supports"}], "rationale": "This cluster corresponds to regulatory T cells (CL:0000815). It expresses the canonical regulatory T cell checkpoint molecule CTLA4 and the key immunosuppressive cytokine IL10, along with TNFRSF1B (TNFR2), which marks functionally suppressive, activated regulatory T cells. It also expresses MAF (c-Maf), a critical transcription factor driving IL-10 production and regulatory T cell specialization, as well as KLRB1 (CD161), DUSP4, IKZF3, and STAT3, which are well-established markers associated with human tissue-resident and activated regulatory T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type 1 regulatory T cell' is not the name of CL:0000906 ('activated CD8-positive, alpha-beta T cell'). Closest names: CL:0000815 (regulatory T cell); CL:0002677 (naive regulatory T cell); CL:0002678 (memory regulatory T cell).", "object id: CL:0000906 (activated CD8-positive, alpha-beta T cell) is defined as having T cell receptor co-receptor CD8 (CD8A/CD8B) on the membrane, but CD8A/CD8B is detected in only 4% of the cluster's cells."], "seconds": 12.5}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b5ea73db74"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "The cluster prominently expresses canonical markers of classical monocytes (CL:0000860), including high levels of CD14, the calprotectin subunits S100A8 and S100A9, lysozyme (LYZ), versican (VCAN), and ficolin-1 (FCN1), alongside other typical myeloid/monocytic markers such as CSF3R, ITGAM (CD11b), CST3, CSTA, and TYROBP, without significant expression of non-classical monocyte markers like FCGR3A (CD16)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b7c75983d8"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "The marker profile is defined by high expression of MHC class II molecules (HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQA1, HLA-DQB1, and invariant chain CD74) alongside hallmark macrophage/myeloid lineage markers including AIF1 (IBA1), MS4A6A, LYZ (lysozyme), TYROBP, and CST3, identifying this cluster as macrophages (CL:0000235)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b864a5744b"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "This cluster is characterized by high expression of TRDC (T cell receptor delta constant) and TRGC2 (T cell receptor gamma constant 2) alongside T cell lineage markers (CD2, CD7), defining them as gamma-delta T cells (CL:0000798). The cells also express a robust cytotoxic and effector program commonly seen in circulating gamma-delta T cells, including cytotoxic molecules (GNLY, NKG7, GZMA, CTSW, CST7), NK/C-type lectin receptors and adaptors (KLRK1/NKG2D, KLRD1/CD94, KLRB1/CD161, HCST), and the effector-associated transcription factor HOPX."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.7}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-b95794dcf3"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "TXNDC5", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "PRDX4", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of immunoglobulin heavy and light chains (IGHA1, IGKC, IGLC1, IGLC2, IGHG1, IGHG3) and canonical plasma cell markers, including JCHAIN, MZB1, DERL3, TXNDC5, FKBP11, and the master unfolded protein response / plasma cell transcription factor XBP1. These markers collectively identify the cluster as plasma cells (CL:0000786)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.5}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ba5f0288e7"} +{"attempts": [{"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 9% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "ITM2A", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CYTIP", "stance": "supports"}], "rationale": "The marker gene profile demonstrates definitive characteristics of CD4-positive, alpha-beta T cells (CL:0000624). The pan-T cell markers CD3D, CD3E, and CD3G together with TCR alpha and beta constant genes TRAC and TRBC2 establish that these cells are alpha-beta T lymphocytes. High expression of IL7R (CD127), LTB, ITM2A, and ICOS, alongside the lack of cytotoxic effector and CD8 lineage markers (such as CD8A, CD8B, PRF1, and GZMB), specifically identifies this population as CD4-positive alpha-beta T cells. Expression of CD69 and IL32 further reflects mucosal tissue-resident and activation states characteristic of colon lamina propria T helper cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.1}, {"answer": {"cell_type_id": "CL:0000789", "cell_type_label": "alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "ITM2A", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}, {"gene": "CYTIP", "stance": "supports"}], "rationale": "The cluster robustly expresses core T cell markers (CD3D, CD3E, CD3G, CD7) along with T cell receptor alpha and beta constant chains (TRAC, TRBC2) in 80-90% of cells, definitively identifying this population as alpha-beta T cells (CL:0000789). While phenotypic markers such as IL7R, LTB, and ICOS suggest a helper/memory T lineage, CD4 transcript dropout in 10x single-cell RNA-seq precludes strict assignment to the CD4+ lineage under ontology definitions requiring detected CD4. Therefore, the cluster is classified at the robust lineage level as alpha-beta T cell (CL:0000789)."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 9% of the cluster's cells."], "seconds": 14.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-be2c0ee626"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000875", "cell_type_label": "non-classical monocyte", "decision": "annotate", "markers": [{"gene": "LST1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "IFITM3", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}], "rationale": "This cluster displays the canonical expression profile of non-classical monocytes (CD16+ monocytes). The top marker by fold change is LST1, which along with FCGR3A (CD16), MS4A7, AIF1, and COTL1, represents the hallmark signature of non-classical monocytes. Core monocyte/myeloid signaling and lysosomal genes such as FCER1G, TYROBP, CST3, CTSS, and SERPINA1 are also strongly expressed (>90% of cells in the cluster). The absence of classical macrophage-specific markers (such as C1QA, C1QB, C1QC, CD163, MRC1) and classical monocyte markers (S100A8, S100A9, VCAN) further distinguishes this cluster as non-classical monocytes (CL:0000875)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 63.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-c5e3a0ec1f"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "The cluster expresses classic pan-T cell markers (CD3D, CD3G, TRAC, TRBC1, TRBC2, CD2) along with the defining lineage transcription factor and surface markers of regulatory T cells: FOXP3 (highly specific, pct_in 0.635 vs pct_out 0.002), IL2RA (CD25), CTLA4, TNFRSF18 (GITR), TNFRSF4 (OX40), and TIGIT."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-c99aec2a45"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}], "rationale": "The cluster shows high and specific expression of canonical B cell lineage markers, including MS4A1 (encoding CD20), CD79A, CD79B, CD19, CD24, FCMR, and VPREB3, alongside prominent expression of MHC class II molecules (HLA-DRA, HLA-DPB1, HLA-DPA1, CD74). These markers consistently and unambiguously identify the cluster as B cells (CL:0000236)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ccd8ad8cc1"} +{"attempts": [{"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster specifically expresses classic mast cell lineage markers, including mast cell secretory granule proteases (TPSAB1, TPSB2, CPA3), histamine synthesis and storage machinery (HDC, SLC18A2), prostaglandin synthesis (HPGDS), the mast cell-associated transcription factor GATA2, and the IL-33 receptor (IL33R/IL1RL1). These markers uniquely identify mast cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.7}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}], "rationale": "The cluster robustly expresses classic granular leukocyte secretory proteases and granule machinery, including tryptases (TPSAB1, TPSB2), carboxypeptidase A3 (CPA3), histidine decarboxylase (HDC), vesicular monoamine transporter 2 (SLC18A2), hematopoietic prostaglandin D synthase (HPGDS), and the transcription factor GATA2. While these markers specifically characterize mast cells, the Cell Ontology definition of mast cell (CL:0000097) includes a formal requirement for C-C chemokine receptor type 3 (CCR3) on the plasma membrane, which is not detected (0% expression) in this cluster. Consequently, annotating to the direct parent ontology term granulocyte (CL:0000094) is consistent with both the cluster's prominent secretory granule expression profile and the Cell Ontology axiomatization."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 78.7}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster exhibits quintessential, highly specific markers of mast cells, including mast cell-specific granule proteases (TPSAB1, TPSB2, CPA3), histamine synthesis machinery (HDC), the vesicular monoamine transporter (SLC18A2), prostaglandin D2 synthase (HPGDS), the mast cell lineage transcription factor GATA2, and the IL-33 receptor (IL33R/IL1RL1). These markers unambiguously identify the cluster as a mast cell (CL:0000097)."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells."], "seconds": 11.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ceffe8616a"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "IL4R", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}], "rationale": "The cluster displays prominent expression of canonical B-cell markers (CD19, CD79A, CD79B, MS4A1, CD72, CD37) along with HLA class II molecules. High co-expression of IGHD and IGHM together with naive B-cell specific markers such as TCL1A, IL4R, FCMR, and VPREB3 clearly identifies this population as naive B cells (CL:0000788). There are no contradicting marker genes present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-d44564d7f6"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}], "rationale": "The top marker genes are canonical markers for monocytes. Highly enriched genes such as S100A8, S100A9, S100A12, FCN1, VCAN, MNDA, and LYZ specifically define monocytes (distinguishing them from resident tissue macrophages, which lack high S100A8/S100A9/VCAN expression and express C1Q/CD163/APOE). Other top markers including CST3, TYROBP, AIF1, CTSS, FCER1G, and HLA-DRA are characteristic of myeloid and antigen-presenting cells. There are no contradicting lineage markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-d7d3163b78"} +{"attempts": [{"codes": ["BEV004"], "evidence": 12, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "PPP1R14A", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}, {"gene": "TPSAB1", "stance": "contradicts"}], "rationale": "This cluster strongly expresses canonical markers of smooth muscle cells (CL:0000192), including TAGLN, ACTA2, TPM2, MYL9, CALD1, PPP1R14A, TPM1, and ADIRF. In addition, the cluster exhibits high expression of TPSB2 and TPSAB1, which are highly specific mast cell markers (tryptases), indicating doublet formation or a mixed cluster with mast cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.3}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-d929ec7963"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical T cell lineage markers (CD3E, TRAC, CD2) along with CD4 and IL7R (CD127), identifying it as a CD4-positive alpha-beta T cell population. Furthermore, high upregulation of CCR7, SELL (CD62L), and CD27 definitively identifies these cells as naive CD4+ T cells (CL:0000895). None of the top marker genes contradict this cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.5}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-e1bfaa2341"} +{"attempts": [{"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 14, "findings": [{"message": "The label 'natural killer T cell' is not the name of CL:0000800 ('mature gamma-delta T cell'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 16, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}], "rationale": "This cluster exhibits strong and specific expression of canonical natural killer (NK) cell markers, including killer cell lectin-like receptors (KLRD1/CD94, KLRC1/NKG2A, KLRB1/CD161), NK-cell chemokines (XCL1, XCL2, CCL4, CCL5), cytotoxic granule-associated and effector molecules (NKG7, GZMA, GZMK, GZMM, CST7), and pan-NK/T signaling components (CD7, CD247) in the absence of lineage-defining markers of other cell types. This profile identifies the cluster as natural killer cells (CL:0000623)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.9}, {"answer": {"cell_type_id": "CL:0000800", "cell_type_label": "natural killer T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}], "rationale": "The cluster co-expresses killer cell lectin-like receptors and NK-associated effector molecules (KLRD1, KLRC1, KLRB1/CD161, NKG7, XCL1, XCL2, GZMA, GZMK, GZMM, CST7, CCL4, CCL5) alongside T-cell lineage components (CD247/CD3zeta, CD7, and CD3E). Pure natural killer cells (CL:0000623) are defined in the Cell Ontology as lacking CD3 epsilon, whereas natural killer T cells (CL:0000800) uniquely combine the NK cell phenotype and cytotoxicity markers with T-cell receptor complex expression (CD3E, CD247)."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35)."], "seconds": 19.5}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "MATK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}], "rationale": "This cluster exhibits high and specific expression of canonical natural killer cell markers, including killer cell lectin-like receptors (KLRD1/CD94, KLRC1/NKG2A, KLRB1), cytolytic and effector molecules (NKG7, GZMA, GZMK, GZMM, CST7), chemokines (XCL1, XCL2, CCL4, CCL5), and NK-associated signaling and surface proteins (CD7, CD247, CMC1, MATK). CD247 (T-cell receptor zeta chain) is standardly expressed in NK cells where it couples to activating receptors such as CD16 and NKp46. Overall, the expression profile definitively identifies this cluster as natural killer cells (CL:0000623)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'natural killer T cell' is not the name of CL:0000800 ('mature gamma-delta T cell'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell)."], "seconds": 12.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-e712a5eb84"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "This cluster displays strong expression of canonical pan-B cell markers (CD19, MS4A1/CD20, CD79A, CD79B) along with prominent co-expression of IGHM and IGHD, which is the defining hallmark of naive B cells. Additional supporting markers include CD24, FCMR, VPREB3, CXCR5, and MHC class II genes (HLA-DRA, HLA-DRB1, HLA-DPB1, HLA-DPA1, CD74). There are no contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-e7ae6683c5"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}], "rationale": "The cluster displays strong and specific expression of the lineage markers CD8A and CD8B, which define CD8-positive, alpha-beta T cells. Additionally, it highly expresses cytotoxic and effector markers such as CCL5, NKG7, GZMK, GZMA, CST7, CCL4, CTSW, and KLRG1, consistent with activated/effector CD8-positive, alpha-beta T cells in tonsil tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ec5325a064"} +{"attempts": [{"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}], "rationale": "The cluster strongly expresses characteristic natural killer (NK) cell markers, including KLRD1 (CD94), NKG7, GNLY, and FGFBP2, as well as cytotoxic effector molecules (PRF1, GZMB, GZMA, CST7) and the NK signaling adaptor HCST (DAP10), with an absence of lineage-defining pan-T cell markers like CD3D or CD3E."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.7}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster demonstrates robust expression of cytotoxic effector molecules (GNLY, NKG7, GZMB, PRF1, GZMA, CST7, CTSW, FGFBP2) alongside KLRD1 and CCL5. While this cytotoxic profile is shared with natural killer cells, the cluster strongly expresses components of the T-cell receptor and CD3 complex, including CD247 (CD3 zeta chain, 95% pct_in) and CD3E (detected in 73% of cluster cells), as well as the TCR signaling kinase FYN. The combination of T-cell identity (CD3/CD247) and cytolytic machinery identifies this cluster as cytotoxic T cells (CL:0000910)."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60)."], "seconds": 51.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ed05c45d83"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}], "rationale": "The cluster exhibits classic, highly specific marker genes for human neutrophils, including the calgranulin family members S100A8, S100A9, and S100A12, the canonical human neutrophil-specific receptor FCGR3B (CD16b), the granulocyte colony-stimulating factor receptor CSF3R, as well as neutrophil-associated genes G0S2, CXCL8, and MNDA."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.2}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}], "rationale": "The cluster expresses hallmark markers of granulocytes, notably the calgranulins (S100A8, S100A9, S100A12), the granulocyte-specific receptor FCGR3B, and the granulocyte colony-stimulating factor receptor CSF3R, alongside G0S2, CXCL8, MNDA, and S100P. Because the formal definition criteria for mature neutrophil (CL:0000775) requiring membrane CEACAM8, ITGAM, and SPN are not detected in the dataset, the cluster is best annotated at the parent ontology level as granulocyte (CL:0000094)."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells."], "seconds": 23.1}, {"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "NAMPT", "stance": "supports"}, {"gene": "GCA", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}], "rationale": "The cluster displays the canonical transcriptional profile of neutrophils (CL:0000775). Key supporting markers include FCGR3B (CD16b, specific to human neutrophils), CSF3R (granulocyte colony-stimulating factor receptor), the calgranulin family (S100A8, S100A9, S100A12), grancalcin (GCA), and other neutrophil-associated activation and survival factors including G0S2, CXCL8, MNDA, NAMPT, and S100P."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells."], "seconds": 27.9}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-f2e4fa20cc"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000904", "cell_type_label": "central memory CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "KLF6", "stance": "supports"}, {"gene": "BTG1", "stance": "supports"}, {"gene": "ZFP36L2", "stance": "supports"}], "rationale": "This cluster represents central memory CD4-positive, alpha-beta T cells (CD4+ TCM). It is characterized by high expression of IL7R (CD127), which is required for the homeostatic maintenance and survival of memory T cells and distinguishes them from tonsil Tfh and Treg subsets (which downregulate IL7R). The cluster also expresses GPR183 (EBI2), which guides CD4+ T cell localization within the secondary lymphoid organ architecture, CXCR4 for lymphoid retention, FYB1 (ADAP) for T cell receptor signaling, and KLRB1 (CD161), a hallmark of antigen-experienced memory T cell subsets. Quiescence and survival transcription factors/regulators typical of resting central memory T cells in lymphoid tissue (KLF6, ZFP36L2, BTG1, TSC22D3, FOS, JUNB) are also enriched. Naive markers (e.g., CCR7, LEF1) and B/myeloid lineage markers are absent, supporting a central memory CD4+ T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-f5551fdf21"} +{"attempts": [{"codes": ["BEV004"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000765", "cell_type_label": "erythroblast", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "HBB", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "ITGA2B", "stance": "contradicts"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "PRDX2", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "CKS2", "stance": "supports"}, {"gene": "CD82", "stance": "supports"}, {"gene": "NPM1", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "MCM5", "stance": "supports"}], "rationale": "The cluster displays strong expression of canonical erythroid lineage markers including hemoglobins (HBB, HBD), transferrin receptor (TFRC/CD71), carbonic anhydrase 1 (CA1), biliverdin reductase B (BLVRB), ferroportin (SLC40A1), and peroxiredoxin 2 (PRDX2), alongside the erythroid/megakaryocytic transcription factor NFE2. In addition, the cluster strongly expresses proliferation and cell cycle markers (STMN1, CDK6, TYMS, PCNA, MCM2, MCM5, CKS2), indicating actively cycling, nucleated erythroid precursors, i.e., erythroblasts (CL:0000765). ITGA2B (CD41) is a characteristic platelet/megakaryocyte marker, likely present due to platelet adherence or doublets, and thus contradicts pure erythroblast identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 80.1}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-f5e849f6ff"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002038", "cell_type_label": "T follicular helper cell", "decision": "annotate", "markers": [{"gene": "TOX2", "stance": "supports"}, {"gene": "PDCD1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "GNG4", "stance": "supports"}], "rationale": "This cluster is characterized by high expression of classic markers of T follicular helper (Tfh) cells in human tonsil. Specifically, TOX2 is a crucial transcription factor governing human Tfh cell programming and survival in germinal centers. PDCD1 (encoding PD-1) is the hallmark surface marker for Tfh cells. MAF encodes c-Maf, a master transcription factor required for Tfh differentiation and function. Additionally, TIGIT is highly expressed on germinal center Tfh cells, and GNG4 is a specific marker enriched in tonsillar germinal center Tfh subsets. There are no contradicting lineage markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.6}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-f6eff45a55"} +{"attempts": [{"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016"], "evidence": 11, "findings": [{"message": "No row of the pinned table has cluster=c13, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 1 (cluster=c13;gene=CD3E)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}], "rationale": "The cluster expresses canonical cytotoxic lymphocyte/natural killer cell markers (GNLY, GZMA), which are hallmark features of endometrial/uterine natural killer (uNK) cells. Concurrently, it displays prominent upregulation of cell-cycle and proliferation markers (STMN1, MKI67, TOP2A, CENPF, TYMS, PCLAF, NUSAP1, HMGB2), identifying this population as proliferating/cycling natural killer cells. In the Cell Ontology, these cells map to natural killer cell (CL:0000623). No markers clearly indicate contamination or an alternative lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.3}, {"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}], "rationale": "The cluster exhibits high expression of cell proliferation and cell cycle markers (STMN1, MKI67, TOP2A, CENPF, PCLAF, TYMS, NUSAP1, HMGB2) alongside cytotoxic effector genes (GNLY, GZMA). While these cytotoxic markers are shared with NK cells, the presence of CD3E confirms T cell lineage commitment and excludes natural killer cells (CL:0000623, which requires the absence of CD3 epsilon). Thus, this population corresponds to proliferating/cycling T cells, mapped in the Cell Ontology to T cell (CL:0000084)."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 29.2}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of cytotoxic effector genes (GNLY, GZMA) along with extensive proliferation and cell cycle markers (STMN1, MKI67, TOP2A, CENPF, PCLAF, TYMS, NUSAP1, HMGB2). In human endometrium, uterine natural killer (uNK) cells represent the predominant cytotoxic lymphocyte population. The co-expression of GNLY and GZMA without T cell receptor/CD3 markers identifies this population as cycling/proliferating natural killer cells, which map to 'natural killer cell' (CL:0000623) in the Cell Ontology."}, "cli_tools": [], "error": null, "feedback": ["evidence 1 (cluster=c13;gene=CD3E): No row of the pinned table has cluster=c13, gene=CD3E."], "seconds": 31.4}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-f7efaf4b7a"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}], "rationale": "The cluster expresses canonical T cell receptor and lineage markers (CD3E, TRAC, CD2), the CD4 co-receptor (CD4), and IL7R (CD127), which strongly identifies it as CD4-positive, alpha-beta T cells. Supporting markers such as CD27, CCR7, and IL32 reflect T cell activation and differentiation states within the CD4+ T cell compartment in human blood. No markers point to non-T cell lineages or contradictory cell types."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.2}], "model": "gemini-flash", "protocol": 3, "task_id": "ct-ff19304f5c"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of classic monocyte markers, particularly CD14, S100A8, S100A9, FCN1, VCAN, and LYZ. In human blood, this gene signature (specifically the presence of CD14, VCAN, and S100 proteins) strongly identifies these cells as monocytes (and more specifically, classical monocytes)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-0094010baa"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}], "rationale": "The cluster expresses classic markers for basophils, including high-affinity IgE receptor (FCER1A), histamine-synthesizing enzyme (HDC), and proteases/granule proteins (CPA3, PRG2, CLC, RNASE2). While some of these markers are shared with mast cells, the origin of the sample (blood) indicates these are circulating basophils rather than tissue-resident mast cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.0}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}], "rationale": "The cluster exhibits a distinct basophil profile, expressing genes for characteristic granule proteins (PRG2, CLC, RNASE2, CPA3), histamine synthesis (HDC), and the high-affinity IgE receptor (FCER1A). Since the term \"basophil\" (CL:0000767) was rejected due to a strict ontology axiom requiring CD40LG expression, the cluster is annotated to the broader parent category \"granulocyte\" which correctly encompasses these cells without violating the constraint."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells."], "seconds": 34.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-0224ef5d63"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "unknown", "cell_type_label": "unknown", "decision": "uncertain", "markers": [], "rationale": "The top marker genes for this cluster are overwhelmingly immediate-early response genes and stress-related transcripts (e.g., NEAT1, FOSB, JUN, FOS, HSP90AA1, DNAJA1, PPP1R15A). This pattern represents a well-known dissociation-induced stress signature (often an artifact of sample preparation in scRNA-seq) rather than a biologically distinct cell type. The few lineage-specific genes present in the list are discordant and expressed only in a minority of the cells (e.g., TAGLN and TPM2 for stromal/smooth muscle cells, TPSB2 for mast cells, all with pct_in < 0.36), which strongly suggests this is a mixed cluster of different cell types that were grouped together primarily because of their shared high expression of stress-induced genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-027de551e6"} +{"attempts": [{"codes": ["BEV004"], "evidence": 12, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IRF7", "stance": "supports"}, {"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}, {"gene": "IGLC2", "stance": "contradicts"}], "rationale": "The cluster is defined by canonical plasmacytoid dendritic cell (pDC) markers. This includes the master transcription factor TCF4 (E2-2), IRF7 (crucial for type I interferon production), the surface marker IL3RA (CD123), and other specific pDC-associated genes like BCL11A, CCDC50, SOX4, and ITM2C. Additionally, pDCs intrinsically express JCHAIN, MZB1, and GZMB. The detection of immunoglobulin light chain genes (IGKC, IGLC2) contradicts the pDC lineage and likely represents ambient RNA contamination from plasma cells, which are highly abundant in the colon."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-0460394dc8"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}], "rationale": "This cluster is characterized by the expression of classic B cell markers, such as MS4A1 (CD20), CD79A, CD79B, CD37, and BANK1. It also features high expression of MHC class II genes (CD74, HLA-DRA, HLA-DRB1, etc.), which are indicative of professional antigen-presenting cells such as B cells, as well as multiple immunoglobulin genes (IGKC, IGHA1, IGLC2, IGHG1). The strong presence of MS4A1 and MHC class II genes confirms these are B cells rather than mature plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.5}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-04f3e6a976"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}], "rationale": "The cluster exhibits high expression of multiple canonical smooth muscle cell markers, particularly contractile proteins such as ACTA2 (alpha-smooth muscle actin), TAGLN (transgelin), MYH11 (smooth muscle myosin heavy chain), MYL9, CALD1, and tropomyosins (TPM1, TPM2). This profile strongly supports its identity as smooth muscle cells, likely representing vascular smooth muscle or myometrial cells in the endometrial sample."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-0919bb7151"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "The cluster expresses classic pan-T cell markers including CD3E and TRAC, which define the cells as alpha-beta T cells. The very strong co-expression of CD8A and CD8B indicates they are of the CD8+ lineage. The presence of IL7R, CD2, and CD27 further supports a T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-15649bcc33"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000451", "cell_type_label": "dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CLEC10A", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}], "rationale": "The cluster exhibits high expression of multiple MHC class II molecules (HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQA1, HLA-DQB1) along with the invariant chain CD74, which are hallmark genes of professional antigen-presenting cells. The expression of CST3, AIF1, the maturation marker CD83, and the myeloid dendritic cell marker CLEC10A strongly points to this cluster being dendritic cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-18bf2c5651"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "The cluster expresses pan-T cell markers (CD3D, CD3E, CD2), T cell receptor alpha and beta chains (TRAC, TRBC1, TRBC2), and CD8 coreceptors (CD8A, CD8B), clearly identifying it as a CD8-positive, alpha-beta T cell. Furthermore, the strong expression of granzymes (GZMA, GZMK) and chemokines (CCL5) highlights its cytotoxic/effector phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-1c3cf91fbc"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}], "rationale": "The top marker genes are highly specific and definitive for mast cells. TPSAB1 and TPSB2 encode mast cell tryptases, while CPA3 encodes mast cell carboxypeptidase A3. MS4A2 encodes the beta subunit of the high-affinity IgE receptor (FcεRI), which is critically specific to mast cells and basophils. Additionally, the cluster expresses HPGDS, an enzyme highly expressed in mast cells for prostaglandin D2 synthesis, and GATA2, a transcription factor essential for mast cell lineage development and maintenance. The profile clearly identifies this cluster as resident mast cells in the kidney."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.0}, {"answer": {"cell_type_id": "CL:0000763", "cell_type_label": "myeloid cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}], "rationale": "The markers TPSAB1, TPSB2, CPA3, HPGDS, MS4A2, and GATA2 strongly indicate a mast cell profile. However, because the specific ontology term 'mast cell' (CL:0000097) is strictly defined as requiring CCR3 expression—which is absent in this cluster—we must fall back to a broader valid lineage term. Mast cells are of myeloid origin, making 'myeloid cell' (CL:0000763) a biologically accurate and ontology-compliant annotation that does not carry the restrictive CCR3 axiom."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 41.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-1cdfab3be0"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}], "rationale": "The cluster exhibits high expression of canonical myeloid/monocyte markers such as S100A8, S100A9, and LYZ. Furthermore, the strong expression of FCN1, VCAN, and MNDA specifically points to monocytes, particularly classical monocytes, as opposed to mature tissue-resident macrophages which typically downregulate these genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.5}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-1dc66b7bae"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical pan-B cell markers including CD79A, CD79B, MS4A1 (CD20), and CD19. The high concurrent expression of IGHM (IgM) and IGHD (IgD), combined with the expression of TCL1A, specifically identifies this cluster as naive B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.2}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-1fdfebb69c"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CD81", "stance": "supports"}, {"gene": "ITGAL", "stance": "supports"}, {"gene": "DUSP2", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The presence of TRDC and TRGC2 is highly specific to gamma-delta T cells, defining the identity of this cluster. The robust expression of cytotoxic genes (NKG7, CST7, GZMA, GNLY, CTSW) and various killer cell lectin-like receptors (KLRB1, KLRK1, KLRF1, KLRD1) along with FCGR3A (CD16) perfectly reflects the innate-like, cytotoxic phenotype characteristic of peripheral blood gamma-delta T cells. All top markers support this cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 73.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-21afd5c734"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The cluster shows high expression of T cell receptor components (TRBC1 and TRDC), which are definitive markers for T cells. The presence of IL7R (CD127) and KLRB1 (CD161) further supports this being a T cell population, likely enriched for tissue-resident or innate-like T cells (such as mucosal-associated invariant T cells or gamma-delta T cells) given the co-expression of CD69 and KLRB1 in the colon. Because both alpha-beta (TRBC1) and gamma-delta (TRDC) T cell receptor constants are highly expressed, the cluster is best annotated broadly as T cells, potentially representing a mixed population of unconventional/tissue-resident T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-227cbde019"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "PLD4", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}], "rationale": "The cluster is characterized by canonical plasmacytoid dendritic cell (pDC) markers, including the master transcription factors TCF4 (E2-2) and IRF7, as well as IRF8, IL3RA (CD123), PLD4, ITM2C, and CCDC50. Furthermore, human pDCs are known to highly express certain genes often associated with B cells or plasma cells, such as JCHAIN, MZB1, and DERL3, all of which are top markers here. This specific combination unambiguously identifies the cluster as plasmacytoid dendritic cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-26fda93c9c"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The cluster highly expresses CD8A and CD8B, along with T cell markers TRAC, CD3E, and CD2, indicating it is a CD8+ T cell population. The high expression of CCR7, SELL (L-selectin), CD27, and IL7R strongly suggests a naive or central memory phenotype, as these genes are critical for homing to secondary lymphoid organs and maintaining a non-effector state. The combination of CD8 lineage markers and naive/memory markers in human blood is characteristic of naive CD8+ T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.3}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-28eb7ea379"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "MRC1", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "F13A1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "MERTK", "stance": "supports"}, {"gene": "STAB1", "stance": "supports"}, {"gene": "COLEC12", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}], "rationale": "The cluster exhibits high expression of classic macrophage markers, including scavenger receptors (CD163, MRC1/CD206, STAB1, COLEC12), complement system components (C1QA, C1QB), and the clearance receptor MERTK. The strong expression of F13A1 and LYVE1 further characterizes these cells as a subpopulation of tissue-resident macrophages (often associated with perivascular locations) that are commonly found across various tissues, including the urinary bladder."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-302af8ae13"} +{"attempts": [{"codes": ["BEV004"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000556", "cell_type_label": "megakaryocyte", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "FCER1A", "stance": "contradicts"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}], "rationale": "The cluster exhibits very strong expression of megakaryocytic lineage markers, including ITGA2B (CD41), PPBP, NFE2, TAL1, and SPARC. The concurrent robust expression of hematopoietic progenitor and proliferation markers like CD34, TYMS, CDK6, and STMN1 strongly indicates that these are proliferating megakaryocyte progenitors or megakaryoblasts, rather than mature anucleate platelets. The presence of FCER1A contradicts the megakaryocyte identity, as it is a classical marker for basophils, mast cells, and type 2 conventional dendritic cells (cDC2s); this may suggest a small fraction of doublets or a mixed subpopulation within the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.2}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-3775a26491"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster exhibits classical mast cell markers including tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the receptor tyrosine kinase KIT, hematopoietic prostaglandin D synthase (HPGDS), and IL33 receptor (IL33R/IL1RL1), which are hallmarks of mast cell identity and function."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.6}, {"answer": {"cell_type_id": "CL:0000766", "cell_type_label": "myeloid leukocyte", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}], "rationale": "The cluster exhibits classical mast cell markers including tryptases (TPSB2, TPSAB1), carboxypeptidase A3 (CPA3), the receptor tyrosine kinase KIT, and hematopoietic prostaglandin D synthase (HPGDS). However, because the specific Cell Ontology term for mast cell (CL:0000097) strictly requires the expression of CCR3 (which is undetected in this cluster, likely due to low expression or dropout in scRNA-seq), we assign the broader parent term 'myeloid leukocyte' (CL:0000766), which encompasses the mast cell lineage without conflicting with the CCR3 expression constraint."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 34.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-3959f97db0"} +{"attempts": [{"codes": ["BEV004"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "FCER1A", "stance": "contradicts"}, {"gene": "CPA3", "stance": "contradicts"}], "rationale": "The presence of CD34 in 94.3% of the cells, along with cell cycle/progenitor markers like CDK6 and STMN1, strongly indicates that this is a cluster of hematopoietic stem/progenitor cells, which are known to circulate in small numbers in peripheral blood. The expression of FCER1A and CPA3 is typically associated with mature basophils or mast cells, which are usually CD34-negative, suggesting these cells might be lineage-primed progenitors (e.g., basophil/mast cell progenitors) or that there is a subset of basophil-committed cells within the progenitor cluster. For a general annotation, 'hematopoietic stem cell' (often used broadly for CD34+ cells) is most appropriate."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 92.2}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-3b8c7f5246"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}], "rationale": "The prominent expression of GZMK strongly indicates a cytotoxic T lymphocyte lineage, typically an effector/memory CD8+ T cell. S100A4 is a well-established marker for memory T cells, and FABP5 is often associated with tissue-resident or activated memory T cells. Furthermore, the strong presence of cytoskeletal and cell cycle-associated genes (STMN1, TUBA1B, TUBB, HMGB2, TYMS) indicates that this is a highly proliferative/cycling subset of these cytotoxic T cells. In humans, activated proliferating T cells also commonly upregulate MHC class II components such as CD74."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.3}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-3daee1395a"} +{"attempts": [{"codes": ["BEV004"], "evidence": 20, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TRGC2", "stance": "contradicts"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CD99", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical T cell markers (CD3E, CD3G, CD2) and the alpha-beta T cell receptor constant gene (TRAC). The high expression of both CD8A and CD8B unequivocally identifies these as CD8-positive, alpha-beta T cells. The cluster also shows a profound effector and cytotoxic signature, expressing granzyme A (GZMA), granulysin (GNLY), CST7, CTSW, and NKG7. Additionally, several NK-associated receptors (KLRK1, KLRF1, KLRD1, FCGR3A, ADGRG1) are highly expressed; these are well-known to be upregulated on mature, effector/cytotoxic CD8+ T cells (such as TEMRA cells) in human blood. TRGC2 is typically a marker for gamma-delta T cells, and its presence might indicate either non-productive transcripts common in alpha-beta T cells or a minor mixture of gamma-delta T cells in the cluster; hence it is listed as contradicting the main alpha-beta lineage assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-4b8439fcc9"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'myeloid progenitor cell' is not the name of CL:0000049 ('common myeloid progenitor'). Closest names: CL:0000038 (erythroid progenitor cell); CL:0011020 (neural progenitor cell); CL:0011026 (progenitor cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000049", "cell_type_label": "myeloid progenitor cell", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}], "rationale": "The cluster expresses classical hematopoietic stem and early progenitor markers including CD34, SPINK2, and PRSS57, indicating an immature progenitor state. The extremely high expression of primary granule genes like MPO and AZU1, along with the myeloid cytokine receptor CSF3R, demonstrates strong commitment to the myeloid/granulocytic lineage. The presence of proliferation-related genes (CDK6, STMN1) further characterizes these as actively dividing progenitors. Taken together, these markers confidently identify the cluster as myeloid progenitor cells, likely Granulocyte-Monocyte Progenitors (GMPs)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.0}, {"answer": {"cell_type_id": "CL:0000049", "cell_type_label": "common myeloid progenitor", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}], "rationale": "The cluster expresses classical hematopoietic stem and early progenitor markers including CD34, SPINK2, and PRSS57, indicating an immature progenitor state. The high expression of early myeloid genes like MPO and AZU1, along with the myeloid cytokine receptor CSF3R, demonstrates commitment to the myeloid lineage. The presence of proliferation-related genes (CDK6, STMN1) further characterizes these as actively dividing progenitors. Taken together, these markers confidently identify the cluster as common myeloid progenitors."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'myeloid progenitor cell' is not the name of CL:0000049 ('common myeloid progenitor'). Closest names: CL:0000038 (erythroid progenitor cell); CL:0011020 (neural progenitor cell); CL:0011026 (progenitor cell)."], "seconds": 17.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-4e9d71ecad"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "FCER1G", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "CTSL", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "CCL20", "stance": "supports"}, {"gene": "AQP9", "stance": "supports"}], "rationale": "This cluster highly expresses several classic myeloid and macrophage markers, including the Fc receptor FCER1G, the lysosomal protease CTSL, and the antigen presentation-related gene IFI30. Additionally, the cells express chemokines typically secreted by activated macrophages such as CXCL8 and CCL20, as well as the aquaporin AQP9, which is characteristic of macrophages and monocytes. The overall profile of high lysosomal activity and chemokine production is consistent with tissue macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.3}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-5169234be6"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The cluster highly expresses T cell receptor delta and gamma constant genes (TRDC, TRGC2) alongside the general T cell marker CD3E, definitively identifying them as gamma-delta T cells. The expression of numerous cytotoxic and natural killer-associated markers (NKG7, CST7, GZMA, CTSW, KLRK1, KLRB1, GNLY) is highly characteristic of the effector phenotype typical of gamma-delta T cells found in human peripheral blood."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-56d8f3ebbf"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "SEL1L3", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC61B", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}], "rationale": "The cluster expresses B-cell lineage markers (CD19, CD79A) alongside incredibly high levels of immunoglobulin-related genes (JCHAIN, IGKC). Crucially, the top markers include key regulators of the unfolded protein response (UPR) and extensive endoplasmic reticulum/secretory machinery (MZB1, XBP1, DERL3, FKBP11, SEC11C, HSP90B1). This massive upregulation of secretory pathways, coupled with the classic surface markers CD27 and CD38, uniquely identifies these cells as plasma cells (or circulating plasmablasts) dedicated to massive antibody production."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.9}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-62995bbc69"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "LAG3", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "PRDM1", "stance": "supports"}, {"gene": "CYTOR", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The cluster displays a canonical signature of activated/effector regulatory T cells (Tregs), featuring high expression of characteristic immune checkpoints and co-stimulatory receptors, including CTLA4, LAG3, TNFRSF4 (OX40), TNFRSF18 (GITR), and TNFRSF1B (TNFR2). Additionally, it expresses PRDM1 (Blimp-1) and the lncRNA CYTOR, which are upregulated in effector Tregs. The expression of KLRB1 (CD161), RORA, and MAF indicates that this is likely a tissue-resident or Th17-like memory Treg subset, which is well-documented in mucosal tissues and tonsils. S100A4 further supports a memory phenotype. There are no clear contradicting markers for this subset."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-62ef0fd4ba"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster is defined by the very strong expression of mast cell-specific proteases such as tryptases (TPSB2, TPSAB1) and carboxypeptidase A3 (CPA3). Furthermore, it expresses MS4A2 (the beta subunit of the high-affinity IgE receptor), HPGDS (hematopoietic prostaglandin D synthase), the transcription factor GATA2, and LTC4S (leukotriene C4 synthase), all of which are classic markers of mast cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.1}, {"answer": {"cell_type_id": "CL:0000766", "cell_type_label": "myeloid leukocyte", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster exhibits a classic mast cell transcriptional profile, characterized by the high expression of proteases like tryptases (TPSB2, TPSAB1) and carboxypeptidase A3 (CPA3), as well as MS4A2 (Fc epsilon receptor beta chain), HPGDS, GATA2, and LTC4S. Biologically, these are mast cells. However, because the cells lack detection of CCR3—which is strictly required by the formal Cell Ontology definition for 'mast cell' (CL:0000097)—we fall back to the more general parent class 'myeloid leukocyte' to accurately annotate the cells without violating the ontology constraints."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 43.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-68351aaa63"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The cluster is characterized by high and specific expression of the complement C1q components (C1QA, C1QB, C1QC), which are classical markers for mature tissue macrophages. It also exhibits high expression of major histocompatibility complex (MHC) class II molecules (HLA-DRA, HLA-DRB1, HLA-DPA1, CD74), consistent with their role as professional antigen-presenting cells. Additional markers include established myeloid and macrophage genes such as TYROBP, AIF1, MS4A7, SELENOP, and CST3, as well as macrophage inflammatory proteins (CCL3, CCL4). Together, this transcriptomic profile unambiguously identifies the cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-6dacd7effa"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}], "rationale": "The cluster highly expresses hallmark T cell markers, most notably components of the T cell receptor complex (CD3D, CD3E, CD3G) and T cell receptor alpha/beta constant regions (TRAC, TRBC2). Additionally, it expresses well-known T cell lineage markers such as CD2, IL7R, and BCL11B. The presence of CD40LG hints that these might be CD4+ T cells, but overall they definitively map to the T cell lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-72757d8950"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "ETS1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "The cluster expresses a strong signature characteristic of T cells. IL7R is a key receptor for T cell development and homeostasis. FYN is an important kinase in T cell receptor signaling. ETS1 is a transcription factor critical for T cell function. CD96 is a surface antigen expressed on T cells. Additionally, the cluster expresses chemokines (CCL5, CCL4) and activation/tissue residency markers (CD69) typical of mature, functional T cells in tissues."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-72dfb189c0"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "SPINK2", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "MSI2", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of well-known hematopoietic stem cell markers, including CD34, PROM1 (CD133), and SPINK2. Other highly enriched genes such as NPR3, CRHBP, EGFL7, and MSI2 are also characteristic of human hematopoietic stem and progenitor cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-75adde23f7"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 12, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000899 (T-helper 17 cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 1% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000899", "cell_type_label": "T helper 17 cell", "decision": "annotate", "markers": [{"gene": "TRBC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "KRT81", "stance": "contradicts"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "The cluster shows very high expression of TRBC1 and CD52, establishing it as a T cell lineage (ruling out Innate Lymphoid Cells, which typically lack rearranged T cell receptors). The specific co-expression of KLRB1 (CD161), IL7R (CD127), the master transcription factor AHR, and IL4I1 strongly points toward a T helper 17 (Th17) cell or a highly related type-3 cytokine-producing T cell. Furthermore, human Th17 cells are uniquely known to express KIT (CD117). TNFRSF4 (OX40) and TNFRSF18 (GITR) also reflect an activated T cell phenotype. The keratins KRT81 and KRT86 clearly contradict a lymphoid identity and are likely due to ambient RNA contamination or epithelial doublets common in mucosal tissue samples like the endometrium."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 71.6}, {"answer": {"cell_type_id": "CL:0000789", "cell_type_label": "alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRBC1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "SLA", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "KRT81", "stance": "contradicts"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "The near-universal expression of TRBC1 and CD52 strongly defines this cluster as an alpha-beta T cell population (ruling out Innate Lymphoid Cells, which lack rearranged T cell receptors despite a similar expression profile). While the cells exhibit a clear type 3/17 immunity signature with high KLRB1, AHR, IL4I1, and KIT, the validator confirmed that CD4 is virtually absent (<1%). This indicates the population is a CD4-negative alpha-beta T cell subset, such as mucosal-associated invariant T (MAIT) cells or Tc17 cells. These innate-like, CD4-negative T cells are prominent in mucosal tissues like the endometrium and characteristically share this Th17-like transcriptional profile. The keratins KRT81 and KRT86 contradict a lymphoid lineage and are likely derived from epithelial doublets or ambient RNA."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000899 (T-helper 17 cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 1% of the cluster's cells."], "seconds": 50.5}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-76fa626271"} +{"attempts": [{"codes": [], "evidence": 3, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}], "rationale": "The cluster is characterized by the strong expression of well-known hematopoietic stem and progenitor cell markers, including CD34, PROM1 (CD133), and SPINK2. Other markers present like STMN1, PCNA, TYMS, and MCM2 indicate that these are highly proliferative cells, typical of a progenitor or stem cell state in early hematopoiesis."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-7a81a9a19f"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}], "rationale": "The high expression of CD3 subunits (CD3D, CD3G, CD3E) and T cell receptor alpha/beta constant chains (TRAC, TRBC2) identifies the cluster as alpha-beta T cells. The strong presence of both CD8 subunits (CD8A and CD8B) specifies them as CD8-positive alpha-beta T cells. Additionally, the presence of cytotoxic effector molecules like granzymes (GZMK, GZMM, GZMH) and CCL5 is highly characteristic of the cytotoxic nature of CD8+ T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.9}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-7c21a7ad85"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "The most definitive marker in this cluster is TRDC (T cell receptor delta constant), which specifically and unambiguously identifies these cells as gamma-delta T cells. The cluster also expresses a strong NK-like/cytotoxic signature (XCL1, XCL2, GNLY, KLRB1/CD161, KLRC1/NKG2A, CTSW, TYROBP, FCER1G), which is highly characteristic of the gamma-delta T cell effector profile. CD7 and IL7R further support the T-lymphoid lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-7ec8cd3664"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "GPX1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}], "rationale": "The cluster exhibits robust expression of C1QA, C1QB, and C1QC, which are classical markers for tissue-resident macrophages. Furthermore, it highly expresses MHC class II genes (HLA-DRA, HLA-DPA1, HLA-DRB1, etc.) and CD74, consistent with professional antigen-presenting cells. The presence of additional myeloid/macrophage lineage markers like CD14, AIF1 (IBA1), TYROBP, MS4A6A, and FCER1G solidifies the identity of this cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-819cfbd986"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). Closest names: CL:0000906 (activated CD8-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}], "rationale": "The cluster shows strong expression of both CD8A and CD8B, clearly identifying it as a CD8-positive T cell population. Furthermore, the high expression of naive T cell markers including CCR7, SELL (CD62L), LEF1, and KLF2, which are important for lymph node homing and maintaining the naive state, strongly supports the annotation of this cluster as naive CD8-positive, alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.5}, {"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}], "rationale": "The cluster shows strong expression of both CD8A and CD8B, clearly identifying it as a CD8-positive T cell population. Furthermore, the high expression of naive T cell markers including CCR7, SELL (CD62L), LEF1, and KLF2, which are important for lymph node homing and maintaining the naive state, strongly supports the annotation of this cluster as naive thymus-derived CD8-positive, alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). Closest names: CL:0000906 (activated CD8-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell)."], "seconds": 42.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-81b1e8f8f5"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "PRDX4", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}], "rationale": "The cluster is highly enriched for immunoglobulin heavy and light chain genes (IGKC, IGHG1, IGHG3, IGLC2, IGHG4, IGHA1, IGHG2, IGLC3, IGLC1, IGHM) as well as JCHAIN, which are classic hallmarks of antibody-secreting plasma cells. It also expresses MZB1 (a well-known plasma cell marker) and XBP1, the master transcriptional regulator essential for plasma cell differentiation. Furthermore, the presence of numerous endoplasmic reticulum and secretory pathway-associated genes (DERL3, SSR4, FKBP11, HERPUD1, SEC11C, PRDX4) reflects the massive protein synthesis and secretory capacity characteristic of plasma cells. CD79A indicates their B-cell lineage origin. Together, these markers unambiguously identify the cluster as plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-879d085000"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}], "rationale": "The cluster expresses high levels of MHC class II genes (HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DQB1, CD74) and classic macrophage/monocyte lineage markers (CD14, LYZ, AIF1, C1QA, CST3, CTSS, IFI30). The robust expression of C1QA specifically points towards tissue-resident macrophages rather than monocytes. These markers strongly identify the cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-89c1241fbf"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}], "rationale": "The cluster is clearly characterized as T cells due to the high expression of definitive T cell markers, including components of the T cell receptor (TRAC, TRBC2) and the CD3 complex (CD3D, CD3E), alongside other classical T cell surface proteins like CD2 and IL7R."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-8ab1b5fbd8"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000875", "cell_type_label": "non-classical monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "NR4A1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}], "rationale": "The cluster exhibits a strong signature of non-classical monocytes. The top marker FCGR3A (CD16) defines this CD14-low/CD16+ monocyte subset. It also highly expresses MS4A7 and LST1, which are canonical markers for non-classical monocytes in scRNA-seq data. Furthermore, NR4A1 is an essential transcription factor for the survival and development of non-classical monocytes. Additional markers such as ITGAX (CD11c), AIF1, TYROBP, CST3, and FCER1G confirm the myeloid/monocyte lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.2}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-8c07cf76ca"} +{"attempts": [{"codes": ["BEV004"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "TRDC", "stance": "contradicts"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}], "rationale": "The cluster shows strong and defining expression of classical natural killer (NK) cell markers, including cytotoxic effector molecules (GNLY, NKG7, CTSW, GZMB), key signaling adaptors (TYROBP, FCER1G), and specific NK cell receptors (KLRD1, KLRC1, KLRF1). Additionally, the chemokines XCL1 and XCL2 are abundantly produced by tonsillar and resting NK cells. TRDC is canonically a T cell receptor gene (gamma-delta T cells); its presence contradicts a pure NK identity, although sterile TRDC transcription is a known phenomenon in NK cells. The absence of canonical pan-T markers like CD3 components in the top marker list strongly favors an NK cell identity over a T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-8d82b1a772"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "The high expression of T cell markers (CD3E, CD3G) and alpha-beta T cell receptor component (TRAC) alongside CD8 coreceptors (CD8A, CD8B) identifies this cluster as CD8-positive, alpha-beta T cells. The presence of cytotoxic effector molecules (NKG7, GZMA, CST7) is characteristic of effector CD8+ T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-95367720e6"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "BACH2", "stance": "supports"}, {"gene": "MEF2C", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "The cluster exhibits high expression of classic B cell markers, including MS4A1 (CD20), CD79A, BANK1, BACH2, and MEF2C. It also highly expresses immunoglobulin genes (IGKC) and numerous MHC class II molecules (HLA-DRA, HLA-DRB1, HLA-DQA1, HLA-DPA1) along with the invariant chain CD74, which is consistent with the antigen-presenting function of B cells. The high expression of MS4A1 (CD20) indicates that these are mature B cells rather than plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-9814423bdc"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}], "rationale": "This cluster exhibits a strong signature for natural killer (NK) cells. It highly expresses classical cytotoxic effector molecules such as GNLY, NKG7, GZMB, PRF1, and GZMA. Additionally, it strongly expresses various killer cell lectin-like receptors (KLRD1, KLRF1, KLRB1) and the mature/cytotoxic NK cell marker FCGR3A (CD16). Other highly expressed genes include TYROBP and FCER1G (adaptor proteins crucial for NK cell signaling), as well as FGFBP2 and SPON2 which are typically associated with mature CD56dim NK cells. The lack of canonical T-cell coreceptor components (like CD3D, CD3E, CD3G) alongside these features confirms the identity as natural killer cells rather than cytotoxic T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 65.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-98402e60db"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "ALOX5AP", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of MHC class II molecules (HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, and CD74), which indicates professional antigen-presenting cells. Furthermore, the strong and specific expression of complement components C1QA, C1QB, and C1QC, along with APOE, TYROBP, LYZ, and ALOX5AP, points directly to macrophages. C1Q genes in particular are classic, highly canonical markers for tissue-resident macrophages that help distinguish them from other antigen-presenting cells such as dendritic cells or B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-9d243229e7"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000836", "cell_type_label": "promyelocyte", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "CDC20", "stance": "supports"}], "rationale": "The cluster exhibits high expression of classic primary (azurophilic) granule genes such as MPO and AZU1, as well as RNASE2 and RNASE3, which are hallmarks of the promyelocyte stage during granulopoiesis. Furthermore, the strong presence of proliferation-associated genes (STMN1, TYMS, PCNA, CDC20) confirms that these are actively dividing progenitor cells rather than mature resting granulocytes. The combination of myeloid lineage markers and proliferation markers points directly to promyelocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-9d2a6afe3f"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'myeloid dendritic cell' is not the name of CL:0001056 ('dendritic cell, human'). 'myeloid dendritic cell' is the name of CL:0000782 (myeloid dendritic cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001056", "cell_type_label": "myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD33", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}], "rationale": "The cluster shows strong expression of MHC class II genes (HLA-DRA, HLA-DRB5, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQB1) as well as the invariant chain CD74, consistent with professional antigen-presenting cells. High expression of specific myeloid/conventional dendritic cell markers such as FCER1A, CD1C, CD33, and ITGAX (CD11c) in the context of human blood indicates these are myeloid dendritic cells, and in particular the cDC2 (CD1c+) subset."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.5}, {"answer": {"cell_type_id": "CL:0000782", "cell_type_label": "myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD33", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}], "rationale": "The cluster shows strong expression of MHC class II genes (HLA-DRA, HLA-DRB5, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQB1) as well as the invariant chain CD74, consistent with professional antigen-presenting cells. High expression of specific myeloid/conventional dendritic cell markers such as FCER1A, CD1C, CD33, and ITGAX (CD11c) in the context of human blood indicates these are myeloid dendritic cells, and in particular the cDC2 (CD1c+) subset."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'myeloid dendritic cell' is not the name of CL:0001056 ('dendritic cell, human'). 'myeloid dendritic cell' is the name of CL:0000782 (myeloid dendritic cell)."], "seconds": 16.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-9e8b98aab5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'transit amplifying cell' is not the name of CL:0000340 ('glioblast (sensu Nematoda and Protostomia)'). 'transit amplifying cell' is the name of CL:0009010 (transit amplifying cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000340", "cell_type_label": "transit amplifying cell", "decision": "annotate", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}], "rationale": "The cluster is defined by the high expression of numerous classic proliferation and cell cycle markers. Genes such as MKI67, TOP2A, CDK1, CENPF, and UBE2C are well-known markers for actively dividing cells (particularly in the G2/M phases of the cell cycle), while TYMS and PCLAF are associated with the S phase. In the context of the normal human colon epithelium, the actively dividing cells are the transit amplifying (TA) cells located in the intestinal crypts. The absence of specific mature lineage markers and the overwhelming dominance of cell cycle genes strongly support annotating this cluster as transit amplifying cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.1}, {"answer": {"cell_type_id": "CL:0009010", "cell_type_label": "transit amplifying cell", "decision": "annotate", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}], "rationale": "The cluster is defined by the high expression of numerous classic proliferation and cell cycle markers. Genes such as MKI67, TOP2A, CDK1, CENPF, and UBE2C are well-known markers for actively dividing cells (particularly in the G2/M phases of the cell cycle), while TYMS and PCLAF are associated with the S phase. In the context of the normal human colon epithelium, the actively dividing cells are the transit amplifying (TA) cells located in the intestinal crypts. The absence of specific mature lineage markers and the overwhelming dominance of cell cycle genes strongly support annotating this cluster as transit amplifying cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'transit amplifying cell' is not the name of CL:0000340 ('glioblast (sensu Nematoda and Protostomia)'). 'transit amplifying cell' is the name of CL:0009010 (transit amplifying cell)."], "seconds": 15.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-a321096724"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}], "rationale": "The cluster shows strong and specific expression of canonical B cell markers, including the B cell antigen receptor complex components CD79A and CD79B. It also expresses various immunoglobulin components such as IGHM (IgM heavy chain) and IGKC (Ig kappa light chain). The presence of IGLL1, VPREB1, and VPREB3 (components of the surrogate light chain), along with SOX4 and TCF4, indicates characteristics of B cell development or a specific state, but they are all fundamentally B cell lineage markers. Additional B cell-associated markers include MZB1, CD24, and CD37. There are no notable markers contradicting a B cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-a33f382e85"} +{"attempts": [{"codes": [], "evidence": 19, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "LY9", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}], "rationale": "The cluster expresses classic, definitive markers of B cells, notably MS4A1 (CD20), CD79A, CD79B, and BANK1. The high expression of various immunoglobulin heavy and light chain genes (IGHM, IGHD, IGKC, IGLC2, IGLC3) confirms their identity as B lymphocytes, with IGHM and IGHD together often delineating naive or unswitched mature B cells. Additional genes such as HLA-DRA and CD74 (MHC class II complex) align with the antigen-presenting role of B cells. The transcription factor SPIB and the B cell survival receptor TNFRSF13C (BAFF-R) further validate the annotation. There are no contradicting markers suggesting mixed clusters."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.2}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ac7ec2b016"} +{"attempts": [{"codes": ["BEV026"], "evidence": 4, "findings": [{"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 4, "findings": [{"message": "CL:0000980 (plasmablast) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 4, "findings": [{"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "The expression of immunoglobulin constant genes (IGKC, IGHG1, IGHG3) strongly indicates this cluster represents plasma cells, which produce large amounts of these transcripts. Additionally, ELL2 is an essential elongation factor required for secretory immunoglobulin production during plasma cell differentiation. Other top markers are largely non-specific lncRNAs, mitochondrial genes, and immediate early genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.2}, {"answer": {"cell_type_id": "CL:0000980", "cell_type_label": "plasmablast", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of immunoglobulin genes (IGKC, IGHG1, IGHG3) and the elongation factor ELL2, which drives secretory immunoglobulin production, indicating an antibody-secreting cell. As syndecan-1 (SDC1) is not highly expressed, this cluster likely represents plasmablasts, which are actively secreting antibodies but are less mature than terminally differentiated SDC1-positive plasma cells."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells."], "seconds": 21.8}, {"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of immunoglobulin genes (IGKC, IGHG1, IGHG3) and the elongation factor ELL2, which drives secretory immunoglobulin production, characteristic of antibody-secreting cells. The lack of CD19 expression (noted by the validator) aligns with terminally differentiated plasma cells, which typically downregulate CD19 compared to plasmablasts."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000980 (plasmablast) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 4% of the cluster's cells."], "seconds": 17.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ad2d591627"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "TRDC", "stance": "contradicts"}], "rationale": "The cluster strongly expresses canonical natural killer (NK) cell markers, particularly cytotoxic granules (GNLY, GZMA, GZMB, PRF1) and characteristic NK receptors/markers (NKG7, KLRC1/NKG2A, KLRD1/CD94, XCL1, XCL2). In the endometrium, these features are highly characteristic of uterine natural killer (uNK) cells, which constitute a major immune population in this tissue. The expression of TRDC is canonically associated with gamma-delta T cells and contradicts an NK cell assignment, though non-functional/sterile TRDC transcripts are sometimes detected in NK cells in scRNA-seq datasets, or this could represent a minor admixture of gamma-delta T cells in the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.6}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}], "rationale": "While the cluster highly expresses cytotoxic markers (GNLY, GZMA, GZMB, PRF1) and NK cell-associated receptors (NKG7, KLRC1, KLRD1), the prominent expression of T cell markers—including TRDC (T cell receptor delta constant), CD247 (CD3Z), and CD3E (as noted in the validation)—clearly identifies these as T cells rather than natural killer cells. The strong expression of TRDC specifically designates this population as gamma-delta T cells. Gamma-delta T cells are a known tissue-resident lymphocyte population in mucosal tissues like the endometrium, and they characteristically exhibit a cytotoxic, NK-like transcriptional profile."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59)."], "seconds": 27.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ae89c1380f"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of genes characteristic of mononuclear phagocytes, particularly monocytes. High expression of S100A8, S100A9, and VCAN is classically associated with classical monocytes. Additionally, the cluster expresses general myeloid/macrophage/monocyte markers such as LYZ, AIF1, TYROBP, IFI30, and the C5a receptor C5AR1. The lack of prominent tissue-resident macrophage markers (like C1Q complex genes or MRC1/CD163) among the top enriched genes further supports the identification as monocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b269766ee9"} +{"attempts": [{"codes": ["BEV017"], "evidence": 5, "findings": [{"message": "The label 'naive thymus-derived CD4-positive, alpha-beta T cell' is not the name of CL:0000898 ('naive T cell'). 'naive thymus-derived CD4-positive, alpha-beta T cell' is the name of CL:0000895 (naive thymus-derived CD4-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}], "rationale": "The cluster expresses high levels of IL7R and LEF1, indicating it belongs to the T cell lineage. Furthermore, it highly expresses CCR7, SELL (L-selectin), and KLF2, which are classical functional markers for naïve T cells that regulate their homing to secondary lymphoid organs like the tonsil. Given its tissue of origin (tonsil), this population corresponds predominantly to naïve CD4-positive T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.3}, {"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}], "rationale": "The cluster expresses high levels of IL7R and LEF1, indicating it belongs to the T cell lineage. Furthermore, it highly expresses CCR7, SELL (L-selectin), and KLF2, which are classical functional markers for naive T cells that regulate their homing to secondary lymphoid organs like the tonsil. Given the absence of specific CD4 or CD8 lineage markers in the top list, it is most accurate to annotate this cluster broadly as naive T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive thymus-derived CD4-positive, alpha-beta T cell' is not the name of CL:0000898 ('naive T cell'). 'naive thymus-derived CD4-positive, alpha-beta T cell' is the name of CL:0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)."], "seconds": 17.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b322bece33"} +{"attempts": [{"codes": ["BEV004"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "HBB", "stance": "contradicts"}], "rationale": "The cluster exhibits strong expression of canonical cytotoxic effector markers such as GNLY, NKG7, granzymes (GZMH, GZMB, GZMA), and PRF1, which are characteristic of cytotoxic T cells and NK cells. The high expression of definitive T cell markers CD3D (85.7%) and CD3G (62.9%) confirms the T cell lineage rather than NK cells. This expression profile strongly aligns with CD8+ cytotoxic T cells. HBB is an erythrocyte marker and its presence is likely due to ambient RNA contamination, contradicting the T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 69.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b51a9f2d53"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 4, "findings": [{"message": "The label 'type 1 regulatory T cell' is not the name of CL:0001053 ('IgD-negative memory B cell'). Closest names: CL:0000815 (regulatory T cell); CL:0002677 (naive regulatory T cell); CL:0002678 (memory regulatory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0001053 (IgD-negative memory B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0001053 (IgD-negative memory B cell) is defined as having membrane-spanning 4-domains subfamily A member 1 (MS4A1) on the membrane, but MS4A1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001053", "cell_type_label": "type 1 regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}], "rationale": "The cluster exhibits high expression of IL10 and its key transcriptional regulator MAF, which are hallmarks of type 1 regulatory T cells (Tr1). Co-expression of the inhibitory receptor CTLA4 and TNFRSF1B further supports a regulatory T cell phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.9}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}], "rationale": "The cluster exhibits high expression of IL10 and its key transcriptional regulator MAF, along with inhibitory receptors CTLA4 and TNFRSF1B, which are hallmarks of regulatory T cells. This specific profile (IL10+, MAF+, KLRB1+) is characteristic of IL-10 producing regulatory T cells such as type 1 regulatory T (Tr1) cells in the tonsil."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type 1 regulatory T cell' is not the name of CL:0001053 ('IgD-negative memory B cell'). Closest names: CL:0000815 (regulatory T cell); CL:0002677 (naive regulatory T cell); CL:0002678 (memory regulatory T cell).", "object id: CL:0001053 (IgD-negative memory B cell) is defined as having CD19 molecule (CD19) on the membrane, but CD19 is detected in only 2% of the cluster's cells.", "object id: CL:0001053 (IgD-negative memory B cell) is defined as having membrane-spanning 4-domains subfamily A member 1 (MS4A1) on the membrane, but MS4A1 is detected in only 8% of the cluster's cells."], "seconds": 25.3}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b5ea73db74"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}], "rationale": "The cluster is highly defined by the expression of CD14, along with S100A8, S100A9, VCAN, and FCN1, which are all canonical markers of classical monocytes in human blood. It also expresses other typical myeloid/monocyte markers like LYZ, CST3, and ITGAM."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.9}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b7c75983d8"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HLA-DMB", "stance": "supports"}], "rationale": "The cluster exhibits robust expression of multiple major histocompatibility complex (MHC) class II genes (HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DRB5, HLA-DMA, HLA-DMB) and the MHC class II invariant chain (CD74), strongly indicating an antigen-presenting cell identity. The high expression of LYZ, CST3, MS4A6A, AIF1, and TYROBP further identifies these cells as macrophages, distinguishing them from other antigen-presenting cells like B cells. These features are characteristic of resident tissue macrophages in the kidney."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 73.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b864a5744b"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "The cluster is identified as gamma-delta T cells due to the strong and specific expression of TRDC and TRGC2, which encode the constant regions of the delta and gamma chains of the T-cell receptor. The presence of pan-T cell markers like CD2 and CD7 confirms the T cell lineage. Furthermore, the cells exhibit a prominent cytotoxic and NK-like gene signature (NKG7, GNLY, KLRK1, KLRF1, KLRB1, KLRD1, GZMA, CTSW, CST7), which is highly characteristic of circulating human gamma-delta T cells (such as the Vγ9Vδ2 subset) that possess innate-like effector functions."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.3}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-b95794dcf3"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "TXNDC5", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}], "rationale": "The cluster exhibits very high expression of multiple immunoglobulin genes (IGKC, IGHA1, IGLC1, IGLC2, IGHG1, etc.) and JCHAIN, which are hallmark features of antibody-secreting plasma cells. Furthermore, it highly expresses genes associated with the endoplasmic reticulum and the unfolded protein response (including XBP1, MZB1, DERL3, FKBP11, and TXNDC5). This signature reflects the massive protein synthesis and secretion machinery required for antibody production, confirming the identity as plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ba5f0288e7"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}], "rationale": "The cluster exhibits ubiquitous expression of core definitive T cell markers, including the CD3 complex genes (CD3D, CD3E, CD3G) and T cell receptor alpha and beta constant genes (TRAC, TRBC2). Additionally, pan-T cell and lymphocyte markers such as CD7 and IL7R are highly expressed. The presence of CD69 and ICOS indicates activation and tissue-resident memory phenotypes typical for mucosal/gut-associated T cells. There are no contradicting marker genes to suggest another lineage or a doublet state."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-be2c0ee626"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}], "rationale": "This cluster robustly expresses classical myeloid lineage and macrophage markers, including AIF1 (IBA1), TYROBP (DAP12), CST3, FCER1G, and MS4A7. The presence of HLA-DRA points towards their role as professional antigen-presenting cells, while FCGR3A (CD16) and FCN1 are widely associated with monocyte-derived macrophages and non-classical monocytes. Collectively, these markers in a kidney cortex tissue sample strongly identify the cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-c5e3a0ec1f"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The presence of classic pan-T cell and T cell receptor markers (CD3D, CD3G, TRAC, CD2) identifies this cluster as a T cell population. The high expression of FOXP3 (the master transcriptional regulator of Tregs), IL2RA (CD25), and CTLA4, along with co-stimulatory/inhibitory molecules constitutively expressed on regulatory T cells like TNFRSF18 (GITR), TNFRSF4 (OX40), and TIGIT, unambiguously identifies this cluster as regulatory T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-c99aec2a45"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}], "rationale": "The cluster is defined by the high expression of canonical B cell markers such as CD79A, CD79B, MS4A1 (CD20), and CD19. It also expresses B-cell receptor components and associated proteins like IGKC and VPREB3. Furthermore, the robust expression of MHC class II genes (HLA-DRA, HLA-DPB1, HLA-DPA1, HLA-DRB5, HLA-DRB1) and CD74 (invariant chain) is characteristic of antigen-presenting cells, which together with the aforementioned markers unequivocally identifies this cluster as B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ccd8ad8cc1"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'myeloid leukocyte' is not the name of CL:0000076 ('squamous epithelial cell'). 'myeloid leukocyte' is the name of CL:0000766 (myeloid leukocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical mast cell markers, including tryptases (TPSAB1, TPSB2) and carboxypeptidase A3 (CPA3). It also expresses enzymes involved in the synthesis of mast cell mediators such as histamine (HDC) and prostaglandin D2 (HPGDS). Furthermore, the presence of GATA2 (a key transcription factor for mast cell development), SLC18A2 (a vesicular transporter for biogenic amines like histamine), and IL33R (the receptor for IL-33, which strongly activates mast cells) further confirms its identity as a mast cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.1}, {"answer": {"cell_type_id": "CL:0000076", "cell_type_label": "myeloid leukocyte", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}], "rationale": "Although the cluster clearly expresses canonical mast cell markers (such as tryptases TPSAB1 and TPSB2, carboxypeptidase CPA3, and enzymes for histamine and prostaglandin synthesis like HDC and HPGDS), the explicit term \"mast cell\" (CL:0000097) is rejected by the ontology due to the absence of detectable CCR3 expression in this dataset (likely a technical dropout in scRNA-seq). Therefore, we back off to the broader parent term \"myeloid leukocyte\" to capture the correct developmental lineage of these cells without violating the strict Cell Ontology surface marker requirements."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 42.7}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}], "rationale": "The cluster exhibits highly specific expression of canonical mast cell markers, including tryptases (TPSAB1, TPSB2), carboxypeptidase A3 (CPA3), histidine decarboxylase (HDC), and hematopoietic prostaglandin D synthase (HPGDS), as well as the transcription factor GATA2, which is critical for mast cell development and function. These strongly identify the cluster as mast cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'myeloid leukocyte' is not the name of CL:0000076 ('squamous epithelial cell'). 'myeloid leukocyte' is the name of CL:0000766 (myeloid leukocyte)."], "seconds": 19.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ceffe8616a"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}], "rationale": "The cluster highly expresses classic pan-B cell markers such as CD79A, CD79B, MS4A1 (CD20), and CD19, establishing its identity as B cells. Furthermore, the strong co-expression of IGHM (IgM) and IGHD (IgD), along with TCL1A and VPREB3, specifically identifies them as naive B cells, as the presence of both IgM and IgD is the canonical signature of mature naive B cells in the peripheral blood."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.9}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-d44564d7f6"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}], "rationale": "The cluster exhibits strong, classic expression of monocyte and myeloid markers. Highly expressed genes such as LYZ, S100A8, S100A9, FCN1, and VCAN represent a canonical signature for monocytes (specifically classical monocytes). The presence of MHC class II molecules (HLA-DRA) and other myeloid markers (TYROBP, AIF1, CST3, CTSS) further support this annotation as a mononuclear phagocyte lineage, distinct from resident tissue macrophages which usually express lower levels of S100A8/9 and VCAN."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.3}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-d7d3163b78"} +{"attempts": [{"codes": ["BEV004"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "PPP1R14A", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}, {"gene": "TPSAB1", "stance": "contradicts"}], "rationale": "The cluster exhibits a strong expression signature characteristic of smooth muscle cells (or myofibroblasts/pericytes), with highly upregulated contractile machinery genes including TAGLN, ACTA2, TPM2, MYL9, TPM1, CALD1, and PPP1R14A. However, it also highly expresses TPSB2 and TPSAB1, which are specific tryptases exclusively produced by mast cells. Since smooth muscle cells and mast cells arise from entirely different lineages but often reside closely together in perivascular niches, this profile indicates a mixed cluster or doublet artifacts consisting of both smooth muscle cells and mast cells. The primary identity is assigned as smooth muscle cell based on the preponderance of muscle-related markers, while the mast cell markers are flagged as contradictory."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.9}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-d929ec7963"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of general T cell markers (TRAC, CD3E, CD2) along with the co-receptor CD4, identifying it as a CD4+ T cell population. It is further characterized by high expression of canonical naive T cell markers, including IL7R, CCR7, CD27, and SELL (which encodes CD62L). The combination of these specific markers points to this cluster being naive CD4+ T cells. No contradictory markers were found among the top marker genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.8}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-e1bfaa2341"} +{"attempts": [{"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical natural killer (NK) cell markers, including killer cell lectin-like receptors (KLRD1, KLRB1, KLRC1), granzymes (GZMA, GZMK, GZMM), chemokines typically secreted by NK cells (XCL1, XCL2, CCL4, CCL5), and NKG7. The presence of CD247 (CD3zeta, which associates with NK cell receptors) and CD7 alongside these markers further supports the identification as NK cells. No contradictory markers pointing to other cell lineages are present among the top markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.9}, {"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "While the cluster heavily expresses markers classically shared with natural killer cells (NKG7, granzymes, KLR-family receptors, XCL1/2), the significant expression of the definitive T-cell marker CD3E (as flagged by the validator) along with CD247 (CD3zeta) and CD7 indicates that this is a T cell population. Specifically, this profile is highly characteristic of cytotoxic effector T cells (such as CD8+ T cells, gamma-delta T cells, or NKT cells) which are abundant in the colon as intraepithelial lymphocytes and often exhibit an NK-like transcriptional signature."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35)."], "seconds": 43.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-e712a5eb84"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB5", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "CD82", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical pan-B cell markers including MS4A1 (CD20), CD19, CD79A, and CD79B. The high expression of immunoglobulin heavy and light chains (IGHM, IGHD, IGKC) is characteristic of B lymphocytes, specifically strongly suggesting a naive B cell phenotype due to the co-expression of IGHM and IGHD. Robust expression of MHC class II molecules (HLA-DRA, HLA-DRB1, CD74, etc.) alongside other well-known B cell surface markers and regulators (CD24, CXCR5, VPREB3, IRF8) solidifies this cluster's identity as B cells. No contradictory markers from other lineages are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.5}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-e7ae6683c5"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "The cluster is characterized by the co-expression of the T-cell co-receptor subunits CD8A and CD8B, clearly identifying them as CD8-positive T cells. Additionally, the cluster expresses a strong signature of effector and cytotoxic molecules, including granzymes (GZMK, GZMA), chemokines (CCL5, CCL4), and other markers of cytotoxicity and activation (NKG7, CST7, CTSW). The high expression of GZMK combined with this cytotoxic profile indicates that these are effector or effector memory CD8+ alpha-beta T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ec5325a064"} +{"attempts": [{"codes": ["BEV026"], "evidence": 11, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of cytotoxic effector molecules (GNLY, GZMB, GZMA, PRF1, NKG7) along with natural killer (NK) cell-associated receptors and signaling adapters (KLRD1/CD94, HCST/DAP10, CD247/CD3Z). The high expression of FGFBP2 is also characteristic of mature, cytotoxic NK cells. The lack of top-ranking defining T cell markers (such as CD3D, CD3E, CD3G, or CD8A/B) further supports the annotation of this cluster as natural killer cells rather than cytotoxic T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.0}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}], "rationale": "The cluster expresses high levels of cytotoxic effector molecules (GNLY, GZMB, GZMA, PRF1, NKG7) along with T-cell associated signaling genes (CD247/CD3Z, FYN). While it shares many markers with natural killer cells (such as KLRD1 and FGFBP2), the significant detection of CD3E in 73% of the cells, as flagged by the validator, alongside CD247, confirms that this is a T cell lineage. The strong cytotoxic gene signature combined with T cell markers identifies this cluster as cytotoxic T cells (or potentially a subset like natural killer T cells / NKT-like cells), distinguishing them from pure NK cells."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60)."], "seconds": 32.7}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ed05c45d83"} +{"attempts": [{"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "GCA", "stance": "supports"}, {"gene": "S100P", "stance": "supports"}], "rationale": "The cluster strongly expresses characteristic markers of neutrophils. S100A8, S100A9, and S100A12 are well-known calprotectin/calgranulin components highly abundant in neutrophils. FCGR3B (CD16b) is a widely recognized neutrophil-specific surface marker. CSF3R is the receptor for G-CSF, which is crucial for neutrophil development and function. Additional genes such as G0S2, MNDA, GCA, and S100P are also highly expressed in the neutrophil lineage. There are no markers that contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}], "rationale": "The cluster expresses classic granulocyte/neutrophil markers such as S100A8, S100A9, FCGR3B, and CSF3R. Since specific surface markers required to formally define neutrophils in the ontology (such as CEACAM8, ITGAM, and SPN) were not detected—likely due to the low RNA capture rate of these transcripts in this single-cell RNA-seq platform—the cluster is annotated with the broader term 'granulocyte'."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells."], "seconds": 55.4}, {"answer": {"cell_type_id": "CL:0000766", "cell_type_label": "myeloid leukocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}], "rationale": "The cluster strongly expresses a myeloid and neutrophil-associated gene profile, highlighted by high expression of S100A8, S100A9, CSF3R, and the neutrophil-specific marker FCGR3B. Because strict Cell Ontology definitions for 'granulocyte' (CL:0000094) and its subtype 'neutrophil' (CL:0000077) require membrane expression of CEACAM8 and ITGAM—which are frequently undetected in 10x 3' scRNA-seq datasets like this one due to low transcript capture—those terms fail validation. To correctly capture the biological lineage while satisfying the strict ontology constraints, the cluster is assigned to the broader parent class 'myeloid leukocyte' (CL:0000766), which is supported by these myeloid markers without explicitly requiring those unobserved adhesion molecules."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells."], "seconds": 54.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-f2e4fa20cc"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "The cluster expresses characteristic T cell markers such as IL7R (CD127) and FYB1, alongside KLRB1 (CD161) which is expressed on specific T cell subsets and NK cells. Additional genes like GPR183 and CXCR4 further support a leukocyte/lymphocyte identity. The cluster is heavily populated by immediate early and activation genes (KLF6, ZFP36, FOS, JUNB, DUSP1, TXNIP), which often denote an activated T cell state or represent a common dissociation-induced stress response in single-cell RNA-seq datasets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-f5551fdf21"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000765", "cell_type_label": "erythroblast", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "PRDX2", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "CKS2", "stance": "supports"}, {"gene": "MCM5", "stance": "supports"}], "rationale": "The cluster exhibits robust expression of mature erythroid lineage markers (HBB, CA1, TFRC/CD71, PRDX2, BLVRB, HBD, SLC40A1) and the erythroid transcription factor NFE2. Additionally, the cluster displays strong expression of multiple cell cycle and proliferation markers (STMN1, CDK6, TYMS, PCNA, MCM2, CKS2, MCM5). The combination of hemoglobin production/iron metabolism genes and active DNA replication/proliferation markers indicates that these are nucleated, dividing red blood cell precursors, or erythroblasts, rather than mature enucleated erythrocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 96.1}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-f5e849f6ff"} +{"attempts": [{"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002038", "cell_type_label": "T follicular helper cell", "decision": "annotate", "markers": [{"gene": "TOX2", "stance": "supports"}, {"gene": "PDCD1", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}], "rationale": "The cluster exhibits a strong T follicular helper (Tfh) cell signature, characterized by the high expression of key Tfh-associated transcription factors (TOX2 and MAF) as well as characteristic surface receptors (PDCD1/PD-1 and TIGIT). This cell type identification is highly consistent with the tissue source (human tonsil). There are no prominent contradictory markers in the top list."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.4}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-f6eff45a55"} +{"attempts": [{"codes": ["BEV026"], "evidence": 20, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "H4C3", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "H2AZ1", "stance": "supports"}, {"gene": "HMGN2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "H1-5", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "H1-3", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "DUT", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}, {"gene": "HMGB1", "stance": "supports"}], "rationale": "The cluster is defined by an extremely strong cell cycle and proliferation signature (MKI67, TOP2A, TYMS, CENPF, NUSAP1, PCLAF, SMC4, STMN1, and multiple histone genes like H4C3, H1-5). Alongside this proliferation machinery, the presence of cytotoxic effector molecules (GNLY, GZMA) clearly points to a lymphocyte lineage, specifically natural killer (NK) cells or cytotoxic T cells. In the human endometrium, uterine NK (uNK) cells are known to constitute a massive proportion of the immune compartment and actively proliferate during the menstrual cycle. Therefore, this cluster represents a highly proliferative subpopulation of natural killer cells. All listed markers support this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.0}, {"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "H4C3", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "H2AZ1", "stance": "supports"}, {"gene": "HMGN2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "H1-5", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "H1-3", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "DUT", "stance": "supports"}, {"gene": "SMC4", "stance": "supports"}, {"gene": "HMGB1", "stance": "supports"}], "rationale": "The cluster exhibits a strong proliferation signature (e.g., MKI67, TOP2A, TYMS, CENPF, STMN1) alongside cytotoxic markers (GNLY, GZMA). The presence of CD3E (as noted by the validator) confirms that it belongs to the T cell lineage rather than being natural killer cells. Thus, this cluster represents a highly proliferative population of T cells, likely with cytotoxic effector function. All listed markers support this identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 24.0}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-f7efaf4b7a"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}], "rationale": "The cluster expresses canonical T cell markers (TRAC, CD3E, CD2) along with the helper T cell marker CD4. High expression of CCR7, CD27, and IL7R is highly characteristic of naive (and central memory) T cells, distinguishing them from effector populations. In human peripheral blood, this profile corresponds to naive CD4+ T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.6}], "model": "gemini-pro", "protocol": 3, "task_id": "ct-ff19304f5c"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}], "rationale": "Strong, nearly universal CD14, FCN1 and VCAN expression, together with S100A8/S100A9 and myeloid markers, identifies classical monocytes. CSF3R alone does not establish a conflicting neutrophil identity; no markers clearly indicate a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-0094010baa"} +{"attempts": [{"codes": ["BEV026"], "evidence": 5, "findings": [{"message": "CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000767", "cell_type_label": "basophil", "decision": "annotate", "markers": [{"gene": "HDC", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "PRG2", "stance": "supports"}], "rationale": "Strong co-enrichment of HDC, FCER1A and CPA3, together with CLC and PRG2, supports basophils in peripheral blood. CLC and PRG2 are shared with eosinophils, but the combined signature favors basophils. No listed marker clearly establishes a conflicting lineage or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.8}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}], "rationale": "The combined signature supports a granulocyte with a basophil-like phenotype. Given the validator’s CD40LG requirement, the broader granulocyte term is the defensible annotation. Undetected CD40LG RNA in a targeted assay does not establish absence of its membrane protein. No listed marker clearly establishes a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000767 (basophil) is defined as having tumor necrosis factor ligand superfamily member 5 (CD40LG) on the membrane, but CD40LG is detected in only 0% of the cluster's cells."], "seconds": 42.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-0224ef5d63"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [], "rationale": "The dominant markers reflect stress or activation (FOS, FOSB, JUN, PPP1R15A) rather than a specific lineage. TAGLN and TPM2 suggest a smooth muscle/myofibroblast component, whereas TPSB2 suggests mast cells; these occur in only 25–36% of the cluster. This profile does not confidently identify one cell type or distinguish a mixed cluster from doublets or ambient RNA."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-027de551e6"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}], "rationale": "The combination of IL3RA, TCF4, BCL11A, IRF7 and GZMB strongly supports plasmacytoid dendritic cells. JCHAIN and MZB1 are also compatible with this identity. IGKC and IGLC2 warrant attention but alone do not establish a mixed cluster or plasma-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-0460394dc8"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "CD79A, CD79B, MS4A1 and BANK1 establish B-cell identity, supported by immunoglobulin light chains and MHC class II expression. IGHA1 and IGHG1 suggest class-switched B cells, but do not establish a specific subtype. No listed markers clearly contradict B-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.0}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-04f3e6a976"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "MYH11", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}], "rationale": "The coordinated contractile signature, particularly MYH11 together with ACTA2, TAGLN, MYL9 and CALD1, supports smooth muscle identity. These markers do not establish a specific anatomical subtype. HLA-DRA alone does not clearly indicate a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-0919bb7151"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "Strong CD8A/CD8B expression together with TRAC and CD3E supports CD8-positive alpha-beta T cells. IL7R and CD27 suggest a less differentiated, potentially memory-like phenotype, but do not resolve the subtype. TRGC2 alone is insufficient to establish a separate gamma-delta population or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-15649bcc33"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "CLEC10A", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "The combination of CLEC10A, GPR183, CST3 and strong MHC class II expression favors conventional type 2 dendritic cells (cDC2). CD83 supports an activated antigen-presenting phenotype. CD1C itself is not listed, so the subtype assignment is inferred from the combined signature. No listed markers clearly contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-18bf2c5651"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "CD3 and alpha-beta T-cell receptor genes establish T-cell identity, with CD8A and CD8B supporting the CD8 subset. GZMK, GZMA and CCL5 suggest an effector-memory-like program, but do not establish a specific memory subtype. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-1c3cf91fbc"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "Strong, widespread expression of mast-cell tryptases TPSAB1 and TPSB2, together with CPA3, HPGDS and MS4A2, identifies mast cells. GATA2 and RGS13 provide additional support. No listed markers clearly indicate a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.7}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "The coordinated expression of mast-cell tryptases TPSAB1 and TPSB2 with CPA3, HPGDS and MS4A2 strongly identifies mast cells. Undetected CCR3 RNA does not establish absence of CCR3 protein on the membrane; a membrane-protein ontology restriction cannot be tested directly by transcript detection alone. The annotation remains mast cell, with membrane CCR3 status unverified. No listed markers clearly support a conflicting identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 32.9}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}], "rationale": "The markers strongly support mast-cell identity. Granulocyte is a broader annotation that avoids the validator's CCR3 restriction on the mast-cell term. Zero detected CCR3 transcripts do not establish absence of membrane CCR3 protein. No listed markers clearly indicate a conflicting identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 42.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-1cdfab3be0"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "RETN", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}], "rationale": "The combined FCN1, VCAN, S100A8/S100A9, LYZ and RETN signature strongly supports classical monocytes. No listed markers clearly indicate a conflicting lineage or mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.0}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-1dc66b7bae"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}], "rationale": "CD19, CD79A/CD79B and MS4A1 establish B-cell identity. Strong IGHM, IGHD and TCL1A expression supports naive B cells. TCL1A and CD24 can also occur in transitional B cells, but these markers do not establish that narrower identity. No listed markers clearly contradict the annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 56.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-1fdfebb69c"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "TRDC and TRGC2 enrichment across much of the cluster supports gamma-delta T-cell identity, with a strong cytotoxic program. FCGR3A and NK-associated receptors are compatible with cytotoxic gamma-delta T cells and do not independently indicate contamination. Confirmation would benefit from CD3 expression or paired gamma-delta TCR evidence."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-21afd5c734"} +{"attempts": [{"codes": ["BEV004"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "TRBC1", "stance": "contradicts"}], "rationale": "TRDC enrichment (78.1% inside versus 7.0% outside) supports gamma-delta T cells. KLRB1, IL7R and CD69 fit a mucosal, tissue-associated phenotype but are not lineage-specific. Widespread TRBC1 expression suggests an alpha-beta T-cell component; cluster-level markers cannot establish whether this reflects admixture or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-227cbde019"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "PLD4", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "CCDC50", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}], "rationale": "The combined IL3RA–TCF4–IRF7–IRF8 signature, reinforced by PLD4 and ITM2C, strongly supports plasmacytoid dendritic cells. JCHAIN and MZB1 are compatible with this identity. Immunoglobulin transcripts alone do not establish a conflicting B-cell identity or a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-26fda93c9c"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}], "rationale": "CD8A/CD8B together with TRAC and CD3E identify CD8 alpha-beta T cells. CCR7, IL7R, CD27 and SELL suggest a naive or central-memory phenotype, but do not reliably distinguish those subsets. KLRK1 and CTSW are compatible with CD8 T cells and do not establish a conflicting NK-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 53.6}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-28eb7ea379"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "MRC1", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "MERTK", "stance": "supports"}, {"gene": "STAB1", "stance": "supports"}, {"gene": "F13A1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "COLEC12", "stance": "supports"}], "rationale": "Coexpression of CD163, MERTK, C1QA and C1QB strongly identifies macrophages. LYVE1, MRC1, F13A1 and SELENOP further suggest a tissue-resident, homeostatic macrophage phenotype. No listed markers clearly indicate a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 65.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-302af8ae13"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000556", "cell_type_label": "megakaryocyte", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "PDLIM1", "stance": "supports"}], "rationale": "Strong ITGA2B expression together with PPBP and the megakaryocytic regulators NFE2 and TAL1 identifies the megakaryocyte lineage. CD34, CDK6, STMN1 and TYMS suggest an immature, proliferative population rather than mature platelets. FCER1A alone is insufficient to establish a competing identity or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-3775a26491"} +{"attempts": [{"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 6, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The strong, highly cluster-enriched expression of mast-cell tryptases TPSB2 and TPSAB1, together with CPA3, KIT and HPGDS, identifies mast cells. IL33R further supports this annotation. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.3}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}], "rationale": "The coordinated enrichment of TPSB2, TPSAB1, CPA3, KIT and HPGDS strongly identifies mast cells. Undetected CCR3 RNA in 10x scRNA-seq does not establish absence of CCR3 membrane protein, so the validator's objection does not justify changing the annotation. No listed markers clearly support a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 33.5}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}], "rationale": "The combined enrichment of mast-cell tryptases TPSB2/TPSAB1, CPA3, KIT and HPGDS strongly identifies mast cells. CCR3 RNA detection in 0% of cells does not establish absence of membrane CCR3 protein; this transcript–protein distinction prevents using the ontology definition as an RNA-expression exclusion rule. No supplied marker clearly supports another cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 71.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-3959f97db0"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}], "rationale": "The combined FCER1A–CPA3 signature with SLC40A1, NPR3 and CRHBP supports mast-cell lineage. Strong CD34 expression suggests circulating immature mast cells or mast-cell progenitors. FCER1A and CPA3 overlap with basophils, so the combined profile is more informative than either marker alone."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-3b8c7f5246"} +{"attempts": [{"codes": [], "evidence": 2, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}], "rationale": "Most consistent with proliferating, activated or memory T cells: GZMK and S100A4 support this interpretation, while STMN1, TYMS and HMGB2 suggest proliferation. These markers do not confidently resolve CD4 versus CD8 identity. CD74 is atypical but alone does not establish a conflicting lineage; confidence is limited by the absence of canonical T-cell markers from the supplied list."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-3daee1395a"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "Strong TRGC2 enrichment in 93.7% of cells, together with CD3E/CD3G, favors gamma-delta T cells with a cytotoxic phenotype. NKG7, KLRK1, CST7, CTSW and GZMA support this phenotype. CD8A/CD8B and TRAC introduce some ambiguity with conventional CD8 T cells; receptor sequencing would confirm lineage. NK-associated markers alone do not establish a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.5}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-4b8439fcc9"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0008001", "cell_type_label": "hematopoietic precursor cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}], "rationale": "CD34, SPINK2, PRSS57 and SOX4 support an immature hematopoietic progenitor identity, with MPO, AZU1 and CSF3R indicating myeloid priming. IGLL1 and CPA3 suggest additional lineage-associated programs but do not alone establish a mixed cluster. A precise progenitor subtype cannot be resolved confidently from these targeted-panel markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-4e9d71ecad"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSL", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "PLIN2", "stance": "supports"}, {"gene": "AQP9", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}], "rationale": "The combined myeloid signaling, lysosomal processing, and lipid-handling signature supports an inflammatory macrophage identity. CCL20, CXCL8, and EREG indicate inflammatory activation. These markers do not securely distinguish a macrophage subtype or exclude closely related activated monocytes; none clearly indicates a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-5169234be6"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "TRDC and TRGC2 expression in nearly all cluster cells strongly identifies gamma-delta T cells, supported by CD3E and CD2. NKG7, GZMA, CST7 and CTSW indicate a cytotoxic program. The NK-associated markers are compatible with gamma-delta T cells and do not clearly suggest a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-56d8f3ebbf"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}], "rationale": "Strong JCHAIN and MZB1 enrichment, together with XBP1, DERL3 and FKBP11, identifies an antibody-secreting plasma-cell program. IGKC and CD79A support B-lineage identity. Circulating plasmablasts are possible, but these markers do not reliably distinguish them from mature plasma cells. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-62995bbc69"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "LAG3", "stance": "supports"}, {"gene": "PRDM1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The combined CTLA4, TNFRSF18, TNFRSF4, TNFRSF1B and LAG3 signature supports an activated regulatory T-cell identity. PRDM1 and MAF reinforce a regulatory program. These markers do not reliably distinguish FOXP3-positive regulatory T cells from a type 1 regulatory T-cell phenotype; the broader ontology term is therefore appropriate."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-62ef0fd4ba"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "Strong enrichment and near-universal expression of the mast-cell proteases TPSB2, TPSAB1 and CPA3, together with MS4A2 and HPGDS, identify mast cells. No listed markers clearly support a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.1}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The coordinated enrichment of TPSB2, TPSAB1, CPA3, MS4A2 and HPGDS strongly identifies mast cells. Undetected CCR3 RNA does not establish absence of membrane CCR3 protein; an ontology protein phenotype should not be enforced as mandatory transcript detection in 10x scRNA-seq. The validator flags a measurement mismatch, not sufficient biological evidence to change the annotation. No listed markers clearly indicate a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 57.1}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "TPSB2, TPSAB1 and CPA3, together with MS4A2 and HPGDS, strongly identify mast cells. Zero detected CCR3 transcripts is a discrepancy with the validator's criterion, but does not demonstrate absence of membrane CCR3 protein. The supplied evidence therefore supports retaining the mast cell annotation; no listed markers clearly support a conflicting identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 45.6}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-68351aaa63"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "Coordinated C1QA/C1QB/C1QC enrichment with MS4A7 and SELENOP strongly supports intestinal macrophages. TYROBP, AIF1 and CST3 reinforce myeloid identity. CCL3/CCL4 suggest an activated state; no listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.0}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-6dacd7effa"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000897", "cell_type_label": "CD4-positive, alpha-beta memory T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}], "rationale": "CD3 genes and TRAC/TRBC2 establish alpha-beta T-cell identity. Strong IL7R together with CD40LG supports a CD4 helper phenotype; S100A4, KLRB1 and GPR183 favor a memory population. The memory CD4 assignment is inferred from the combined profile; no listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-72757d8950"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CBLB", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The combined IL7R, CD96, FYN, CAMK4 and T-cell signaling signature supports T cells, with an IL7R-high memory-like phenotype. CD69 and CCL5 suggest activation or tissue residency. These markers do not reliably distinguish CD4 from CD8 T cells; none clearly establishes a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-72dfb189c0"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "MSI2", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}], "rationale": "Strong CD34 and SPINK2 expression together with PROM1, CRHBP, NPR3, MSI2 and HOPX supports a primitive hematopoietic stem-cell identity. These markers favor HSCs within the stem/progenitor compartment, although a targeted expression panel cannot establish functional stemness or fully exclude closely related multipotent progenitors. No listed marker clearly establishes a contradictory lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 50.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-75adde23f7"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'group 3 innate lymphoid cell' is not the name of CL:0001070 ('beige adipocyte'). 'group 3 innate lymphoid cell' is the name of CL:0001071 (group 3 innate lymphoid cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0001070", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "TRBC1", "stance": "contradicts"}], "rationale": "The combined KIT, IL7R, KLRB1 and AHR signature favors group 3 innate lymphoid cells (ILC3). However, TRBC1 expression in 97.6% of cells strongly indicates a T-cell program, conflicting with a pure ILC3 identity and raising concern for T-cell admixture, doublets, or an alternative T-cell annotation. This assignment is provisional."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.3}, {"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "TRBC1", "stance": "contradicts"}], "rationale": "The combined KIT, IL7R, KLRB1 and AHR signature supports group 3 innate lymphoid cells. However, TRBC1 expression in 97.6% of cells conflicts with a pure ILC3 identity and suggests an alternative T-cell identity or mixed population; the annotation remains provisional."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'group 3 innate lymphoid cell' is not the name of CL:0001070 ('beige adipocyte'). 'group 3 innate lymphoid cell' is the name of CL:0001071 (group 3 innate lymphoid cell)."], "seconds": 31.6}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-76fa626271"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}], "rationale": "The strong CD34, SPINK2 and PROM1 signature supports an immature hematopoietic stem/progenitor population. STMN1, TYMS, PCNA and MCM2 indicate proliferation. IGLL1 suggests possible lymphoid priming but does not independently establish a separate lineage. This annotation is provisional: these markers cannot reliably distinguish true stem cells from early progenitors."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.5}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-7a81a9a19f"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}], "rationale": "CD3 genes together with TRAC and TRBC2 establish alpha-beta T-cell identity, while CD8A and CD8B support the CD8-positive subtype. CCL5 and granzymes indicate a cytotoxic/effector program. No listed markers clearly contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-7c21a7ad85"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}], "rationale": "TRDC enrichment in 78.6% of cells strongly supports gamma-delta T-cell identity. CD7 and KLRB1 support the lymphocyte phenotype, while CTSW, GNLY, XCL1/XCL2 and KLRC1 indicate an innate-like cytotoxic program. NK-associated markers can occur in gamma-delta T cells and do not independently establish a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.0}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-7ec8cd3664"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}], "rationale": "Strong, coordinated C1QA/C1QB/C1QC enrichment together with myeloid markers identifies macrophages. HLA class II and CD74 expression supports their antigen-presenting function. No marker combination clearly indicates a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-819cfbd986"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "CD8A and CD8B support CD8 T-cell identity. CCR7, SELL, LEF1 and KLF2 together favor a naive, lymphoid-homing state. Central memory CD8 T cells remain a possible alternative, but the overall signature favors naive cells. No listed marker clearly establishes a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-81b1e8f8f5"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}], "rationale": "Abundant immunoglobulin transcripts together with JCHAIN, MZB1, DERL3 and the XBP1-associated secretory program strongly support antibody-secreting plasma cells. CD79A supports B-lineage identity. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-879d085000"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "C1QA together with CD14, AIF1 and LYZ supports macrophage identity. Abundant lysosomal genes and strong MHC class II expression indicate antigen-presenting macrophages. Although MHC class II genes are shared with dendritic cells, the combined profile favors macrophages. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.6}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-89c1241fbf"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000789", "cell_type_label": "alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}], "rationale": "TRAC and TRBC2, together with CD3D/CD3E and CD2, identify alpha-beta T cells. Strong IL7R suggests a helper/memory-like population, but these markers do not conclusively establish CD4 identity or a specific memory subtype. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-8ab1b5fbd8"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000875", "cell_type_label": "non-classical monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "NR4A1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}], "rationale": "Strong, nearly universal FCGR3A expression together with MS4A7, LST1 and NR4A1 supports CD16-positive non-classical monocytes. The accompanying myeloid markers reinforce this assignment. No listed markers clearly contradict it. Distinction from intermediate monocytes is less definitive without CD14 expression data."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-8c07cf76ca"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}], "rationale": "The combined NK-receptor, innate-signaling and cytotoxic marker program strongly supports natural killer cells. TRDC raises a γδ T-cell alternative, but can occur in NK cells and alone does not establish a conflicting lineage or mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-8d82b1a772"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}], "rationale": "Coexpression of T-cell receptor/CD3 genes and cytotoxic-effector markers supports CD8-enriched cytotoxic T cells. Strong TRGC2 expression leaves alpha-beta versus gamma-delta lineage unresolved, so the broader cytotoxic T-cell term is appropriate; it does not by itself establish a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-95367720e6"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "BACH2", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "MS4A1, CD79A, BANK1 and IGKC form a strong B-cell signature, supported by BACH2 and MHC class II antigen-presentation genes. The markers do not establish a specific B-cell subtype or clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-9814423bdc"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "The combination of NK receptors KLRD1 and KLRF1, cytotoxic genes GNLY, NKG7, PRF1 and GZMB, and signaling adaptors TYROBP and FCER1G strongly supports natural killer cells. FCGR3A and FGFBP2 suggest a mature CD16-positive cytotoxic NK phenotype. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-98402e60db"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CTSD", "stance": "supports"}], "rationale": "Near-universal C1QA/C1QB/C1QC expression, together with APOE and myeloid markers TYROBP and LYZ, strongly supports macrophages. High CD74 and HLA class II expression indicates an antigen-presenting phenotype. No listed markers clearly suggest a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.0}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-9d243229e7"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}], "rationale": "The profile supports immature, proliferating granulocytes: MPO and AZU1 indicate primary granule production, while STMN1, TYMS, PCNA and CDC20 indicate cycling. RNASE2 and RNASE3 suggest eosinophilic differentiation, but the combined profile does not securely resolve the granulocyte subtype. These markers alone do not establish a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.5}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-9d2a6afe3f"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CD33", "stance": "supports"}], "rationale": "Strong FCER1A and CD1C enrichment, together with ITGAX and abundant MHC class II expression, identifies conventional type 2 dendritic cells (cDC2). LYZ and CD33 are compatible with this myeloid identity; no listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-9e8b98aab5"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "", "cell_type_label": "Cycling cells; lineage unresolved", "decision": "uncertain", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}], "rationale": "These markers support active proliferation, including DNA replication and mitosis, rather than a specific cell lineage. Colon epithelial progenitors are plausible, but cycling immune or stromal cells cannot be excluded. No lineage-defining markers are provided, so a specific Cell Ontology term cannot be assigned. There is no clear evidence of a mixed cluster or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.4}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-a321096724"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'pre-B cell' is not the name of CL:0000817 ('precursor B cell'). Closest names: CL:0000956 (pre-B-I cell); CL:0000826 (pro-B cell); CL:0000955 (pre-B-II cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000817", "cell_type_label": "pre-B cell", "decision": "annotate", "markers": [{"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}], "rationale": "Strong IGLL1 and VPREB1 expression indicates the surrogate light-chain program characteristic of pre-B cells. Together with IGHM, CD79A/CD79B and VPREB3, this supports a developing B-cell identity. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 53.5}, {"answer": {"cell_type_id": "CL:0000817", "cell_type_label": "precursor B cell", "decision": "annotate", "markers": [{"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}], "rationale": "Strong IGLL1 and VPREB1 expression supports a surrogate light-chain program in developing B cells, together with IGHM, CD79A/CD79B and VPREB3. The broader term precursor B cell is supported without assigning an insufficiently resolved developmental stage. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pre-B cell' is not the name of CL:0000817 ('precursor B cell'). Closest names: CL:0000956 (pre-B-I cell); CL:0000826 (pro-B cell); CL:0000955 (pre-B-II cell)."], "seconds": 26.5}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-a33f382e85"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}], "rationale": "MS4A1 and CD79A/CD79B establish B-cell identity. Strong IGHM, IGHD and TCL1A expression supports a naive B-cell phenotype. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ac7ec2b016"} +{"attempts": [{"codes": ["BEV026"], "evidence": 4, "findings": [{"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "Immunoglobulin enrichment together with ELL2, a regulator of secretory immunoglobulin processing, favors IgG-producing plasma cells. Confidence is moderate because additional canonical plasma-cell markers are not listed. Isolated HDC expression is insufficient to establish a conflicting mast-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.4}, {"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "IGKC, IGHG1 and IGHG3 support a class-switched B-lineage identity. ELL2 suggests differentiation toward antibody secretion, but sparse SDC1 detection and insufficient additional plasma-cell markers favor the broader B cell annotation. Isolated HDC does not establish a conflicting mast-cell identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells."], "seconds": 36.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ad2d591627"} +{"attempts": [{"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016"], "evidence": 10, "findings": [{"message": "No row of the pinned table has cluster=c07, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 2 (cluster=c07;gene=CD3E)"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}], "rationale": "The combined NK-receptor, cytotoxic-effector and XCL1/XCL2 signature supports natural killer cells in endometrium. TRDC raises a gamma-delta T-cell alternative but can occur in uterine NK cells; without a accompanying CD3/T-cell-receptor program, it does not clearly contradict this annotation. The supplied markers do not establish a specific uterine NK subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.0}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "TRDC expression in 89.4% of cells, together with enriched CD3E expression in 65%, supports gamma-delta T cells with a strong cytotoxic program. NK-associated receptors and cytotoxic effectors are also expressed by gamma-delta T cells and do not clearly contradict this annotation. Cluster-level summaries cannot exclude mixed populations, but the additional CD3E evidence makes the previous NK-cell annotation inappropriate."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 65% of the cluster's cells, more than in the others (logfc 0.59)."], "seconds": 39.3}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "Enriched TRDC expression in 89.4% of cluster cells supports gamma-delta T cells with a strong cytotoxic program. The NK-associated markers are compatible with cytotoxic gamma-delta T cells and do not clearly contradict this annotation. However, these shared markers cannot independently distinguish T cells from NK cells. CD3E was not provided; its inclusion and expression percentage in the previous answer were unsupported."}, "cli_tools": [], "error": null, "feedback": ["evidence 2 (cluster=c07;gene=CD3E): No row of the pinned table has cluster=c07, gene=CD3E."], "seconds": 53.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ae89c1380f"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "Strong VCAN and S100A8/S100A9 expression, together with LYZ, C5AR1 and IL1R2, supports inflammatory classical monocytes. AIF1 and TYROBP reinforce myeloid identity. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b269766ee9"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LINC00861", "stance": "supports"}], "rationale": "CCR7 and SELL indicate lymphoid homing, while LEF1, KLF2 and IL7R support a resting naive T-cell phenotype. These markers favor naive T cells, although central memory T cells share part of this signature. CD4 versus CD8 identity cannot be resolved from the supplied markers; none clearly contradict the annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.6}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b322bece33"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}], "rationale": "TRGC2 enrichment together with widespread CD3D and CD3G expression favors cytotoxic gamma-delta T cells. NKG7, GNLY, GZMB and PRF1 support their cytotoxic program; these shared NK/T-cell markers do not independently contradict this annotation. Cluster-level expression cannot establish that every cell is gamma-delta."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b51a9f2d53"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "IL10 enrichment together with CTLA4, MAF and TNFRSF1B supports regulatory T cells. The IL10–MAF–KLRB1 pattern suggests a type 1 regulatory T (Tr1)-like population, but these markers alone do not firmly establish that subtype. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b5ea73db74"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "CD14", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "Strong, widespread CD14, FCN1 and VCAN expression together with S100A8/S100A9 and LYZ identifies classical monocytes. CSF3R and RNASE2 overlap with granulocyte programs but do not clearly contradict the coherent monocyte signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b7c75983d8"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "MS4A6A", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "The combined myeloid signature (MS4A6A, AIF1, TYROBP, LYZ, CST3) and strong MHC class II expression favor antigen-presenting macrophages. These markers overlap with dendritic cells, so the assignment is not definitive; no listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b864a5744b"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "TRDC expression in 96.1% and TRGC2 in 80.5% of cluster cells strongly supports gamma-delta T-cell identity. The cytotoxic genes and NK-associated receptors indicate a cytotoxic phenotype compatible with this lineage; they do not independently imply a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-b95794dcf3"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "MZB1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}], "rationale": "Strong immunoglobulin expression together with MZB1, JCHAIN, XBP1 and DERL3 identifies antibody-secreting plasma cells. Prominent IGHA1 suggests an IgA-enriched population. No listed markers clearly contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ba5f0288e7"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}], "rationale": "Strong, coherent CD3 and T-cell receptor expression identifies T cells. IL7R and ICOS suggest a helper/memory phenotype, but these markers do not establish CD4 lineage or a specific memory subtype. No listed markers clearly contradict T-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.2}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-be2c0ee626"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}], "rationale": "Strong FCN1 expression together with LST1, AIF1, SERPINA1, FCGR3A and MS4A7 supports monocytes. FCER1G, TYROBP and CTSS reinforce myeloid identity. The markers do not establish a specific monocyte subtype or clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-c5e3a0ec1f"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "FOXP3 enrichment (63.5% within versus 0.2% outside), together with IL2RA, CTLA4, TIGIT and TNFRSF18, strongly supports regulatory T cells. TRAC and CD3 genes establish T-cell identity. No listed markers clearly support a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-c99aec2a45"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}], "rationale": "Strong, coherent expression of B-cell receptor components CD79A/CD79B, MS4A1 (CD20), CD19 and IGKC identifies B cells. The markers do not confidently resolve a B-cell subtype. JCHAIN alone does not establish a plasma-cell identity or indicate a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ccd8ad8cc1"} +{"attempts": [{"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The combined expression of mast-cell tryptases TPSAB1 and TPSB2, CPA3, and histamine-synthesis enzyme HDC strongly identifies mast cells. These markers are expressed in 85–100% of cluster cells and virtually absent outside it. No listed markers clearly support a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.2}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}], "rationale": "The combined tryptase (TPSAB1, TPSB2), CPA3 and histamine-synthesis (HDC) signature strongly identifies mast cells. Undetected CCR3 RNA does not establish absence of membrane CCR3 protein, so the validator's objection does not justify rejecting this annotation. No listed markers clearly indicate a conflicting identity. IL33R is omitted because it is not an approved HGNC symbol."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 51.4}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}], "rationale": "The tryptase, CPA3 and histamine synthesis signature strongly supports mast cells. Granulocyte provides a broader annotation compatible with the validator's restriction on the mast cell term. Undetected CCR3 RNA does not establish absence of membrane CCR3 protein. No listed markers clearly support a conflicting identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 34.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ceffe8616a"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}], "rationale": "CD19, CD79A/CD79B and MS4A1 establish B-cell identity. Near-universal IGHM and IGHD expression together with strong TCL1A supports a naive B-cell phenotype. The markers do not clearly distinguish transitional from mature naive B cells, and none clearly indicates a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.0}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-d44564d7f6"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}], "rationale": "FCN1 and VCAN enrichment together with strong S100A8, S100A9 and S100A12 expression supports classical monocytes. LYZ, LST1, TYROBP and AIF1 reinforce myeloid identity. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-d7d3163b78"} +{"attempts": [{"codes": ["BEV004"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "PPP1R14A", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}, {"gene": "TPSAB1", "stance": "contradicts"}], "rationale": "The coordinated contractile markers support smooth muscle identity. However, strong TPSB2 and TPSAB1 expression in most cells indicates a substantial mast-cell signal, raising concern for doublets or a mixed cluster. This is a provisional annotation; cluster-level markers cannot resolve the conflicting identities."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-d929ec7963"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}], "rationale": "The T-cell markers TRAC, CD3E and CD2, together with CD4 and strong CCR7, SELL, CD27 and IL7R expression, favor naive CD4 T cells. Central memory CD4 T cells share this profile, so the naive designation is provisional without additional differentiation markers. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-e1bfaa2341"} +{"attempts": [{"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "Strong, widespread expression of NKG7 together with KLRD1 and KLRC1, supported by XCL1/XCL2 and cytotoxic effector genes, identifies an NK-cell cluster. No listed markers clearly contradict this identity; the evidence does not establish a specific NK subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.0}, {"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CD3E", "stance": "contradicts"}], "rationale": "The supporting markers indicate an NK-like phenotype, but CD3E expression in 50% of cells contradicts a confident natural killer cell annotation. These data cannot distinguish cytotoxic T cells expressing NK receptors from an NK/T mixture or doublets. They also do not establish a natural killer T-cell identity; additional T-cell receptor/CD3 markers and per-cell coexpression are needed."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35)."], "seconds": 32.9}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-e712a5eb84"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}], "rationale": "CD79A, CD79B, MS4A1 and CD19 establish B-cell identity. Strong, widespread IGHM and IGHD expression favors naive B cells. These markers do not fully distinguish naive from unswitched memory B cells, but none clearly indicates a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-e7ae6683c5"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000794", "cell_type_label": "CD8-positive, alpha-beta cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}], "rationale": "CD8A/CD8B together with the cytotoxic gene program support CD8 cytotoxic T cells. Strong GZMK expression suggests an effector-memory-like state. CD74 alone does not establish a conflicting lineage or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ec5325a064"} +{"attempts": [{"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016"], "evidence": 8, "findings": [{"message": "No row of the pinned table has cluster=c09, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 1 (cluster=c09;gene=CD3E)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "Strong GNLY, NKG7 and KLRD1 expression together with FGFBP2 and the perforin/granzyme cytotoxic program supports natural killer cells. CD247 is also expressed by NK cells and does not contradict this annotation. No listed marker clearly indicates a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.4}, {"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "CD3E expression in 73% of cells supports T-cell identity, while the perforin/granzyme program indicates a cytotoxic phenotype. GNLY, KLRD1 and FGFBP2 indicate NK-like features but can occur in cytotoxic T cells. These data do not establish a specific NKT or CD8 T-cell subtype; T cell is the defensible annotation. No marker unequivocally establishes a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60)."], "seconds": 36.9}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "The combined GNLY, KLRD1, NKG7 and FGFBP2 enrichment, together with perforin and granzymes, strongly supports natural killer cells. CD247 is shared with NK cells and does not establish T-cell identity. The previous CD3E evidence was unsupported: CD3E is not in the supplied table. No listed marker clearly contradicts NK-cell identity."}, "cli_tools": [], "error": null, "feedback": ["evidence 1 (cluster=c09;gene=CD3E): No row of the pinned table has cluster=c09, gene=CD3E."], "seconds": 48.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ed05c45d83"} +{"attempts": [{"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}], "rationale": "FCGR3B and CSF3R strongly support neutrophil identity, reinforced by abundant S100A8/S100A9 and enrichment of S100A12, G0S2, and MNDA. CXCL8 is consistent with an inflammatory activation state. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.0}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}], "rationale": "Granulocyte is a conservative broader annotation under the validator's constraints. FCGR3B and CSF3R strongly favor neutrophils, supported by S100A8/S100A9 and S100A12. Undetected CEACAM8, ITGAM, and SPN transcripts do not establish absence of their membrane proteins in sparse 10x RNA data. No listed markers clearly support a conflicting identity."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells."], "seconds": 46.8}, {"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}], "rationale": "FCGR3B and CSF3R, together with S100A8, S100A9 and S100A12, identify neutrophils more specifically than granulocytes. No listed markers clearly indicate a conflicting identity. Zero detected CEACAM8 or ITGAM RNA does not establish absence of membrane proteins. Neutrophils inherit granulocyte properties, so this biologically supported revision may still fail a validator that treats undetected transcripts as absent proteins."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells."], "seconds": 37.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-f2e4fa20cc"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000897", "cell_type_label": "CD4-positive, alpha-beta memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}, {"gene": "ZFP36L2", "stance": "supports"}], "rationale": "The IL7R–KLRB1–GPR183 combination favors a memory CD4 T-cell phenotype, with FYB1 and ZFP36L2 supporting T-cell biology. This is a provisional assignment: these markers are not exclusive to CD4 memory T cells, and definitive lineage markers are absent from the supplied top-marker list. No listed marker clearly contradicts this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.8}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-f5551fdf21"} +{"attempts": [{"codes": ["BEV004"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000765", "cell_type_label": "erythroblast", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "PRDX2", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "ITGA2B", "stance": "contradicts"}], "rationale": "The coordinated hemoglobin, erythroid metabolism, and iron-handling signature supports erythroblasts. Strong proliferation markers (STMN1, TYMS, PCNA, MCM2, MCM5) indicate cycling immature cells. ITGA2B points toward megakaryocytic differentiation and raises possible lineage overlap or mixing, but alone does not establish doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.1}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-f5e849f6ff"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002038", "cell_type_label": "T follicular helper cell", "decision": "annotate", "markers": [{"gene": "TOX2", "stance": "supports"}, {"gene": "PDCD1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "GNG4", "stance": "supports"}], "rationale": "TOX2, PDCD1 and MAF together strongly support a follicular helper T-cell identity in tonsil. TIGIT and GNG4 provide additional support. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.5}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-f6eff45a55"} +{"attempts": [{"codes": ["BEV026"], "evidence": 2, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016"], "evidence": 3, "findings": [{"message": "No row of the pinned table has cluster=c13, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 1 (cluster=c13;gene=CD3E)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 2, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "Most consistent with proliferating natural killer cells. GNLY and GZMA support cytotoxic lymphocyte identity, while MKI67, TOP2A, TYMS, PCLAF and CENPF indicate active cycling. These markers favor NK cells but do not definitively exclude cytotoxic T cells or establish a specific uterine NK subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.0}, {"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "CD3E expression in 78% of cells, enriched relative to other cells, supports T-cell identity and argues against the previous NK-cell annotation. GNLY and GZMA support a cytotoxic phenotype; MKI67, TOP2A and TYMS indicate proliferation. These data support proliferating cytotoxic T cells but do not establish a specific T-cell subtype."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 65.3}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "GNLY and GZMA support an NK-cell identity, with MKI67, TOP2A, TYMS and other cell-cycle genes indicating proliferation. This cluster is most consistent with proliferating natural killer cells. Cytotoxic T cells cannot be definitively excluded from this marker list; CD3E was absent from the supplied table and was incorrectly cited previously."}, "cli_tools": [], "error": null, "feedback": ["evidence 1 (cluster=c13;gene=CD3E): No row of the pinned table has cluster=c13, gene=CD3E."], "seconds": 40.7}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-f7efaf4b7a"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}], "rationale": "TRAC, CD3E and CD2 establish T-cell identity, with CD4 supporting the CD4-positive lineage. Strong IL7R, CCR7 and CD27 suggest a naive or central-memory phenotype, but do not reliably distinguish these states. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.3}], "model": "gpt-astra", "protocol": 3, "task_id": "ct-ff19304f5c"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'classical monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'classical monocyte' is the name of CL:0000860 (classical monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001054", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}], "rationale": "The combination of strong FCN1, CD14, VCAN, S100A8/S100A9, LYZ and CST3 expression is characteristic of classical CD14-positive monocytes. CSF3R is also compatible with an inflammatory/classical monocyte state; no marker clearly indicates a distinct cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 53.2}, {"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "FCN1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}], "rationale": "Strong FCN1, CD14, VCAN, S100A8/S100A9, LYZ and CST3 expression supports a classical monocyte identity. CSF3R is compatible with an inflammatory classical-monocyte state; no marker clearly indicates a distinct cell type or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'classical monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'classical monocyte' is the name of CL:0000860 (classical monocyte)."], "seconds": 25.3}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-0094010baa"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000771 (eosinophil) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 6% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'eosinophil precursor cell' is not the name of CL:0000911 ('effector T cell'). Closest names: CL:0000611 (eosinophil progenitor cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000771", "cell_type_label": "eosinophil", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}], "rationale": "The cluster is an eosinophil population, possibly with an immature or proliferative state. PRG2 and CLC are especially characteristic eosinophil granule markers, supported by RNASE2, HDC, CPA3, FCER1A, PRSS57 and NFE2. STMN1, CDK6 and TYMS indicate cell-cycle activity but do not define a different lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.7}, {"answer": {"cell_type_id": "CL:0000911", "cell_type_label": "eosinophil precursor cell", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "ITGA2B", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}], "rationale": "PRG2, CLC, HDC, CPA3, RNASE2 and PRSS57 strongly support eosinophilic differentiation, while STMN1, CDK6 and TYMS indicate a proliferative immature state. ITGA2B and NFE2 are also compatible with an eosinophil precursor population. The markers do not clearly indicate a separate lineage or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000771 (eosinophil) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 6% of the cluster's cells."], "seconds": 41.1}, {"answer": {"cell_type_id": "CL:0000611", "cell_type_label": "eosinophil progenitor cell", "decision": "annotate", "markers": [{"gene": "PRG2", "stance": "supports"}, {"gene": "CLC", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}], "rationale": "PRG2, CLC, HDC, CPA3, RNASE2, PRSS57 and FCER1A strongly support eosinophil-lineage differentiation, while STMN1, CDK6 and TYMS indicate a proliferative progenitor state. The marker set does not clearly indicate a separate lineage or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'eosinophil precursor cell' is not the name of CL:0000911 ('effector T cell'). Closest names: CL:0000611 (eosinophil progenitor cell)."], "seconds": 35.0}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-0224ef5d63"} +{"attempts": [{"codes": ["BEV004"], "evidence": 3, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}], "rationale": "TAGLN and TPM2 support a contractile smooth-muscle phenotype. TPSB2 is a mast-cell marker and may indicate mast-cell contamination or doublets, but the cluster lacks a coherent mast-cell signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-027de551e6"} +{"attempts": [{"codes": ["BEV004"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "BCL11A", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "JCHAIN", "stance": "contradicts"}, {"gene": "MZB1", "stance": "contradicts"}, {"gene": "IGKC", "stance": "contradicts"}, {"gene": "IGLC2", "stance": "contradicts"}], "rationale": "The combination of IL3RA, GZMB, TCF4, BCL11A, IRF7 and SOX4 is characteristic of human plasmacytoid dendritic cells. JCHAIN, MZB1 and immunoglobulin genes instead indicate antibody-secreting/plasma-cell biology, suggesting ambient RNA contamination or a possible mixed population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.6}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-0460394dc8"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}], "rationale": "The cluster is clearly B-lineage: CD79A, CD79B, MS4A1, BANK1, CD37 and IRF8 support B-cell identity, while CD74 and multiple HLA class II genes indicate antigen presentation typical of B cells. IGHA1, IGHG1, IGKC and IGLC2 suggest immunoglobulin expression and possible class-switched B-cell features, but MS4A1/CD79A expression does not support calling this a plasma-cell cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-04f3e6a976"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000192", "cell_type_label": "smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}], "rationale": "The cluster shows a coherent contractile smooth-muscle program: TAGLN, ACTA2, MYH11, MYL9, TPM2, CALD1, and TPM1. MYH11 and CALD1 particularly support mature smooth-muscle identity rather than pericytes; no clear marker indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.0}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-0919bb7151"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRGC2", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "The cluster is clearly T-lineage, with strong TRAC, CD3E, CD2 and CD27 expression. TRGC2 together with KLRK1, CTSW, NKG7, HCST and CST7 supports a cytotoxic gamma-delta T-cell identity. CD8A/CD8B and IL7R suggest a CD8-like, less terminally differentiated subset. No marker clearly indicates a contaminating alternative cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-15649bcc33"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'CD1c-positive myeloid dendritic cell' is not the name of CL:0001056 ('dendritic cell, human'). 'CD1c-positive myeloid dendritic cell' is the name of CL:0002399 (CD1c-positive myeloid dendritic cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001056", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "CLEC10A", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}], "rationale": "The cluster shows uniform high MHC class II and CD74 expression, together with CLEC10A, GPR183, CD83, CST3, and AIF1, supporting an activated CD1c-positive conventional/myeloid dendritic-cell identity. No marker clearly indicates a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.5}, {"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "CLEC10A", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CD83", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}], "rationale": "The cluster shows uniformly high MHC class II and CD74 expression, together with CLEC10A, GPR183, CD83, CST3, and AIF1, supporting a CD1c-positive myeloid dendritic-cell identity. The corrected Cell Ontology mapping is CL:0002399. No marker clearly indicates a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD1c-positive myeloid dendritic cell' is not the name of CL:0001056 ('dendritic cell, human'). 'CD1c-positive myeloid dendritic cell' is the name of CL:0002399 (CD1c-positive myeloid dendritic cell)."], "seconds": 28.2}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-18bf2c5651"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 15, "findings": [{"message": "The label 'Memory T cell (GZMK-positive CD8 effector-memory T cell)' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell').", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as lacking T cell receptor co-receptor CD8 (CD8A), but CD8A is detected in 50% of the cluster's cells, more than in the others (logfc 0.85).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017", "BEV026"], "evidence": 14, "findings": [{"message": "The label 'effector memory CD8-positive, alpha-beta T cell' is not the name of CL:0000907 ('central memory CD8-positive, alpha-beta T cell'). 'effector memory CD8-positive, alpha-beta T cell' is the name of CL:0000913 (effector memory CD8-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000907 (central memory CD8-positive, alpha-beta T cell) is defined as having C-C chemokine receptor type 7 (CCR7) on the membrane, but CCR7 is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "Memory T cell (GZMK-positive CD8 effector-memory T cell)", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}], "rationale": "The cluster is a CD8-positive memory/effector-memory T-cell population, characterized by T-cell receptor and CD3 genes (TRAC, TRBC1/2, CD3D, CD3E), CD8A/CD8B, and cytotoxic-memory markers CCL5, GZMK, GZMA, CCL4, and CST7. CD69 and RGS1 indicate an activated state. The profile does not clearly support a separate cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.2}, {"answer": {"cell_type_id": "CL:0000907", "cell_type_label": "effector memory CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The cluster is a CD8-positive alpha-beta T-cell population with an effector-memory/cytotoxic profile. CD8A and CD8B support CD8 lineage, while TRAC, TRBC1/2, CD3D, CD3E, and CD2 support alpha-beta T-cell identity. CCL5, GZMK, GZMA, CCL4, CST7, and activated-state CD69 support an effector-memory phenotype. No marker clearly indicates a different cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'Memory T cell (GZMK-positive CD8 effector-memory T cell)' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell').", "object id: CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 2% of the cluster's cells.", "object id: CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as lacking T cell receptor co-receptor CD8 (CD8A), but CD8A is detected in 50% of the cluster's cells, more than in the others (logfc 0.85)."], "seconds": 28.7}, {"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "effector memory CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The markers identify an activated effector-memory CD8-positive alpha-beta T-cell population. CD8A and CD8B support CD8 lineage; TRAC, TRBC1, TRBC2, CD3D, CD3E, and CD2 support alpha-beta T-cell identity; and CCL5, GZMK, GZMA, CCL4, CST7, and CD69 support an effector-memory/activated cytotoxic program. The low CCR7 representation argues against central memory CD8-positive T cells. No marker clearly indicates a different cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'effector memory CD8-positive, alpha-beta T cell' is not the name of CL:0000907 ('central memory CD8-positive, alpha-beta T cell'). 'effector memory CD8-positive, alpha-beta T cell' is the name of CL:0000913 (effector memory CD8-positive, alpha-beta T cell).", "object id: CL:0000907 (central memory CD8-positive, alpha-beta T cell) is defined as having C-C chemokine receptor type 7 (CCR7) on the membrane, but CCR7 is detected in only 2% of the cluster's cells."], "seconds": 45.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-1c3cf91fbc"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'connective tissue mast cell' is not the name of CL:0000098 ('sensory epithelial cell'). Closest names: CL:0000484 (connective tissue type mast cell); CL:0002320 (connective tissue cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000484 (connective tissue type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}], "rationale": "The cluster is a mast cell population, supported by the highly specific mast-cell proteases TPSAB1, TPSB2, and CPA3, together with HPGDS, MS4A2, GATA2, and RGS13. No markers clearly indicate a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.5}, {"answer": {"cell_type_id": "CL:0000098", "cell_type_label": "connective tissue mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}], "rationale": "The cluster is clearly a mast-cell population, with highly specific mast-cell proteases TPSAB1, TPSB2, and CPA3, plus HPGDS, MS4A2, GATA2, and RGS13. The connective-tissue mast-cell term fits these tissue mast-cell markers without requiring CCR3, which is absent from the cluster."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 33.2}, {"answer": {"cell_type_id": "CL:0000484", "cell_type_label": "connective tissue type mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "RGS13", "stance": "supports"}, {"gene": "RHEX", "stance": "supports"}], "rationale": "The cluster is a clear mast-cell population, supported by highly specific mast-cell proteases TPSAB1, TPSB2, and CPA3, together with HPGDS, MS4A2, GATA2, RGS13, and RHEX. The appropriate Cell Ontology term is connective tissue type mast cell (CL:0000484)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'connective tissue mast cell' is not the name of CL:0000098 ('sensory epithelial cell'). Closest names: CL:0000484 (connective tissue type mast cell); CL:0002320 (connective tissue cell)."], "seconds": 25.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-1cdfab3be0"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'inflammatory monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'inflammatory monocyte' is the name of CL:0000860 (classical monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001054", "cell_type_label": "inflammatory monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "RETN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The strong S100A8/S100A9, FCN1, VCAN, RETN, LYZ and CST3 signature is characteristic of inflammatory/classical monocytes, with no clear markers indicating a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.7}, {"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "RETN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The strong S100A8/S100A9, FCN1, VCAN, RETN, LYZ and CST3 signature supports a classical monocyte identity. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'inflammatory monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'inflammatory monocyte' is the name of CL:0000860 (classical monocyte)."], "seconds": 34.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-1dc66b7bae"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}], "rationale": "The cluster shows a coherent mature B-cell program (CD19, CD79A, CD79B, MS4A1, CD72) together with strong IGHM and IGHD expression. Uniform TCL1A, VPREB3, and CD24 expression is characteristic of antigen-inexperienced naive B cells, particularly the circulating naive B-cell compartment. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 57.5}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CD72", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}], "rationale": "The cluster has a coherent B-cell program (CD19, CD79A, CD79B, MS4A1, CD72) with uniform IGHM and strong IGHD, indicating an unswitched mature B-cell population. The combination of TCL1A, VPREB3, and CD24 strongly supports naive B cells. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell)."], "seconds": 43.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-1fdfebb69c"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}], "rationale": "The cluster is best annotated as cytotoxic gamma-delta T cells: TRDC and TRGC2 provide direct gamma-delta T-cell evidence, while NKG7, GNLY, CTSW, GZMA, KLRD1, KLRK1, KLRF1, FCGR3A, and ADGRG1 support an activated cytotoxic innate-like phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-21afd5c734"} +{"attempts": [{"codes": ["BEV004"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRBC1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "KRT86", "stance": "contradicts"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "TRDC together with TRBC1 identifies a T-cell receptor gamma-delta population. IL7R, KLRB1, RORA, TMIGD2 and ID2 support an IL7R+ CD161+ mucosal-like gamma-delta T-cell phenotype. KRT86 and LST1 are epithelial- and myeloid-associated markers, respectively, suggesting possible ambient RNA or a small doublet/contamination component."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.3}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-227cbde019"} +{"attempts": [{"codes": ["BEV004"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000784", "cell_type_label": "plasmacytoid dendritic cell", "decision": "annotate", "markers": [{"gene": "IL3RA", "stance": "supports"}, {"gene": "TCF4", "stance": "supports"}, {"gene": "PLD4", "stance": "supports"}, {"gene": "IRF8", "stance": "supports"}, {"gene": "IRF7", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "JCHAIN", "stance": "contradicts"}, {"gene": "MZB1", "stance": "contradicts"}, {"gene": "DERL3", "stance": "contradicts"}, {"gene": "IGKC", "stance": "contradicts"}, {"gene": "IGHM", "stance": "contradicts"}], "rationale": "IL3RA, TCF4, PLD4, IRF8, IRF7 and FCER1A support a plasmacytoid dendritic-cell identity. However, uniform JCHAIN with MZB1, DERL3 and immunoglobulin expression strongly suggests antibody-secreting/plasma-cell contamination or doublets, so the cluster may be mixed."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-26fda93c9c"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "The cluster shows a strong CD8 T-cell program (CD8A, CD8B, TRAC, CD3E) with CCR7, IL7R, CD27, and SELL indicating a less-differentiated/central-memory-like phenotype. KLRK1 and CTSW support cytotoxic-leaning CD8 T-cell identity, but the markers do not require a more specific subtype annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-28eb7ea379"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "MRC1", "stance": "supports"}, {"gene": "F13A1", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "STAB1", "stance": "supports"}, {"gene": "MERTK", "stance": "supports"}, {"gene": "COLEC12", "stance": "supports"}], "rationale": "The cluster shows a strong tissue-resident, MRC1-positive macrophage program: CD163, C1QA/C1QB, MERTK, STAB1, SELENOP, F13A1, LYVE1 and MRC1. RNASE1 and COLEC12 may reflect vascular/perivascular localization, but the dominant macrophage program does not require calling a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 74.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-302af8ae13"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'megakaryocyte-erythroid progenitor cell' is not the name of CL:0000892 ('smooth muscle cell derived foam cell'). 'megakaryocyte-erythroid progenitor cell' is the name of CL:0000050 (megakaryocyte-erythroid progenitor cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000892", "cell_type_label": "megakaryocyte-erythroid progenitor cell", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "FERMT3", "stance": "supports"}, {"gene": "GUCY1B1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}], "rationale": "The cluster shows a proliferative, CD34-positive megakaryocytic progenitor program. ITGA2B, PPBP, FERMT3, GUCY1B1 and NFE2 support megakaryocyte/platelet lineage, while CD34, STMN1, CDK6 and TYMS indicate an immature cycling progenitor state. SLC40A1 and TAL1 are also consistent with megakaryocyte-erythroid progenitor biology."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 55.9}, {"answer": {"cell_type_id": "CL:0000050", "cell_type_label": "megakaryocyte-erythroid progenitor cell", "decision": "annotate", "markers": [{"gene": "ITGA2B", "stance": "supports"}, {"gene": "PPBP", "stance": "supports"}, {"gene": "FERMT3", "stance": "supports"}, {"gene": "GUCY1B1", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "TAL1", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}], "rationale": "The corrected Cell Ontology mapping is CL:0000050. Strong ITGA2B, PPBP, FERMT3, GUCY1B1 and NFE2 expression supports megakaryocytic lineage, while CD34, STMN1, CDK6 and TYMS indicate an immature proliferating progenitor state. TAL1 and SLC40A1 are compatible with megakaryocyte-erythroid progenitor biology."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'megakaryocyte-erythroid progenitor cell' is not the name of CL:0000892 ('smooth muscle cell derived foam cell'). 'megakaryocyte-erythroid progenitor cell' is the name of CL:0000050 (megakaryocyte-erythroid progenitor cell)."], "seconds": 33.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-3775a26491"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'connective tissue mast cell' is not the name of CL:0000099 ('interneuron'). Closest names: CL:0000484 (connective tissue type mast cell); CL:0002320 (connective tissue cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000484 (connective tissue type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL18R1", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster is a mast cell population, supported by highly specific mast-cell markers TPSB2, TPSAB1, CPA3, KIT, and HPGDS. IL18R1 and IL33R are also compatible with mast-cell identity. No markers clearly indicate a conflicting cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}, {"answer": {"cell_type_id": "CL:0000099", "cell_type_label": "connective tissue mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "SLC24A3", "stance": "supports"}], "rationale": "The cluster is clearly a mast-cell population, with strong expression of TPSB2, TPSAB1, CPA3, KIT, and HPGDS. Its tissue-resident/connective-tissue phenotype is consistent with IL33R and SLC24A3. No markers clearly indicate a different cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 53.6}, {"answer": {"cell_type_id": "CL:0000484", "cell_type_label": "connective tissue type mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}, {"gene": "SLC24A3", "stance": "supports"}], "rationale": "The cluster is clearly composed of mast cells, with strong expression of TPSB2, TPSAB1, CPA3, KIT, and HPGDS. IL33R and SLC24A3 support a tissue-resident connective-tissue mast-cell phenotype. No markers clearly indicate another cell type or a mixed-cell doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'connective tissue mast cell' is not the name of CL:0000099 ('interneuron'). Closest names: CL:0000484 (connective tissue type mast cell); CL:0002320 (connective tissue cell)."], "seconds": 39.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-3959f97db0"} +{"attempts": [{"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'mast cell progenitor' is not the name of CL:0000985 ('IgG plasma cell'). 'mast cell progenitor' is the name of CL:0000831 (mast cell progenitor).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000831 (mast cell progenitor) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 9% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000985", "cell_type_label": "mast cell progenitor", "decision": "annotate", "markers": [{"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "The combination of strong CPA3 and FCER1A expression with CD34 and cell-cycle markers supports an immature, proliferating mast-cell lineage rather than mature mast cells. NPR3 and SLC40A1 are also compatible with this progenitor-like myeloid program."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 67.0}, {"answer": {"cell_type_id": "CL:0000831", "cell_type_label": "mast cell progenitor", "decision": "annotate", "markers": [{"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}], "rationale": "Strong CPA3 and FCER1A identify the mast-cell lineage, while CD34 together with CDK6 and STMN1 supports an immature, proliferating progenitor state. NPR3 and SLC40A1 are compatible with this mast-cell progenitor profile."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'mast cell progenitor' is not the name of CL:0000985 ('IgG plasma cell'). 'mast cell progenitor' is the name of CL:0000831 (mast cell progenitor)."], "seconds": 33.0}, {"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "CPA3", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "CPA3 and FCER1A strongly support mast-cell identity, with NPR3 providing additional support. CD34, CDK6, and STMN1 indicate an immature and proliferative state, but the available markers do not meet the more specific mast-cell-progenitor definition."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000831 (mast cell progenitor) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 9% of the cluster's cells."], "seconds": 25.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-3b8c7f5246"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'activated T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). Closest names: CL:0000898 (naive T cell); CL:0000064 (ciliated cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'dividing T cell' is not the name of CL:0000910 ('cytotoxic T cell').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "activated T cell", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CD99", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}], "rationale": "The combination of GZMK and S100A4 supports an activated memory/effector T-cell program, while STMN1, TUBA1B, TUBB, HMGB2, and TYMS indicate strong cell-cycle/proliferative activity. CD74 is not sufficiently specific here to establish an antigen-presenting cell identity or a doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 50.8}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "dividing T cell", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}], "rationale": "STMN1, TUBA1B, TUBB, HMGB2, and TYMS indicate a strongly proliferative/dividing state, while GZMK and S100A4 support T-cell identity. CD74 is not sufficient to call a separate antigen-presenting lineage or a doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'activated T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). Closest names: CL:0000898 (naive T cell); CL:0000064 (ciliated cell)."], "seconds": 27.7}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "GZMK", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TUBA1B", "stance": "supports"}, {"gene": "TUBB", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}], "rationale": "GZMK and S100A4 support a cytotoxic T-cell identity, while STMN1, TUBA1B, TUBB, HMGB2, and TYMS indicate that these cells are actively dividing. CD74 may reflect activation and does not clearly establish a separate lineage or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'dividing T cell' is not the name of CL:0000910 ('cytotoxic T cell')."], "seconds": 23.3}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-3daee1395a"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "The combination of TRGC2 with CD3E, TRAC and CD3G identifies a gamma-delta T-cell receptor lineage. Strong NKG7, KLRK1, FCGR3A, KLRF1, KLRD1, GNLY, CST7 and CTSW expression indicates a cytotoxic NK-like gamma-delta T-cell state. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.2}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-4b8439fcc9"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'granulocyte-monocyte progenitor' is not the name of CL:0000050 ('megakaryocyte-erythroid progenitor cell'). 'granulocyte-monocyte progenitor' is the name of CL:0000557 (granulocyte monocyte progenitor cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000050", "cell_type_label": "granulocyte-monocyte progenitor", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "RNASE2", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}], "rationale": "The combination of MPO, CD34, SPINK2, PRSS57, AZU1, CSF3R and strong cell-cycle genes indicates an immature granulocytic/myeloid progenitor population. CPA3 and RNASE2 support early granulocyte-lineage differentiation, while IGLL1 can mark immature hematopoietic progenitors. The markers do not clearly establish a distinct contaminating cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.9}, {"answer": {"cell_type_id": "CL:0000557", "cell_type_label": "granulocyte monocyte progenitor cell", "decision": "annotate", "markers": [{"gene": "MPO", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "PRSS57", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}], "rationale": "The combination of immature hematopoietic/proliferation markers (CD34, SPINK2, PRSS57, STMN1) with strong myeloid/granulocytic markers (MPO, AZU1, CSF3R, NFE2) supports a granulocyte-monocyte progenitor population. No markers clearly indicate a separate contaminating cell type or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'granulocyte-monocyte progenitor' is not the name of CL:0000050 ('megakaryocyte-erythroid progenitor cell'). 'granulocyte-monocyte progenitor' is the name of CL:0000557 (granulocyte monocyte progenitor cell)."], "seconds": 29.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-4e9d71ecad"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "FCER1G", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "CTSL", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "AQP9", "stance": "supports"}, {"gene": "PLIN2", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "CCL20", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "EREG", "stance": "supports"}, {"gene": "SOD2", "stance": "supports"}], "rationale": "The combination of FCER1G, IFI30, CTSL, PLAUR, AQP9 and PLIN2 supports a macrophage-lineage myeloid identity. CCL20, CXCL8, EREG, KYNU and SOD2 suggest an activated/inflammatory macrophage state. No marker clearly contradicts this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-5169234be6"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}], "rationale": "TRDC and TRGC2 are highly specific markers of gamma-delta T-cell receptor expression, while CD3E confirms T-cell identity. NKG7, KLRK1, KLRD1, CTSW, GZMA, and GNLY support a cytotoxic/NK-like gamma-delta T-cell phenotype. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-56d8f3ebbf"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'plasma cell' is not the name of CL:0000091 ('Kupffer cell'). 'plasma cell' is the name of CL:0000786 (plasma cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "The cluster shows a strong antibody-secreting plasma-cell program: JCHAIN, MZB1, DERL3, FKBP11, XBP1, and SEC11C indicate immunoglobulin production and endoplasmic-reticulum specialization, with CD38, CD27, CD79A, CD19, and IGKC supporting B-lineage plasma-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.9}, {"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "CD38", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "The cluster has a strong antibody-secreting plasma-cell program: JCHAIN, MZB1, DERL3, FKBP11, XBP1, and SEC11C indicate immunoglobulin production and endoplasmic-reticulum specialization, while CD38, CD27, CD79A, and IGKC support B-lineage plasma-cell identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'plasma cell' is not the name of CL:0000091 ('Kupffer cell'). 'plasma cell' is the name of CL:0000786 (plasma cell)."], "seconds": 42.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-62995bbc69"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "LAG3", "stance": "supports"}, {"gene": "PRDM1", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}], "rationale": "The cluster shows an activated regulatory T-cell program, with TNFRSF4, TNFRSF18, CTLA4, LAG3, PRDM1, and MAF. KLRB1 and RORA suggest a mucosal/Th17-like regulatory T-cell state. No marker clearly indicates a separate cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-62ef0fd4ba"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'mucosal mast cell' is not the name of CL:0000868 ('lymph node macrophage'). Closest names: CL:0000485 (mucosal type mast cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000485 (mucosal type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster is a mast cell population, supported by the highly specific mast-cell proteases TPSB2, TPSAB1, and CPA3, along with MS4A2, HPGDS, GATA2, and LTC4S. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 53.6}, {"answer": {"cell_type_id": "CL:0000868", "cell_type_label": "mucosal mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster is clearly a mast-cell population, based on highly specific mast-cell proteases TPSB2, TPSAB1, and CPA3, together with MS4A2, HPGDS, GATA2, and LTC4S. The mucosal mast cell term is more appropriate than the rejected generic mast cell term because CCR3 is not detected. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 32.6}, {"answer": {"cell_type_id": "CL:0000485", "cell_type_label": "mucosal type mast cell", "decision": "annotate", "markers": [{"gene": "TPSB2", "stance": "supports"}, {"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "MS4A2", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "LTC4S", "stance": "supports"}], "rationale": "The cluster is clearly a mast-cell population, supported by highly specific mast-cell proteases TPSB2, TPSAB1, and CPA3, together with HPGDS, MS4A2, GATA2, and LTC4S. These markers support the Cell Ontology term mucosal type mast cell (CL:0000485). No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'mucosal mast cell' is not the name of CL:0000868 ('lymph node macrophage'). Closest names: CL:0000485 (mucosal type mast cell)."], "seconds": 26.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-68351aaa63"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "CST3", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "FCGRT", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "The cluster shows a coherent macrophage program: near-universal CST3 and C1Q genes, plus SELENOP, TYROBP, MS4A7, FCGRT, AIF1, NPC2, and antigen-presentation genes HLA-DRA/HLA-DRB1/HLA-DPA1/CD74. CCL3 and CCL4 suggest an activated inflammatory state, but no markers clearly indicate a different cell type or a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-6dacd7effa"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000899", "cell_type_label": "T-helper 17 cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "RORA", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "The cluster is clearly an activated CD4 T-cell population, with IL7R, KLRB1, RORA, CD40LG and GPR183 supporting a Th17-like phenotype. CD3D/E/G, TRAC, TRBC2, CD2 and BCL11B confirm T-cell identity. No markers clearly indicate a competing cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-72757d8950"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 7, "findings": [{"message": "The label 'CD4-positive, alpha-beta memory T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). 'CD4-positive, alpha-beta memory T cell' is the name of CL:0000897 (CD4-positive, alpha-beta memory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 7% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as lacking T cell receptor co-receptor CD8 (CD8A), but CD8A is detected in 68% of the cluster's cells, more than in the others (logfc 1.09).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017", "BEV026"], "evidence": 7, "findings": [{"message": "The label 'effector memory CD8-positive, alpha-beta T cell' is not the name of CL:0000907 ('central memory CD8-positive, alpha-beta T cell'). 'effector memory CD8-positive, alpha-beta T cell' is the name of CL:0000913 (effector memory CD8-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000907 (central memory CD8-positive, alpha-beta T cell) is defined as having C-C chemokine receptor type 7 (CCR7) on the membrane, but CCR7 is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "CD4-positive, alpha-beta memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "The strong IL7R signal is characteristic of memory CD4 T cells, while CD96, CCL5, CCL4, STAT4, and CD69 indicate an activated, cytotoxic-leaning memory T-cell state. No marker clearly requires assignment to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.8}, {"answer": {"cell_type_id": "CL:0000907", "cell_type_label": "effector memory CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "The cluster is best classified as an effector-memory CD8-positive alpha-beta T-cell population: CD8A is enriched and detected in most cells, while CCL5, CCL4, CD96, STAT4, and CD69 indicate an activated effector/cytotoxic program. IL7R supports a memory T-cell state. The low CD4 detection argues against a CD4-defined effector-memory annotation."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD4-positive, alpha-beta memory T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). 'CD4-positive, alpha-beta memory T cell' is the name of CL:0000897 (CD4-positive, alpha-beta memory T cell).", "object id: CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 7% of the cluster's cells.", "object id: CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as lacking T cell receptor co-receptor CD8 (CD8A), but CD8A is detected in 68% of the cluster's cells, more than in the others (logfc 1.09)."], "seconds": 50.9}, {"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "effector memory CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CD96", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "STAT4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "FYN", "stance": "supports"}, {"gene": "CBLB", "stance": "supports"}], "rationale": "The cluster is best classified as an effector memory CD8-positive alpha-beta T-cell population. IL7R indicates a memory T-cell program, while CD96, CCL5, CCL4, STAT4, and CD69 support activated effector/cytotoxic T-cell biology. The very low CCR7 signal argues against central memory T cells; no marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'effector memory CD8-positive, alpha-beta T cell' is not the name of CL:0000907 ('central memory CD8-positive, alpha-beta T cell'). 'effector memory CD8-positive, alpha-beta T cell' is the name of CL:0000913 (effector memory CD8-positive, alpha-beta T cell).", "object id: CL:0000907 (central memory CD8-positive, alpha-beta T cell) is defined as having C-C chemokine receptor type 7 (CCR7) on the membrane, but CCR7 is detected in only 4% of the cluster's cells."], "seconds": 50.0}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-72dfb189c0"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "SPINK2", "stance": "supports"}, {"gene": "CD34", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "MSI2", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "The cluster shows a strong primitive hematopoietic stem/progenitor program, especially SPINK2, CD34, NPR3, CRHBP, EGFL7, PROM1, MSI2, and HOPX. STMN1 and CDK6 suggest some proliferative activity, but no markers clearly indicate a different lineage or a doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 54.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-75adde23f7"} +{"attempts": [{"codes": ["BEV004", "BEV026"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 1% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV004", "BEV017"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'mucosal invariant T cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'mucosal invariant T cell' is the name of CL:0000940 (mucosal-associated invariant T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "TRBC1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}, {"gene": "KRT81", "stance": "contradicts"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "The near-universal TRBC1 expression establishes a T-cell identity, while IL7R, KLRB1, LTB, TNFRSF4 and TNFRSF18 support an activated CD4-positive alpha-beta T-cell phenotype. High LST1 suggests myeloid signal, and KRT81/KRT86 indicate epithelial contamination or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.9}, {"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "mucosal invariant T cell", "decision": "annotate", "markers": [{"gene": "TRBC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}, {"gene": "KRT81", "stance": "contradicts"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "TRBC1 establishes a T-cell identity, while the combination of KLRB1, IL7R, KIT, AHR and TMIGD2 is characteristic of a mucosal-associated invariant T (MAIT-like) population rather than a conventional CD4-positive T-cell annotation. LST1 suggests myeloid signal, and KRT81/KRT86 suggest epithelial contamination or doublets."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 1% of the cluster's cells."], "seconds": 57.5}, {"answer": {"cell_type_id": "CL:0000940", "cell_type_label": "mucosal-associated invariant T cell", "decision": "annotate", "markers": [{"gene": "TRBC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "AHR", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}, {"gene": "KRT81", "stance": "contradicts"}, {"gene": "KRT86", "stance": "contradicts"}], "rationale": "TRBC1 supports T-cell identity, while KLRB1, IL7R, KIT, AHR, and TMIGD2 support a mucosal-associated invariant T-cell phenotype. LST1 suggests myeloid contamination, and KRT81/KRT86 suggest epithelial contamination or a mixed/doublet population."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'mucosal invariant T cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'mucosal invariant T cell' is the name of CL:0000940 (mucosal-associated invariant T cell)."], "seconds": 33.6}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-76fa626271"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000037", "cell_type_label": "hematopoietic stem cell", "decision": "annotate", "markers": [{"gene": "CD34", "stance": "supports"}, {"gene": "PROM1", "stance": "supports"}, {"gene": "SPINK2", "stance": "supports"}, {"gene": "NPR3", "stance": "supports"}, {"gene": "EGFL7", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}], "rationale": "The cluster shows a proliferating hematopoietic stem/progenitor program: strong CD34, PROM1, SPINK2, NPR3, and EGFL7 expression, with STMN1, CDK6, TYMS, PCNA, and MCM2 indicating active cycling. IGLL1 is compatible with an early progenitor state."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-7a81a9a19f"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 13, "findings": [{"message": "The label 'cytotoxic T cell' is not the name of CL:0000913 ('effector memory CD8-positive, alpha-beta T cell'). 'cytotoxic T cell' is the name of CL:0000910 (cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as lacking interleukin-2 receptor subunit alpha (IL2RG), but IL2RG is detected in 71% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "LIME1", "stance": "supports"}], "rationale": "The cluster is a CD8-positive cytotoxic T-cell population, supported by T-cell receptor and CD3 genes (TRAC, CD3D, CD3G, CD2), CD8A/CD8B, and cytotoxic effector genes (CCL5, GZMK, GZMM, GZMH, CST7)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 54.9}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "BCL11B", "stance": "supports"}, {"gene": "LIME1", "stance": "supports"}], "rationale": "The cluster is best annotated as a cytotoxic T cell (CL:0000910), with strong T-cell receptor and CD3 expression, CD8A/CD8B, and cytotoxic effector genes including CCL5, GZMK, GZMM, GZMH, and CST7. IL2RG expression argues against the previously assigned effector memory CD8-positive, alpha-beta T-cell term CL:0000913, but does not indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cytotoxic T cell' is not the name of CL:0000913 ('effector memory CD8-positive, alpha-beta T cell'). 'cytotoxic T cell' is the name of CL:0000910 (cytotoxic T cell).", "object id: CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as lacking interleukin-2 receptor subunit alpha (IL2RG), but IL2RG is detected in 71% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 38.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-7c21a7ad85"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'gamma-delta T cell' is not the name of CL:0000814 ('mature NK T cell'). 'gamma-delta T cell' is the name of CL:0000798 (gamma-delta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000814", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "TRDC is a defining marker of gamma-delta T cells. The combination of KLRB1, IL7R, CD7 and cytotoxic/NK-associated genes including XCL1, XCL2, GNLY, CTSW and KLRC1 supports an activated, NK-like gamma-delta T-cell phenotype. TYROBP and FCER1G can occur in cytotoxic gamma-delta T cells and do not by themselves establish a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.3}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "TRDC is a defining gamma-delta T-cell marker. KLRB1 and IL7R support a mucosal/innate-like gamma-delta T-cell phenotype, while XCL1, XCL2, GNLY, CTSW, and KLRC1 indicate cytotoxic NK-like activation. No marker clearly establishes a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'gamma-delta T cell' is not the name of CL:0000814 ('mature NK T cell'). 'gamma-delta T cell' is the name of CL:0000798 (gamma-delta T cell)."], "seconds": 30.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-7ec8cd3664"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "The strong C1Q program (C1QA/B/C), SELENOP, TYROBP, FCER1G, AIF1, CD14, and MS4A6A expression identifies a tissue macrophage population, with HLA-II genes indicating antigen-presentation activity. No markers clearly indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-819cfbd986"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). Closest names: CL:0000906 (activated CD8-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "TXNIP", "stance": "supports"}, {"gene": "NELL2", "stance": "supports"}], "rationale": "CD8A/CD8B identify the CD8 T-cell lineage, while CCR7, SELL, LEF1, KLF2, TXNIP, and NELL2 support a naive or central-naive phenotype. No markers clearly indicate a conflicting cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.2}, {"answer": {"cell_type_id": "CL:0000900", "cell_type_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "TXNIP", "stance": "supports"}, {"gene": "NELL2", "stance": "supports"}], "rationale": "CD8A and CD8B support the CD8-positive T-cell lineage. CCR7, SELL, LEF1, KLF2, TXNIP, and NELL2 support a naive thymus-derived phenotype. No markers clearly indicate a conflicting cell type or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). Closest names: CL:0000906 (activated CD8-positive, alpha-beta T cell); CL:0000625 (CD8-positive, alpha-beta T cell); CL:0000896 (activated CD4-positive, alpha-beta T cell)."], "seconds": 28.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-81b1e8f8f5"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}], "rationale": "The cluster shows a strong antibody-secreting plasma-cell program: abundant immunoglobulin heavy and light chains, JCHAIN, MZB1, DERL3, FKBP11, XBP1, PRDX4, and SEC11C. The immunoglobulin profile is particularly consistent with class-switched, predominantly IgG-expressing plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-879d085000"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}], "rationale": "The cluster shows a coherent macrophage/mononuclear phagocyte program: CD14, LYZ, C1QA, AIF1, CST3, CTSB and CTSS, together with strong antigen-presentation genes HLA-DRA, HLA-DRB1, CD74, HLA-DPA1 and HLA-DPB1. The high C1QA and CD14 expression support macrophages over a generic dendritic-cell annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-89c1241fbf"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017", "BEV026"], "evidence": 9, "findings": [{"message": "The label 'memory T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). 'memory T cell' is the name of CL:0000813 (memory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The cluster shows a clear T-cell receptor/CD3 program (TRAC, TRBC2, CD3D, CD3E, CD2) with IL7R and KLRB1, consistent with a CD4-positive alpha-beta T-cell population, likely an IL7R-positive memory/helper-like subset. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.4}, {"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The cluster has a clear T-cell receptor/CD3 program (TRAC, TRBC2, CD3D, CD3E, CD2) together with IL7R, LTB, and KLRB1, consistent with an IL7R-positive memory T-cell population. Because CD4 is detected in only a small minority of cells, a broader memory T-cell annotation is better supported than a CD4-positive T-cell term."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000624 (CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 8% of the cluster's cells."], "seconds": 37.5}, {"answer": {"cell_type_id": "CL:0000813", "cell_type_label": "memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The cluster shows a clear alpha-beta T-cell program through TRAC, TRBC2, CD3D, CD3E, and CD2, with IL7R, LTB, and KLRB1 supporting a memory T-cell phenotype. The data do not support the more specific effector memory CD4-positive term because CD4 is not among the reported markers and is detected in only a small fraction of cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'memory T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). 'memory T cell' is the name of CL:0000813 (memory T cell).", "object id: CL:0000905 (effector memory CD4-positive, alpha-beta T cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 8% of the cluster's cells."], "seconds": 32.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-8ab1b5fbd8"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'CD16-positive monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). Closest names: CL:0001054 (CD14-positive monocyte); CL:0001022 (CD115-positive monocyte); CL:0002396 (CD14-low, CD16-positive monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001054", "cell_type_label": "CD16-positive monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "NR4A1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CD86", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}], "rationale": "The combination of strong FCGR3A (CD16), MS4A7, LST1, FCER1G, TYROBP, and NR4A1 expression is characteristic of human CD16-positive/non-classical monocytes. ITGAX, CD86, and MPEG1 further support an activated or dendritic-like monocyte state, but do not outweigh the coherent monocyte program. No clearly contradictory markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.5}, {"answer": {"cell_type_id": "CL:0002396", "cell_type_label": "CD14-low, CD16-positive monocyte", "decision": "annotate", "markers": [{"gene": "FCGR3A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}, {"gene": "NR4A1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CD86", "stance": "supports"}, {"gene": "MPEG1", "stance": "supports"}], "rationale": "The strong FCGR3A program together with NR4A1, MS4A7, LST1, TYROBP, FCER1G, ITGAX, and CD86 is characteristic of CD14-low, CD16-positive (non-classical/intermediate-spectrum) monocytes. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD16-positive monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). Closest names: CL:0001054 (CD14-positive monocyte); CL:0001022 (CD115-positive monocyte); CL:0002396 (CD14-low, CD16-positive monocyte)."], "seconds": 43.6}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-8c07cf76ca"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}], "rationale": "The cluster shows a strong cytotoxic innate-like lymphocyte program, with TRDC specifically supporting gamma-delta T-cell identity and GNLY, NKG7, CTSW, KLRD1, KLRC1, XCL1/XCL2, TYROBP, FCER1G, and GZMB supporting its NK-like cytotoxic phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.2}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-8d82b1a772"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The combination of TRGC2 with CD3/T-cell receptor genes identifies a gamma-delta T-cell lineage. NKG7, KLRK1, GZMA, CTSW, CST7, and CD8A/B support a cytotoxic, CD8-associated phenotype. No marker clearly indicates a different cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.0}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-95367720e6"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "AFF3", "stance": "supports"}, {"gene": "RALGPS2", "stance": "supports"}], "rationale": "The cluster shows a coherent B-cell program: MS4A1 (CD20), CD79A, BANK1, AFF3, and RALGPS2, together with immunoglobulin light chain IGKC and strong MHC class II antigen-presentation genes (CD74, HLA-DRA, HLA-DRB1, HLA-DQA1, HLA-DPA1). No clear markers indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-9814423bdc"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}], "rationale": "The cluster shows a strong cytotoxic NK-cell program: GNLY, NKG7, GZMB, PRF1, KLRD1, KLRF1, FGFBP2, FCGR3A, TYROBP, and FCER1G are characteristic of natural killer cells, with high expression across most cells in the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-98402e60db"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000235", "cell_type_label": "macrophage", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "PLXDC2", "stance": "supports"}], "rationale": "The strong C1Q complement signature (C1QA/B/C), APOE, TYROBP, LYZ, CST3 and NPC2 supports a tissue macrophage identity. High HLA-DRA/CD74 and HLA-DP/DQ expression indicates an MHC-II-high antigen-presenting macrophage state. No markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-9d243229e7"} +{"attempts": [{"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000771 (eosinophil) is defined as having CD69 molecule (CD69) on the membrane, but CD69 is detected in only 9% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000771 (eosinophil) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'eosinophil precursor' is not the name of CL:0002390 ('uninucleate blastconidium').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000771 (eosinophil) is defined as having CD69 molecule (CD69) on the membrane, but CD69 is detected in only 9% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000771 (eosinophil) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000771", "cell_type_label": "eosinophil", "decision": "annotate", "markers": [{"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "CDC20", "stance": "supports"}], "rationale": "RNASE2 and RNASE3 are highly characteristic eosinophil markers, while MPO, AZU1, and LYZ support an immature granulocytic program. STMN1, TYMS, PCNA, and CDC20 indicate that the cluster is proliferating/cycling, consistent with proliferating or immature eosinophils."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.2}, {"answer": {"cell_type_id": "CL:0002390", "cell_type_label": "eosinophil precursor", "decision": "annotate", "markers": [{"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "CDC20", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}], "rationale": "RNASE2 and RNASE3 indicate eosinophil lineage, while MPO and AZU1 support an immature granulocytic program. STMN1, TYMS, PCNA, and CDC20 show active proliferation, favoring an eosinophil precursor rather than a mature eosinophil. No marker clearly indicates a distinct cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000771 (eosinophil) is defined as having CD69 molecule (CD69) on the membrane, but CD69 is detected in only 9% of the cluster's cells.", "object id: CL:0000771 (eosinophil) is defined as having CD9 molecule (CD9) on the membrane, but CD9 is detected in only 2% of the cluster's cells."], "seconds": 38.9}, {"answer": {"cell_type_id": "CL:0000771", "cell_type_label": "eosinophil", "decision": "annotate", "markers": [{"gene": "RNASE2", "stance": "supports"}, {"gene": "RNASE3", "stance": "supports"}, {"gene": "MPO", "stance": "supports"}, {"gene": "AZU1", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "CDC20", "stance": "supports"}], "rationale": "RNASE2 and RNASE3 are characteristic eosinophil-lineage markers, with MPO and AZU1 supporting an immature granulocytic program. STMN1, TYMS, PCNA, and CDC20 indicate active proliferation, suggesting a cycling or immature eosinophil population. No markers clearly indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'eosinophil precursor' is not the name of CL:0002390 ('uninucleate blastconidium')."], "seconds": 31.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-9d2a6afe3f"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "CD1C", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "ITGAX", "stance": "supports"}], "rationale": "The combination of strong FCER1A and CD1C expression with uniformly high MHC class II genes (HLA-DRA, HLA-DP, HLA-DR, and CD74), plus myeloid markers CST3 and LYZ, is characteristic of human CD1c-positive myeloid dendritic cells (cDC2)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-9e8b98aab5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'cycling cell' is not the name of CL:0000955 ('pre-B-II cell'). Closest names: CL:4033069 (cycling T cell); CL:4033068 (cycling B cell); CL:4047002 (cycling glial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'proliferating cell' is not the name of CL:0000128 ('oligodendrocyte').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'cycling cell' is not the name of CL:0008034 ('mural cell'). Closest names: CL:4033069 (cycling T cell); CL:4033068 (cycling B cell); CL:4047002 (cycling glial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000955", "cell_type_label": "cycling cell", "decision": "annotate", "markers": [{"gene": "TOP2A", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}], "rationale": "The cluster is strongly proliferative, with canonical cell-cycle and mitosis markers including MKI67, TOP2A, CENPF, PCLAF, TYMS, NUSAP1, UBE2C, CDK1, and ASPM. No lineage-specific markers are present, so it is best assigned as a cycling cell rather than a specific colon lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.5}, {"answer": {"cell_type_id": "CL:0000128", "cell_type_label": "proliferating cell", "decision": "annotate", "markers": [{"gene": "TOP2A", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "The cluster is defined by strong proliferation and mitosis programs, including MKI67, TOP2A, CENPF, PCLAF, TYMS, NUSAP1, UBE2C, CDK1, ASPM, and STMN1. No lineage-specific markers identify a particular colon cell type, so the appropriate annotation is the generic Cell Ontology term proliferating cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cycling cell' is not the name of CL:0000955 ('pre-B-II cell'). Closest names: CL:4033069 (cycling T cell); CL:4033068 (cycling B cell); CL:4047002 (cycling glial cell)."], "seconds": 54.5}, {"answer": {"cell_type_id": "CL:0008034", "cell_type_label": "cycling cell", "decision": "annotate", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "PCLAF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "ASPM", "stance": "supports"}], "rationale": "The cluster shows a strong cell-cycle and mitotic program, with MKI67, TOP2A, CENPF, PCLAF, TYMS, NUSAP1, UBE2C, CDK1, ASPM, and STMN1. No lineage-specific markers identify a particular colon cell type, supporting the generic Cell Ontology term cycling cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'proliferating cell' is not the name of CL:0000128 ('oligodendrocyte')."], "seconds": 26.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-a321096724"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'immature B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'immature B cell' is the name of CL:0000816 (immature B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "immature B cell", "decision": "annotate", "markers": [{"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}], "rationale": "The cluster shows a coherent immature/pre-B-cell program: B-cell receptor components CD79A/CD79B, surface IgM (IGHM), and surrogate light-chain genes IGLL1, VPREB1, and VPREB3. CD24 and SOX4 further support an immature B-cell state. No marker clearly indicates a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.7}, {"answer": {"cell_type_id": "CL:0000816", "cell_type_label": "immature B cell", "decision": "annotate", "markers": [{"gene": "CD79B", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGLL1", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "VPREB1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}], "rationale": "The cluster has a coherent immature B-cell program, including B-cell receptor components CD79A/CD79B and IGHM, surrogate light-chain genes IGLL1 and VPREB1/VPREB3, plus CD24 and SOX4. The correct Cell Ontology term for immature B cell is CL:0000816."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'immature B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'immature B cell' is the name of CL:0000816 (immature B cell)."], "seconds": 42.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-a33f382e85"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}], "rationale": "The cluster shows a coherent mature B-cell program (MS4A1, CD79A, CD79B, CD37, HLA-DRA) with strong naive B-cell features, including IGHM, IGHD, TCL1A, VPREB3, TNFRSF13C, BANK1, and SPIB. There are no clear markers indicating a different cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.4}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "TNFRSF13C", "stance": "supports"}, {"gene": "BANK1", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}], "rationale": "The cluster is a coherent B-cell population marked by MS4A1, CD79A, CD79B, CD37 and HLA-DRA, with strong naive B-cell features including IGHM, IGHD, TCL1A, VPREB3, TNFRSF13C, BANK1 and SPIB. No markers clearly indicate another cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell)."], "seconds": 39.3}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ac7ec2b016"} +{"attempts": [{"codes": ["BEV026"], "evidence": 4, "findings": [{"message": "CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "The coordinated expression of immunoglobulin constant regions (IGHG1, IGHG3, IGKC) and ELL2, a regulator associated with antibody-secreting plasma cells, supports an IgG-producing plasma-cell identity. HDC is not sufficiently specific or prevalent here to establish a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.0}, {"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "ELL2", "stance": "supports"}], "rationale": "IGKC together with class-switched immunoglobulin genes IGHG1 and IGHG3 supports a mature immunoglobulin-expressing B-lineage identity, while ELL2 is consistent with immunoglobulin secretion and plasma-cell differentiation. Because SDC1 is detected in only a small fraction of cells and canonical plasma-cell markers are not present, a conservative B-cell annotation is better supported than plasma cell."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000786 (plasma cell) is defined as having syndecan-1 (SDC1) on the membrane, but SDC1 is detected in only 8% of the cluster's cells."], "seconds": 42.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ad2d591627"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "The strong TRDC signal identifies a gamma-delta T-cell lineage, while GNLY, NKG7, KLRD1, KLRC1, GZMB, PRF1 and CTSW indicate a cytotoxic NK-like effector state."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ae89c1380f"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'inflammatory monocyte' is not the name of CL:0002553 ('fibroblast of lung'). 'inflammatory monocyte' is the name of CL:0000860 (classical monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002553", "cell_type_label": "inflammatory monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "THBS1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "EREG", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "KYNU", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "IFI30", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "The strong S100A8/S100A9, VCAN, LYZ, C5AR1, IL1R2, EREG, TYROBP and AIF1 program is characteristic of activated inflammatory/classical monocytes. No marker clearly indicates a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.9}, {"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "C5AR1", "stance": "supports"}, {"gene": "EREG", "stance": "supports"}, {"gene": "IL1R2", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}], "rationale": "The strong S100A8/S100A9, VCAN, LYZ and C5AR1 program, together with EREG, IL1R2, TYROBP and AIF1, supports annotation as a classical monocyte. No markers clearly indicate a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'inflammatory monocyte' is not the name of CL:0002553 ('fibroblast of lung'). 'inflammatory monocyte' is the name of CL:0000860 (classical monocyte)."], "seconds": 27.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b269766ee9"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "KLF2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LINC00861", "stance": "supports"}, {"gene": "FLT3LG", "stance": "supports"}], "rationale": "CCR7, SELL, LEF1, KLF2, and LINC00861 support a naive/resting T-cell state, while IL7R and FLT3LG are consistent with naive CD4-positive T cells. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b322bece33"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'natural killer T cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "natural killer T cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}], "rationale": "The cluster combines strong NK-like cytotoxic markers (GNLY, NKG7, GZMH, GZMB, KLRD1, PRF1, FGFBP2) with T-cell receptor markers (CD3D, CD3G, TRGC2), supporting a cytotoxic natural killer T-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.2}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRGC2", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}], "rationale": "The combination of T-cell markers CD3D, CD3G and especially TRGC2 with strong NK-like cytotoxic markers GNLY, NKG7, GZMH, GZMB, KLRD1, PRF1 and FGFBP2 supports a cytotoxic gamma-delta T-cell identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'natural killer T cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell)."], "seconds": 53.0}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b51a9f2d53"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 7, "findings": [{"message": "The label 'regulatory T cell' is not the name of CL:0000913 ('effector memory CD8-positive, alpha-beta T cell'). 'regulatory T cell' is the name of CL:0000815 (regulatory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as having T cell receptor co-receptor CD8 (CD8A/CD8B) on the membrane, but CD8A/CD8B is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as having interleukin-7 receptor subunit alpha (IL7R) on the membrane, but IL7R is detected in only 4% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The combination of IL10, CTLA4, TNFRSF1B, IKZF3, MAF, and RGS1 supports an activated regulatory T-cell phenotype, with KLRB1 consistent with a mucosal/effector-memory regulatory T-cell state. No marker clearly requires assignment to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.1}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "IL10", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "IKZF3", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}], "rationale": "IL10 and CTLA4 are strong regulatory T-cell markers, supported by TNFRSF1B, MAF, IKZF3, and RGS1, consistent with an activated/effector regulatory T-cell phenotype. The prior CD8-positive effector-memory assignment is not supported because CD8A/CD8B and IL7R are scarcely detected."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'regulatory T cell' is not the name of CL:0000913 ('effector memory CD8-positive, alpha-beta T cell'). 'regulatory T cell' is the name of CL:0000815 (regulatory T cell).", "object id: CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as having T cell receptor co-receptor CD8 (CD8A/CD8B) on the membrane, but CD8A/CD8B is detected in only 4% of the cluster's cells.", "object id: CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as having interleukin-7 receptor subunit alpha (IL7R) on the membrane, but IL7R is detected in only 4% of the cluster's cells."], "seconds": 38.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b5ea73db74"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'classical monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'classical monocyte' is the name of CL:0000860 (classical monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001054", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "The strong S100A8/S100A9, LYZ, VCAN, FCN1 and CD14 program is characteristic of inflammatory classical CD14-positive monocytes. TYROBP, FCER1G, CST3 and ITGAM further support a myeloid-monocyte identity. RNASE2 is somewhat atypical but does not outweigh the coherent monocyte marker program."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.3}, {"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "CD14", "stance": "supports"}, {"gene": "CSTA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "ITGAM", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "The strong S100A8/S100A9, LYZ, VCAN, FCN1 and CD14 expression defines a classical CD14-positive monocyte program. CSTA, CST3, TYROBP, ITGAM and FCER1G provide additional monocyte/myeloid support. RNASE2 and CSF3R are atypical but do not outweigh the coherent classical-monocyte signature."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'classical monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'classical monocyte' is the name of CL:0000860 (classical monocyte)."], "seconds": 37.2}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b7c75983d8"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000451", "cell_type_label": "dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HLA-DMB", "stance": "supports"}], "rationale": "The cluster shows a strong antigen-presenting myeloid program, with near-universal MHC class II and CD74 expression plus CST3, LYZ, AIF1, MS4A6A, and TYROBP. This is most consistent with dendritic cells, likely a conventional myeloid dendritic-cell population. No listed marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b864a5744b"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDC", "stance": "supports"}, {"gene": "TRGC2", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRK1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "TRDC and TRGC2 directly support a gamma-delta T-cell identity. The strong cytotoxic and NK-associated program (NKG7, GNLY, CTSW, KLRD1, KLRK1, KLRF1, GZMA) is consistent with an activated/cytotoxic gamma-delta T-cell subset. No markers clearly indicate a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-b95794dcf3"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}], "rationale": "Strong immunoglobulin secretion and unfolded-protein-response markers (JCHAIN, MZB1, XBP1, DERL3, FKBP11, SEC11C) identify antibody-secreting plasma cells. IGHA1 and JCHAIN suggest an IgA-skewed plasma-cell state."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.5}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ba5f0288e7"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 11, "findings": [{"message": "The label 'memory T cell' is not the name of CL:0000899 ('T-helper 17 cell'). 'memory T cell' is the name of CL:0000813 (memory T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000899 (T-helper 17 cell) is defined as having C-C chemokine receptor type 6 (CCR6) on the membrane, but CCR6 is detected in only 8% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000899 (T-helper 17 cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 9% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000899", "cell_type_label": "memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster shows a clear T-cell receptor/CD3 program together with IL7R, ICOS, and CD69, consistent with an activated memory T-cell population, likely IL7R-positive helper-like memory T cells. No markers clearly indicate a competing lineage or a mixed/doublet cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.2}, {"answer": {"cell_type_id": "CL:0000813", "cell_type_label": "memory T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "ICOS", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TRBC2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster has a strong T-cell receptor/CD3 program, with IL7R, ICOS, and CD69 supporting an activated memory T-cell state. The appropriate Cell Ontology term is memory T cell (CL:0000813); the sparse CCR6 and CD4 detection does not support assigning it specifically as a T-helper 17 cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'memory T cell' is not the name of CL:0000899 ('T-helper 17 cell'). 'memory T cell' is the name of CL:0000813 (memory T cell).", "object id: CL:0000899 (T-helper 17 cell) is defined as having C-C chemokine receptor type 6 (CCR6) on the membrane, but CCR6 is detected in only 8% of the cluster's cells.", "object id: CL:0000899 (T-helper 17 cell) is defined as having CD4 molecule (CD4) on the membrane, but CD4 is detected in only 9% of the cluster's cells."], "seconds": 45.2}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-be2c0ee626"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "The cluster shows a strong myeloid/monocyte program: LST1, AIF1, FCER1G, TYROBP, CTSS, FCN1, SERPINA1, FCGR3A, and MS4A7. FCN1 and SERPINA1 support a monocyte identity, while FCGR3A suggests a more differentiated/non-classical component."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.3}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-c5e3a0ec1f"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "IL2RA", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "TNFRSF4", "stance": "supports"}, {"gene": "TNFRSF18", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD3G", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "The cluster is a T-cell population with strong regulatory T-cell markers: FOXP3, IL2RA, CTLA4, TIGIT, TNFRSF4 (OX40), and TNFRSF18 (GITR). TRAC, CD3D, CD3G, CD2, and IL32 support its T-cell identity. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-c99aec2a45"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000788 (naive B cell) is defined as lacking CD27 molecule (CD27), but CD27 is detected in 63% of the cluster's cells, more than in the others (logfc 1.30).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'memory B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'memory B cell' is the name of CL:0000787 (memory B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "The cluster shows a coherent mature B-cell program (CD79A, MS4A1, CD79B, CD19, CD37, CD74/HLA-II) with CD24, VPREB3, and FCMR supporting a naive B-cell phenotype. JCHAIN is present in a subset, but the strong MS4A1/CD79A program and absence of plasma-cell markers do not support a plasma-cell annotation or a mixed-cell interpretation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.9}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "The cluster has a coherent mature B-cell program marked by CD79A, MS4A1, CD79B, CD19, CD74/HLA class II, and CD37. CD24, VPREB3, and FCMR support a naive B-cell phenotype. JCHAIN is present in a subset, but the dominant MS4A1/CD79A program and lack of plasma-cell markers do not establish a mixed cluster or a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell)."], "seconds": 23.8}, {"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "memory B cell", "decision": "annotate", "markers": [{"gene": "CD27", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}], "rationale": "The cluster is a coherent mature B-cell population with strong CD79A, MS4A1, CD79B, CD19, CD74/HLA class II, and CD37 expression. CD27 is detected in 63% of cells and is enriched versus other cells, arguing against naive B cell and supporting a memory B-cell identity. JCHAIN occurs in a substantial subset and may reflect an IgM/JCHAIN-expressing memory-like subset, but the dominant MS4A1/CD79A program does not indicate a plasma-cell cluster."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000788 (naive B cell) is defined as lacking CD27 molecule (CD27), but CD27 is detected in 63% of the cluster's cells, more than in the others (logfc 1.30)."], "seconds": 23.6}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ccd8ad8cc1"} +{"attempts": [{"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'mucosal mast cell' is not the name of CL:0000860 ('classical monocyte'). Closest names: CL:0000485 (mucosal type mast cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000485 (mucosal type mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000097", "cell_type_label": "mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster is a mast cell population, supported by the highly specific combination of tryptases TPSAB1/TPSB2, CPA3, histidine decarboxylase HDC, mast-cell transcription factor GATA2, HPGDS, and vesicular monoamine transporter SLC18A2. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.6}, {"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "mucosal mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster is a mucosal mast cell population, supported by the highly specific mast-cell markers TPSAB1, TPSB2, CPA3, HDC, HPGDS, GATA2, SLC18A2, and IL33R. Its colon origin and absence of markers indicating another lineage favor this mucosal mast-cell subtype. No markers clearly contradict the annotation."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000097 (mast cell) is defined as having C-C chemokine receptor type 3 (CCR3) on the membrane, but CCR3 is detected in only 0% of the cluster's cells."], "seconds": 38.5}, {"answer": {"cell_type_id": "CL:0000485", "cell_type_label": "mucosal type mast cell", "decision": "annotate", "markers": [{"gene": "TPSAB1", "stance": "supports"}, {"gene": "CPA3", "stance": "supports"}, {"gene": "TPSB2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "HDC", "stance": "supports"}, {"gene": "GATA2", "stance": "supports"}, {"gene": "SLC18A2", "stance": "supports"}, {"gene": "IL33R", "stance": "supports"}], "rationale": "The cluster shows a strong mast-cell program, with near-universal CPA3 and HPGDS expression and highly specific TPSAB1, TPSB2, HDC, GATA2, SLC18A2, and IL33R expression, supporting a mucosal type mast cell identity. No markers clearly indicate a second cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'mucosal mast cell' is not the name of CL:0000860 ('classical monocyte'). Closest names: CL:0000485 (mucosal type mast cell)."], "seconds": 36.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ceffe8616a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "The cluster shows a coherent mature B-cell program (CD19, MS4A1, CD79A/CD79B) together with strong unswitched immunoglobulin expression (IGHM, IGHD) and TCL1A, characteristic of human naive B cells. No clear markers indicate a mixed or doublet population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.3}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "TCL1A", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}], "rationale": "The cluster has a coherent mature B-cell program (MS4A1, CD19, CD79A, CD79B) with strong unswitched immunoglobulin expression (IGHM, IGHD) and TCL1A, supporting the Cell Ontology term naive B cell (CL:0000788). No markers clearly indicate a mixed or doublet population."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell)."], "seconds": 49.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-d44564d7f6"} +{"attempts": [{"codes": ["BEV017"], "evidence": 14, "findings": [{"message": "The label 'classical monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'classical monocyte' is the name of CL:0000860 (classical monocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0001054", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}], "rationale": "The strong LYZ, S100A8/S100A9/S100A12, FCN1, and VCAN expression identifies an inflammatory/classical monocyte population. TYROBP, FCER1G, LST1, AIF1, CTSS, and CST3 further support myeloid-monocyte identity. No clear markers indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.1}, {"answer": {"cell_type_id": "CL:0000860", "cell_type_label": "classical monocyte", "decision": "annotate", "markers": [{"gene": "LYZ", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "FCN1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "VCAN", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}], "rationale": "The combination of LYZ, S100A8/S100A9/S100A12, FCN1, VCAN, and myeloid genes TYROBP, FCER1G, LST1, AIF1, CTSS, and CST3 supports a classical monocyte identity. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'classical monocyte' is not the name of CL:0001054 ('CD14-positive monocyte'). 'classical monocyte' is the name of CL:0000860 (classical monocyte)."], "seconds": 27.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-d7d3163b78"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "CL:0000186", "cell_type_label": "smooth muscle cell", "decision": "uncertain", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "TPM1", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "PPP1R14A", "stance": "supports"}, {"gene": "TPSB2", "stance": "contradicts"}, {"gene": "TPSAB1", "stance": "contradicts"}], "rationale": "TAGLN, ACTA2, TPM2, MYL9, CALD1, TPM1, and PPP1R14A strongly support a smooth-muscle identity. However, TPSB2 and TPSAB1 are highly prevalent mast-cell markers in the cluster, indicating a likely smooth-muscle/mast-cell mixed cluster or doublets; therefore the annotation is uncertain."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 56.0}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-d929ec7963"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'naive T cell' is not the name of CL:0000895 ('naive thymus-derived CD4-positive, alpha-beta T cell'). 'naive T cell' is the name of CL:0000898 (naive T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000895", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}], "rationale": "The combination of CD4, IL7R, CCR7, SELL, CD27, and FCMR supports a naive/resting CD4-positive T-cell phenotype, with TRAC and CD3E confirming T-cell identity. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.6}, {"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "TRAC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD4", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}], "rationale": "TRAC, CD3E, and CD2 establish T-cell identity, while IL7R, CCR7, SELL, CD27, CD4, FCMR, and TESPA1 support a resting naive T-cell phenotype. The correct Cell Ontology term for the label 'naive T cell' is CL:0000898."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive T cell' is not the name of CL:0000895 ('naive thymus-derived CD4-positive, alpha-beta T cell'). 'naive T cell' is the name of CL:0000898 (naive T cell)."], "seconds": 43.7}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-e1bfaa2341"} +{"attempts": [{"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016", "BEV017"], "evidence": 16, "findings": [{"message": "No row of the pinned table has cluster=c06, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 16 (cluster=c06;gene=CD3E)"}, {"message": "The label 'natural killer T cell' is not the name of CL:0000911 ('effector T cell'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 14, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "The cluster shows a coherent NK-cell cytotoxic program: universal NKG7, strong KLRD1 and KLRC1, XCL1/XCL2, CCL4/CCL5, granzymes, CMC1, CST7, CD247, and CD7. KLRB1 and GZMK indicate an activated or memory-like NK-cell state, but do not outweigh the overall NK-cell signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.7}, {"answer": {"cell_type_id": "CL:0000911", "cell_type_label": "natural killer T cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}], "rationale": "The cluster has a strong NK-like cytotoxic program, including NKG7, KLRD1, KLRC1, XCL1/XCL2, CCL4/CCL5, granzymes, CMC1 and CST7, but CD3E is detected in a substantial fraction of cells and is enriched versus the rest of the dataset. This combination supports a natural killer T-cell annotation rather than a conventional natural killer cell annotation."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 50% of the cluster's cells, more than in the others (logfc 0.35)."], "seconds": 55.6}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMM", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "The cluster shows a coherent natural-killer-cell cytotoxic program: universal NKG7, strong KLRD1 and KLRC1, XCL1/XCL2, CCL4/CCL5, granzymes, CMC1, CST7, CD247 and CD7. No marker in the provided table clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": ["evidence 16 (cluster=c06;gene=CD3E): No row of the pinned table has cluster=c06, gene=CD3E.", "object label: The label 'natural killer T cell' is not the name of CL:0000911 ('effector T cell'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell)."], "seconds": 59.9}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-e712a5eb84"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}], "rationale": "The cluster shows a coherent mature B-cell program (CD79A, CD79B, MS4A1, CD19) with strong unswitched immunoglobulin expression (IGHM and IGHD) and naive B-cell-associated markers including CD24, FCMR, VPREB3, and CXCR5. No markers clearly indicate a conflicting cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.7}, {"answer": {"cell_type_id": "CL:0000788", "cell_type_label": "naive B cell", "decision": "annotate", "markers": [{"gene": "IGHM", "stance": "supports"}, {"gene": "IGHD", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "CD19", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "FCMR", "stance": "supports"}, {"gene": "VPREB3", "stance": "supports"}, {"gene": "CXCR5", "stance": "supports"}], "rationale": "The cluster has a coherent mature B-cell program marked by MS4A1, CD79A, CD79B, and CD19, with strong unswitched immunoglobulin expression (IGHM and IGHD) and naive B-cell-associated markers including CD24, FCMR, VPREB3, and CXCR5. CL:0000788 is the Cell Ontology term for naive B cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive B cell' is not the name of CL:0000945 ('lymphocyte of B lineage'). 'naive B cell' is the name of CL:0000788 (naive B cell)."], "seconds": 36.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-e7ae6683c5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'CD8-positive, alpha-beta T cell (GZMK+ effector-memory-like)' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell (GZMK+ effector-memory-like)", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster shows a coherent CD8 cytotoxic/effector-memory program: CD8A/CD8B with CCL5, NKG7, GZMK, GZMA, CST7, CCL4, CTSW, CXCR3, and KLRG1. No marker clearly indicates a different cell type or an obvious doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 54.6}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "KLRG1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster has a coherent CD8 T-cell cytotoxic/effector-memory program, marked by CD8A/CD8B together with CCL5, NKG7, GZMK, GZMA, CST7, CCL4, CTSW, CXCR3, and KLRG1. No marker clearly indicates a distinct cell type or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD8-positive, alpha-beta T cell (GZMK+ effector-memory-like)' is not the name of CL:0000625 ('CD8-positive, alpha-beta T cell')."], "seconds": 32.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ec5325a064"} +{"attempts": [{"codes": ["BEV026"], "evidence": 9, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016", "BEV017"], "evidence": 10, "findings": [{"message": "No row of the pinned table has cluster=c09, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 1 (cluster=c09;gene=CD3E)"}, {"message": "The label 'natural killer T cell' is not the name of CL:0000814 ('mature NK T cell'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 10, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "The cluster shows a strong cytotoxic NK-cell program: near-universal NKG7 and KLRD1, high GNLY, GZMB, PRF1, FGFBP2, CCL5, CST7, and CTSW. The absence of clear T-cell receptor genes supports natural killer cells rather than conventional T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.4}, {"answer": {"cell_type_id": "CL:0000814", "cell_type_label": "natural killer T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}], "rationale": "The cluster has a strong cytotoxic NK-like program, including NKG7, KLRD1, GNLY, GZMB, PRF1, FGFBP2, CCL5, CST7, and CTSW, while CD3E is detected in 73% of cells and is enriched versus other cells. The combination supports natural killer T cells rather than conventional NK cells, which lack CD3 expression."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 73% of the cluster's cells, more than in the others (logfc 0.60)."], "seconds": 32.6}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster shows a strong conventional cytotoxic NK-cell program: NKG7, KLRD1, GNLY, GZMB, PRF1, FGFBP2, CCL5, CST7, CTSW, and HCST are highly enriched. No T-cell marker such as CD3D, CD3E, or CD3G is present in the provided marker table, so natural killer cell is better supported than mature NK T cell."}, "cli_tools": [], "error": null, "feedback": ["evidence 1 (cluster=c09;gene=CD3E): No row of the pinned table has cluster=c09, gene=CD3E.", "object label: The label 'natural killer T cell' is not the name of CL:0000814 ('mature NK T cell'). Closest names: CL:0000623 (natural killer cell); CL:0000937 (pre-natural killer cell); CL:0000824 (mature natural killer cell)."], "seconds": 29.4}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-ed05c45d83"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'neutrophil' is not the name of CL:0000099 ('interneuron'). 'neutrophil' is the name of CL:0000775 (neutrophil).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000094 (granulocyte) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}, {"message": "CL:0000094 (granulocyte) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000099", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}], "rationale": "The combination of strong S100A8/S100A9/S100A12 expression with FCGR3B and CSF3R is characteristic of neutrophils, with CXCL8 supporting an activated inflammatory neutrophil state. No clear contradictory lineage markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 55.5}, {"answer": {"cell_type_id": "CL:0000775", "cell_type_label": "neutrophil", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}], "rationale": "The strong S100A8/S100A9/S100A12 inflammatory program together with FCGR3B and CSF3R is characteristic of neutrophils. CXCL8 and G0S2 further support an activated neutrophil state. No clear contradictory lineage markers are present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'neutrophil' is not the name of CL:0000099 ('interneuron'). 'neutrophil' is the name of CL:0000775 (neutrophil)."], "seconds": 45.8}, {"answer": {"cell_type_id": "CL:0000094", "cell_type_label": "granulocyte", "decision": "annotate", "markers": [{"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "S100A12", "stance": "supports"}, {"gene": "FCGR3B", "stance": "supports"}, {"gene": "CSF3R", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "MNDA", "stance": "supports"}], "rationale": "The S100A8/S100A9/S100A12 inflammatory granulocyte program, together with FCGR3B, CSF3R, CXCL8, and G0S2, supports a granulocyte identity. The more specific neutrophil label is not retained because CEACAM8, ITGAM, and SPN are absent from the supplied marker table."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000775 (neutrophil) is defined as having cell adhesion molecule CEACAM8 (CEACAM8) on the membrane, but CEACAM8 is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having integrin alpha-M (ITGAM) on the membrane, but ITGAM is detected in only 0% of the cluster's cells.", "object id: CL:0000775 (neutrophil) is defined as having leukosialin (SPN) on the membrane, but SPN is detected in only 0% of the cluster's cells."], "seconds": 47.6}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-f2e4fa20cc"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'memory CD4-positive, alpha-beta T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). Closest names: CL:0000904 (central memory CD4-positive, alpha-beta T cell); CL:0000624 (CD4-positive, alpha-beta T cell); CL:0001044 (effector CD4-positive, alpha-beta T cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "memory CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "ZFP36L2", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "IL7R, KLRB1 and GPR183 support a memory CD4-positive T-cell phenotype, with ZFP36L2 and FYB1 consistent with T-cell identity. No markers clearly indicate a conflicting lineage or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.9}, {"answer": {"cell_type_id": "CL:0000905", "cell_type_label": "effector memory CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "ZFP36L2", "stance": "supports"}, {"gene": "FYB1", "stance": "supports"}], "rationale": "IL7R, KLRB1, and GPR183 support an effector-memory CD4-positive T-cell phenotype; CXCR4 is consistent with tissue-homing memory T cells, while ZFP36L2 and FYB1 support T-cell identity. No listed marker clearly indicates a conflicting lineage or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'memory CD4-positive, alpha-beta T cell' is not the name of CL:0000905 ('effector memory CD4-positive, alpha-beta T cell'). Closest names: CL:0000904 (central memory CD4-positive, alpha-beta T cell); CL:0000624 (CD4-positive, alpha-beta T cell); CL:0001044 (effector CD4-positive, alpha-beta T cell)."], "seconds": 29.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-f5551fdf21"} +{"attempts": [{"codes": ["BEV017"], "evidence": 12, "findings": [{"message": "The label 'erythroblast' is not the name of CL:0000766 ('myeloid leukocyte'). 'erythroblast' is the name of CL:0000765 (erythroblast).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000766", "cell_type_label": "erythroblast", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "ITGA2B", "stance": "supports"}], "rationale": "The cluster is an actively proliferating erythroblast population. HBB, HBD, CA1, BLVRB, SLC40A1, TFRC, and NFE2 support erythroid identity, while STMN1, TYMS, PCNA, MCM2, CDK6, and CKS2 indicate strong cell-cycle activity. ITGA2B can occur in erythro-megakaryocytic progenitors but is not sufficient here to call a mixed cluster or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.1}, {"answer": {"cell_type_id": "CL:0000765", "cell_type_label": "erythroblast", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "TFRC", "stance": "supports"}, {"gene": "NFE2", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "PCNA", "stance": "supports"}, {"gene": "MCM2", "stance": "supports"}, {"gene": "CDK6", "stance": "supports"}, {"gene": "CKS2", "stance": "supports"}], "rationale": "The correct Cell Ontology identifier for erythroblast is CL:0000765. The cluster shows strong erythroid markers (HBB, HBD, CA1, BLVRB, SLC40A1, TFRC, and NFE2) together with a pronounced proliferative program (STMN1, TYMS, PCNA, MCM2, CDK6, and CKS2), consistent with a proliferating erythroblast population. ITGA2B is compatible with an erythro-megakaryocytic progenitor state but, without additional megakaryocyte markers, does not clearly establish a mixed cluster or doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'erythroblast' is not the name of CL:0000766 ('myeloid leukocyte'). 'erythroblast' is the name of CL:0000765 (erythroblast)."], "seconds": 27.8}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-f5e849f6ff"} +{"attempts": [{"codes": ["BEV017", "BEV026"], "evidence": 5, "findings": [{"message": "The label 'T follicular helper cell' is not the name of CL:0000915 ('CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell'). 'T follicular helper cell' is the name of CL:0002038 (T follicular helper cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000915 (CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell) is defined as having T-cell surface glycoprotein CD8 alpha chain (CD8A) on the membrane, but CD8A is detected in only 2% of the cluster's cells.", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000915", "cell_type_label": "T follicular helper cell", "decision": "annotate", "markers": [{"gene": "TOX2", "stance": "supports"}, {"gene": "PDCD1", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "GNG4", "stance": "supports"}], "rationale": "The combination of TOX2, PDCD1, TIGIT, and MAF strongly supports an activated/exhausted follicular helper T-cell phenotype typical of tonsil. No marker clearly indicates a different cell type or a mixed-cell doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.4}, {"answer": {"cell_type_id": "CL:0002038", "cell_type_label": "T follicular helper cell", "decision": "annotate", "markers": [{"gene": "TOX2", "stance": "supports"}, {"gene": "PDCD1", "stance": "supports"}, {"gene": "TIGIT", "stance": "supports"}, {"gene": "MAF", "stance": "supports"}, {"gene": "GNG4", "stance": "supports"}], "rationale": "TOX2, PDCD1, TIGIT, and MAF support an activated tonsillar T follicular helper-cell phenotype. The corrected Cell Ontology term is CL:0002038; the prior CL:0000915 identifier was mismatched and describes CD8-alpha-alpha-positive intraepithelial T cells, which are not supported by this marker set."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'T follicular helper cell' is not the name of CL:0000915 ('CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell'). 'T follicular helper cell' is the name of CL:0002038 (T follicular helper cell).", "object id: CL:0000915 (CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell) is defined as having T-cell surface glycoprotein CD8 alpha chain (CD8A) on the membrane, but CD8A is detected in only 2% of the cluster's cells."], "seconds": 24.1}], "model": "gpt-luna", "protocol": 3, "task_id": "ct-f6eff45a55"} +{"attempts": [{"codes": ["BEV026"], "evidence": 7, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}, {"codes": ["BEV016", "BEV017", "BEV026"], "evidence": 8, "findings": [{"message": "No row of the pinned table has cluster=c13, gene=CD3E.", "rule_id": "BEV016", "where": "evidence 1 (cluster=c13;gene=CD3E)"}, {"message": "The label 'cytotoxic T cell' is not the name of CL:0000913 ('effector memory CD8-positive, alpha-beta T cell'). 'cytotoxic T cell' is the name of CL:0000910 (cytotoxic T cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "CL:0000913 (effector memory CD8-positive, alpha-beta T cell) is defined as lacking interleukin-2 receptor subunit alpha (IL2RG), but IL2RG is detected in 87% of the cluster's cells, more than in the others (logfc 0.40).", "rule_id": "BEV026", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV026"], "evidence": 8, "findings": [{"message": "CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42).", "rule_id": "BEV026", "where": "object id"}], "status": "review_required", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}], "rationale": "GNLY and GZMA support an NK-cell identity, while MKI67, TOP2A, CENPF, TYMS, STMN1 and other cell-cycle genes indicate a proliferating/cycling NK-cell state. No marker clearly contradicts this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 59.5}, {"answer": {"cell_type_id": "CL:0000913", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}], "rationale": "CD3E expression in most cluster cells supports T-cell identity and argues against annotating this as a conventional natural killer cell, which lacks CD3E. GNLY and GZMA support a cytotoxic lymphocyte program, while MKI67, TOP2A, CENPF, TYMS, and STMN1 indicate a proliferating state. Overall this is best labeled a proliferating cytotoxic T-cell cluster."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0000623 (natural killer cell) is defined as lacking CD3 epsilon (CD3E), but CD3E is detected in 78% of the cluster's cells, more than in the others (logfc 0.42)."], "seconds": 50.2}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}], "rationale": "GNLY and GZMA indicate a cytotoxic natural-killer-cell program, while MKI67, TOP2A, CENPF, TYMS, STMN1, and NUSAP1 indicate active proliferation. The table does not provide T-cell-specific markers such as CD3D, CD3E, or TRBC1/2, so natural killer cell is the best-supported Cell Ontology annotation, with a proliferating state."}, "cli_tools": [], "error": null, "feedback": ["evidence 1 (cluster=c13;gene=CD3E): No row of the pinned table has cluster=c13, gene=CD3E.", "object label: The label 'cytotoxic T cell' is not the name of CL:0000913 ('effector memory CD8-positive, alpha-beta T cell'). 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0.0, + 0.0453 + ] + }, + "with_identifier_or_marker_error": { + "events": 33, + "n": 80, + "rate": 0.4125, + "wilson_95": [ + 0.3111, + 0.522 + ] + }, + "wrong": { + "events": 43, + "n": 81, + "rate": 0.5309, + "wilson_95": [ + 0.4233, + 0.6357 + ] + } + } + } + }, + "revised": 131, + "split": "external" +} diff --git a/evaluation/llm_benchmark/results/celltype-external/summary.md b/evaluation/llm_benchmark/results/celltype-external/summary.md new file mode 100644 index 0000000..4e017b7 --- /dev/null +++ b/evaluation/llm_benchmark/results/celltype-external/summary.md @@ -0,0 +1,40 @@ +# Single-cell cell-type annotation (external set, protocol 3) + +Each model annotates one cluster from its top 20 marker genes with a Cell Ontology term and the markers that support it. Compared with the authors' term: exact, coarser (an ancestor), finer (a descendant) or wrong; an identifier that is not a current cell type term is invalid. + +| Model | View | Answered | Exact | Coarser | Finer | Wrong | Invalid ID | Answers with an identifier or marker error | Routed to a person | +|---|---|---:|---:|---:|---:|---:|---:|---:|---:| +| Claude Opus 5.5 | Model alone (first answer) | 79/81 | 35/81 | 12/81 | 8/81 | 24/81 | 0/81 | 0/79 | 0/81 | +| Claude Opus 5.5 | Model + bioevidence gate (first answer) | 62/81 | 24/81 | 12/81 | 8/81 | 18/81 | 0/81 | 0/62 | 17/81 | +| Claude Opus 5.5 | Model + gate without the definition check (first answer) | 75/81 | 34/81 | 12/81 | 8/81 | 21/81 | 0/81 | 0/75 | 4/81 | +| Claude Opus 5.5 | Model + bioevidence feedback loop (last answer) | 70/81 | 24/81 | 15/81 | 8/81 | 23/81 | 0/81 | 0/70 | 9/81 | +| GPT-6-Astra | Model alone (first answer) | 79/81 | 33/81 | 11/81 | 5/81 | 30/81 | 0/81 | 2/79 | 0/81 | +| GPT-6-Astra | Model + bioevidence gate (first answer) | 63/81 | 25/81 | 11/81 | 5/81 | 22/81 | 0/81 | 0/63 | 16/81 | +| GPT-6-Astra | Model + gate without the definition check (first answer) | 74/81 | 32/81 | 11/81 | 5/81 | 26/81 | 0/81 | 0/74 | 5/81 | +| GPT-6-Astra | Model + bioevidence feedback loop (last answer) | 67/81 | 26/81 | 11/81 | 5/81 | 25/81 | 0/81 | 0/67 | 12/81 | +| Gemini 3.1 Pro | Model alone (first answer) | 80/81 | 32/81 | 16/81 | 1/81 | 31/81 | 0/81 | 6/80 | 0/81 | +| Gemini 3.1 Pro | Model + bioevidence gate (first answer) | 55/81 | 23/81 | 15/81 | 1/81 | 16/81 | 0/81 | 0/55 | 25/81 | +| Gemini 3.1 Pro | Model + gate without the definition check (first answer) | 65/81 | 29/81 | 15/81 | 1/81 | 20/81 | 0/81 | 0/65 | 15/81 | +| Gemini 3.1 Pro | Model + bioevidence feedback loop (last answer) | 70/81 | 23/81 | 20/81 | 2/81 | 25/81 | 0/81 | 0/70 | 10/81 | +| Claude Haiku 4.5 | Model alone (first answer) | 81/81 | 17/81 | 18/81 | 5/81 | 40/81 | 1/81 | 23/81 | 0/81 | +| Claude Haiku 4.5 | Model + bioevidence gate (first answer) | 40/81 | 9/81 | 18/81 | 1/81 | 12/81 | 0/81 | 0/40 | 41/81 | +| Claude Haiku 4.5 | Model + gate without the definition check (first answer) | 45/81 | 14/81 | 18/81 | 1/81 | 12/81 | 0/81 | 0/45 | 36/81 | +| Claude Haiku 4.5 | Model + bioevidence feedback loop (last answer) | 59/81 | 13/81 | 21/81 | 5/81 | 20/81 | 0/81 | 0/59 | 22/81 | +| GPT-5.6-Luna | Model alone (first answer) | 80/81 | 20/81 | 10/81 | 7/81 | 43/81 | 0/81 | 33/80 | 0/81 | +| GPT-5.6-Luna | Model + bioevidence gate (first answer) | 31/81 | 11/81 | 3/81 | 1/81 | 16/81 | 0/81 | 0/31 | 49/81 | +| GPT-5.6-Luna | Model + gate without the definition check (first answer) | 42/81 | 17/81 | 3/81 | 1/81 | 21/81 | 0/81 | 0/42 | 38/81 | +| GPT-5.6-Luna | Model + bioevidence feedback loop (last answer) | 64/81 | 16/81 | 6/81 | 9/81 | 33/81 | 0/81 | 0/64 | 16/81 | +| Gemini 3.8 Flash | Model alone (first answer) | 80/81 | 32/81 | 13/81 | 3/81 | 32/81 | 0/81 | 6/80 | 0/81 | +| Gemini 3.8 Flash | Model + bioevidence gate (first answer) | 51/81 | 22/81 | 11/81 | 2/81 | 16/81 | 0/81 | 0/51 | 29/81 | +| Gemini 3.8 Flash | Model + gate without the definition check (first answer) | 61/81 | 28/81 | 11/81 | 2/81 | 20/81 | 0/81 | 0/61 | 19/81 | +| Gemini 3.8 Flash | Model + bioevidence feedback loop (last answer) | 60/81 | 23/81 | 12/81 | 3/81 | 22/81 | 0/81 | 0/60 | 20/81 | +| All models | Model alone (first answer) | 479/486 | 169/486 | 80/486 | 29/486 | 200/486 | 1/486 | 70/479 | 0/486 | +| All models | Model + bioevidence gate (first answer) | 302/486 | 114/486 | 70/486 | 18/486 | 100/486 | 0/486 | 0/302 | 177/486 | +| All models | Model + gate without the definition check (first answer) | 362/486 | 154/486 | 70/486 | 18/486 | 120/486 | 0/486 | 0/362 | 117/486 | +| All models | Model + bioevidence feedback loop (last answer) | 390/486 | 125/486 | 85/486 | 32/486 | 148/486 | 0/486 | 0/390 | 89/486 | + +Errors in the models' first answers (all models): label mismatch 69/479, marker not in data 0/479, no markers 0/479, not a cell type 0/479, obsolete id 1/479, unapproved symbol 0/479, unknown id 0/479. + +486 episodes, 673 model calls (0 failed), 131 revised after feedback. Rule codes raised across all records: BEV004 69, BEV016 7, BEV017 95, BEV023 1, BEV026 140. + +First answers the definition check flagged, by comparison with the authors' term: exact 43, finer 4, wrong 41. diff --git a/examples/singlecell_celltype/README.md b/examples/singlecell_celltype/README.md index 55cce4d..36f6ffb 100644 --- a/examples/singlecell_celltype/README.md +++ b/examples/singlecell_celltype/README.md @@ -54,6 +54,12 @@ in about one answer in five. Bioevidence admitted none of these errors. In its f - answers compatible with the authors' term rose from 176 to 205 of 276; - 8% of the annotations went to a person. +The external split, six datasets from other studies (81 clusters, mostly immune), tested the Cell Ontology +definition check (protocol 3). The result was negative. Protein-level definitions such as "a mast cell has +CCR3" or "an NK cell lacks CD3 epsilon" do not hold for transcripts. The check therefore flagged correct +annotations as often as wrong ones, and fed back to the models it turned correct answers into wrong ones. +The identifier layer held there too: 70 of 479 answers had an identifier error, and none was admitted. + ## Limits - Author labels are the reference, at the granularity each study chose ("myeloid leukocyte", "stem cell"). diff --git a/examples/singlecell_celltype/prepare_source.py b/examples/singlecell_celltype/prepare_source.py index 3df2573..00bf7b6 100644 --- a/examples/singlecell_celltype/prepare_source.py +++ b/examples/singlecell_celltype/prepare_source.py @@ -19,6 +19,11 @@ cell type with a CL identifier, and its gene biomarkers under their current HGNC symbols. 4. Tasks. One per cluster: the tissue, the assay and the top PROMPT_GENES markers with their statistics. Per dataset, clusters in keyed-hash order go to the pilot split (PILOT_PER_DATASET) and the rest to the test split. +5. Definition panels. For every cluster, `pct_in` and `logfc` of every gene that a Cell Ontology presence or + absence axiom mentions (`bioevidence_validator.definitions`), whether or not it is a marker of the cluster. +6. External datasets. When DIR also holds `selected-v2.json` and `h5ad-v2/`, six more datasets from other + studies are added the same way, all of their clusters in the `external` split: a held-out set for checks + designed on the first six. Outputs in sources/: `snapshots/..gz` (marker tables, the Cell Ontology release, the HGNC set, the ASCT+B reference), `tasks.jsonl`, `truth.jsonl`, `manifest.json` and `ATTRIBUTION.md`. @@ -37,6 +42,7 @@ import numpy as np import scipy.sparse as sp +from bioevidence_validator.definitions import MarkerDefinitions from bioevidence_validator.identifiers import Genes, Ontology ROOT = Path(__file__).resolve().parent @@ -66,8 +72,8 @@ def tsv(columns: list[str], rows: list[dict]) -> bytes: return out.getvalue().encode() -def markers(path: Path, genes: Genes, ontology: Ontology) -> tuple[list[dict], list[dict]]: - """(marker rows, clusters) for one dataset.""" +def markers(path: Path, genes: Genes, ontology: Ontology, panel: set[str]) -> tuple[list[dict], list[dict], list[dict]]: + """(marker rows, clusters, definition panel rows) for one dataset.""" data = anndata.read_h5ad(path) counts = data.raw.X if data.raw is not None else data.X var = data.raw.var if data.raw is not None else data.var @@ -89,7 +95,8 @@ def markers(path: Path, genes: Genes, ontology: Ontology) -> tuple[list[dict], l labels = dict(zip(terms, data.obs["cell_type"].astype(str), strict=True)) total, total_expressed, cells = (np.asarray(normalised.sum(axis=0)).ravel(), np.asarray(expressed.sum(axis=0)).ravel(), len(terms)) - rows, clusters = [], [] + rows, clusters, panel_rows = [], [], [] + measured = [i for i, g in enumerate(symbols) if g in panel] usable = sorted(t for t in set(terms) if t.startswith("CL:") and (terms == t).sum() >= MIN_CELLS) for n, term in enumerate(usable, start=1): mask = terms == term @@ -102,6 +109,8 @@ def markers(path: Path, genes: Genes, ontology: Ontology) -> tuple[list[dict], l ranked = sorted((i for i in range(len(symbols)) if pct_in[i] >= MIN_PCT and logfc[i] > 0), key=lambda i: (-round(logfc[i], 6), symbols[i]))[:TOP_GENES] cluster = f"c{n:02d}" + panel_rows += [{"cluster": cluster, "gene": symbols[i], "pct_in": f"{pct_in[i]:.3f}", "logfc": f"{logfc[i]:.3f}"} + for i in sorted(measured, key=lambda i: symbols[i])] rows += [{"cluster": cluster, "gene": symbols[i], "rank": rank, "logfc": f"{logfc[i]:.3f}", "pct_in": f"{pct_in[i]:.3f}", "pct_out": f"{pct_out[i]:.3f}"} for rank, i in enumerate(ranked, start=1)] truth, note = term, "" @@ -111,7 +120,7 @@ def markers(path: Path, genes: Genes, ontology: Ontology) -> tuple[list[dict], l clusters.append({"cluster": cluster, "author_term": term, "author_label": labels[term], "term": truth, "label": ontology.terms[truth].name if truth in ontology.terms else labels[term], "cells": int(inside), "note": note}) - return rows, clusters + return rows, clusters, panel_rows def asctb(directory: Path, genes: Genes) -> list[dict]: @@ -142,6 +151,8 @@ def main(argv: list[str] | None = None) -> int: data = args.data cl_bytes, hgnc_bytes = (data / "ref/cl.obo").read_bytes(), (data / "ref/hgnc_complete_set.txt").read_bytes() ontology, genes = Ontology.from_obo(cl_bytes), Genes.from_hgnc(hgnc_bytes) + definitions = MarkerDefinitions(ontology, genes) + panel = {g for t in ontology.terms if t.startswith("CL:") for _, _, gs in definitions.of(t) for g in gs} manifest = {"key": KEY, "parameters": {"min_cells": MIN_CELLS, "top_genes": TOP_GENES, "prompt_genes": PROMPT_GENES, "min_pct": MIN_PCT, "pilot_per_dataset": PILOT_PER_DATASET}, "cell_ontology": {"version": ontology.version, "sha256": pin(cl_bytes, "obo")}, @@ -151,21 +162,27 @@ def main(argv: list[str] | None = None) -> int: manifest["asctb"] = {"organs": sorted(set(ORGANS.values())), "release": "ccf-releases v2.0", "assertions": len(reference), "sha256": pin(tsv(["subject", "predicate", "object", "object_label", "organ"], reference), "tsv")} tasks, truth = [], [] - for meta in json.loads((data / "selected.json").read_text(encoding="utf-8")): - h5ad = data / "h5ad" / f"{meta['name']}.h5ad" - rows, clusters = markers(h5ad, genes, ontology) + groups = [("development", data / "selected.json", data / "h5ad"), ("external", data / "selected-v2.json", data / "h5ad-v2")] + selected = [(group, meta, folder) for group, listing, folder in groups if listing.exists() + for meta in json.loads(listing.read_text(encoding="utf-8"))] + manifest["parameters"]["definition_panel_genes"] = len(panel) + for group, meta, folder in selected: + h5ad = folder / f"{meta['name']}.h5ad" + rows, clusters, panel_rows = markers(h5ad, genes, ontology, panel) table = pin(tsv(["cluster", "gene", "rank", "logfc", "pct_in", "pct_out"], rows), "tsv") + panel_table = pin(tsv(["cluster", "gene", "pct_in", "logfc"], panel_rows), "tsv") manifest["datasets"].append({**{k: meta[k] for k in ("name", "dataset_id", "dataset_version_id", "title", "collection_name", "collection_doi", "cell_count", "url")}, "tissue": meta["tissue"][0], "assay": [a["label"] for a in meta["assay"]], "h5ad_sha256": sha256(h5ad.read_bytes()), "markers_sha256": table, - "clusters": len(clusters)}) + "panel_sha256": panel_table, "clusters": len(clusters), "group": group}) order = sorted(clusters, key=lambda c: sha256(f"{KEY}:{meta['dataset_id']}:{c['cluster']}".encode())) pilot = {c["cluster"] for c in order[:PILOT_PER_DATASET]} for c in clusters: task_id = "ct-" + sha256(f"{meta['dataset_id']}:{c['cluster']}".encode())[:10] top = [r for r in rows if r["cluster"] == c["cluster"]][:PROMPT_GENES] - tasks.append({"task_id": task_id, "split": "pilot" if c["cluster"] in pilot else "test", + split = "external" if group == "external" else "pilot" if c["cluster"] in pilot else "test" + tasks.append({"task_id": task_id, "split": split, "dataset": meta["name"], "cluster": c["cluster"], "tissue": meta["tissue"][0]["label"], "assay": ", ".join(a["label"] for a in meta["assay"]), "species": "Homo sapiens", "markers_sha256": table, @@ -176,7 +193,8 @@ def main(argv: list[str] | None = None) -> int: newline="\n") (SOURCES / "manifest.json").write_text(json.dumps(manifest, indent=2, sort_keys=True) + "\n", encoding="utf-8", newline="\n") - print(f"{len(tasks)} tasks ({sum(t['split'] == 'pilot' for t in tasks)} pilot), {len(reference)} ASCT+B assertions") + splits = {s: sum(t["split"] == s for t in tasks) for s in ("pilot", "test", "external")} + print(f"{len(tasks)} tasks {splits}, {len(reference)} ASCT+B assertions, {len(panel)} definition panel genes") return 0 diff --git a/examples/singlecell_celltype/sources/ATTRIBUTION.md b/examples/singlecell_celltype/sources/ATTRIBUTION.md index 04e50c6..06c2c4b 100644 --- a/examples/singlecell_celltype/sources/ATTRIBUTION.md +++ b/examples/singlecell_celltype/sources/ATTRIBUTION.md @@ -15,6 +15,17 @@ redistributed; `manifest.json` records each file's SHA-256 and dataset version. | skin | Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming | *Commun Biol* 2020, [10.1038/s42003-020-0922-4](https://doi.org/10.1038/s42003-020-0922-4) | | lung_t_nk_ilc | T, NK and ILC, in *A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates* | *Cell* 2022, [10.1016/j.cell.2022.11.005](https://doi.org/10.1016/j.cell.2022.11.005) | +External datasets (the `external` split), from other studies: + +| Name | Dataset | Publication | +|---|---|---| +| blood_bone_marrow | blood and bone marrow from a healthy young donor, in *Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states* (a targeted gene panel) | *Nat Immunol* 2021, [10.1038/s41590-021-01059-0](https://doi.org/10.1038/s41590-021-01059-0) | +| tonsil_t | Human tonsil T cells scRNA, in *Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics* | *Sci Immunol* 2021, [10.1126/sciimmunol.abe6291](https://doi.org/10.1126/sciimmunol.abe6291) | +| kidney_immune | Mature kidney dataset: immune, in *Spatiotemporal immune zonation of the human kidney* | *Science* 2019, [10.1126/science.aat5031](https://doi.org/10.1126/science.aat5031) | +| endometrium_immune | Immune cells from five healthy donors, in *Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women* | *PNAS* 2024, [10.1073/pnas.2404775121](https://doi.org/10.1073/pnas.2404775121) | +| bladder_immune | Adult bladder immune subset, in *Exploring the Utility of snRNA-seq in Profiling Human Bladder Tissue: A Comprehensive Comparison with scRNA-seq* | *iScience*, [10.1016/j.isci.2024.111628](https://doi.org/10.1016/j.isci.2024.111628) | +| fetal_intestine | Immune, in *Spatiotemporal analysis of human intestinal development at single-cell resolution* | *Cell* 2021, [10.1016/j.cell.2020.12.016](https://doi.org/10.1016/j.cell.2020.12.016) | + Reference releases, redistributed unchanged (gzip-compressed) in `snapshots/`: - **Cell Ontology**, release 2026-06-08, full `cl.obo` diff --git a/examples/singlecell_celltype/sources/manifest.json b/examples/singlecell_celltype/sources/manifest.json index 00022e8..08dce91 100644 --- a/examples/singlecell_celltype/sources/manifest.json +++ b/examples/singlecell_celltype/sources/manifest.json @@ -26,9 +26,11 @@ "collection_name": "Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations", "dataset_id": "a43aa46b-bd16-47fe-bc3e-19a052624e79", "dataset_version_id": "9681a962-f2d0-4d53-8127-7ac87f2bd799", + "group": "development", "h5ad_sha256": "9d9c24983830f1948033c4fcf0c139e735e35e05db50e3778f64c7f8b3db7bee", "markers_sha256": "fe2ff2cb67d700473d6285d4b052a1d892278cfc5377937a37152123c8c6b98d", "name": "liver", + "panel_sha256": "4edd4b4d17ed3bdb5e59aae56733e0d2c155169a4ffc9a4a5e77c64c65192820", "tissue": { "label": "caudate lobe of liver", "ontology_term_id": "UBERON:0001117", @@ -47,9 +49,11 @@ "collection_name": "Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response", "dataset_id": "f801b7a9-80a6-4d09-9161-71474deb58ae", "dataset_version_id": "5f0b9675-aed8-4870-8ad8-7a3f38037486", + "group": "development", "h5ad_sha256": "3215543bd2dc490db5ef247d082632aaa12392cac536e6cad41dd7f991b33f49", "markers_sha256": "a8bc60d1f3d0c6496eba01eb18f3f2ec0226f329ff4fdc52033e41486fc3a58b", "name": "kidney", + "panel_sha256": "b4e35c41cb49cb37e2a7dceeb4d61d443972b9c07eea0c2108bf4cdf5a4026db", "tissue": { "label": "kidney", "ontology_term_id": "UBERON:0002113", @@ -68,9 +72,11 @@ "collection_name": "Charting human development using a multi-endodermal organ atlas and organoid models", "dataset_id": "ee195b7d-184d-4dfa-9b1c-51a7e601ac11", "dataset_version_id": "1f896487-282d-4303-a948-3cbdd1b721b0", + "group": "development", "h5ad_sha256": "c42a9fcf76fbc2905d8fe1fc24d29e88677298dea722fa1d7c2a268f0ad41b89", "markers_sha256": "a468f9b74afc3d0b358e28c1b514c558558d49f69d688fe1758ac3348d6c6e56", "name": "duodenum", + "panel_sha256": "aa2a0366a1d3fa6f27d05ada922287277680229eb68b82f5e8f980bb7588f078", "tissue": { "label": "duodenum", "ontology_term_id": "UBERON:0002114", @@ -89,9 +95,11 @@ "collection_name": "Muraro Pancreas", "dataset_id": "b07e5164-baf6-43d2-bdba-5a249d0da879", "dataset_version_id": "ac56150b-add4-4336-9059-6d3d3ce17f3b", + "group": "development", "h5ad_sha256": "183673651cfa8c473a26641d42011d43be44eb2fea44e6e6ab8e2b0065d07483", "markers_sha256": "c627f49dc8fd53ee164a2fab9a818d857d695937291aa809f194b4006b1a4c7d", "name": "pancreas", + "panel_sha256": "04149afa4ad2c3d69b62c2ae573f8ac7ae921e5cd07a6ee52b4052414ef0eb80", "tissue": { "label": "pancreas", "ontology_term_id": "UBERON:0001264", @@ -110,9 +118,11 @@ "collection_name": "Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming", "dataset_id": "124744b8-4681-474a-9894-683896122708", "dataset_version_id": "1a6bbe2b-4eed-477a-97c9-f7a74d4874d7", + "group": "development", "h5ad_sha256": "0968cb3ccad509198e0aa37541c3f2301abcbfe81eefeec781abac80c15bc8ad", "markers_sha256": "1dacf640d2c4d41b43f2b7e7d3b7a1fc13fe72ac383760d336886501afacfa1b", "name": "skin", + "panel_sha256": "27b93845077ff60795eaaed588b0fb18a9dc08fd1b300ae0b7e2435c1cd1e020", "tissue": { "label": "zone of skin", "ontology_term_id": "UBERON:0000014", @@ -131,9 +141,11 @@ "collection_name": "A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates", "dataset_id": "62315937-e268-4fa5-a032-8f7d776f3a3f", "dataset_version_id": "03a99fe4-e8ce-47c6-b912-d088271cc319", + "group": "development", "h5ad_sha256": "889617850ca9ba1ab7cec31d57bf11d6eec11b563fc07182e4f4b03695f838a3", "markers_sha256": "0973035c1880e60359ca8af87b55d8fa125ff19bf059144cfc00ee98b3f2bbd3", "name": "lung_t_nk_ilc", + "panel_sha256": "47581619b67b2cbd7cd9534044529a0d47f8bc40ae49bae9c584801db4dd0e72", "tissue": { "label": "lung", "ontology_term_id": "UBERON:0002048", @@ -141,6 +153,145 @@ }, "title": "T, NK and ILC", "url": "https://datasets.cellxgene.cziscience.com/03a99fe4-e8ce-47c6-b912-d088271cc319.h5ad" + }, + { + "assay": [ + "BD Rhapsody Targeted mRNA" + ], + "cell_count": 15502, + "clusters": 27, + "collection_doi": "10.1038/s41590-021-01059-0", + "collection_name": "Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states", + "dataset_id": "d3566d6a-a455-4a15-980f-45eb29114cab", + "dataset_version_id": "89982e3f-db80-4f08-8a15-acd80f106658", + "group": "external", + "h5ad_sha256": "d8778165d66e036416dbb3490443fac58971f9c5c832608999235d2faf4d8675", + "markers_sha256": "fefc4d5efecffd34bc1e5834e139db7ee008f1e403400505d14dc8ae575b3531", + "name": "blood_bone_marrow", + "panel_sha256": "a26148a4559f60fbcd65a70b2083cacc46cbb704627e37aeb8124dda248349d4", + "tissue": { + "label": "blood", + "ontology_term_id": "UBERON:0000178", + "tissue_type": "tissue" + }, + "title": "blood and bone marrow from a healthy young donor", + "url": "https://datasets.cellxgene.cziscience.com/89982e3f-db80-4f08-8a15-acd80f106658.h5ad" + }, + { + "assay": [ + "10x 3' v2", + "10x 5' v1" + ], + "cell_count": 8753, + "clusters": 10, + "collection_doi": "10.1126/sciimmunol.abe6291", + "collection_name": "Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics", + "dataset_id": "f54647ec-0c03-4775-8dac-5a477c10a3f5", + "dataset_version_id": "033d8138-e31b-4e1d-9faf-539c65779a44", + "group": "external", + "h5ad_sha256": "ca644159b119bf9092e284c90df74d0420450ced4ce1a0eb9774398bb19763c1", + "markers_sha256": "667841e432e47092938264f7024acbaa3c36ffaee96f919fc813a653f814d2b2", + "name": "tonsil_t", + "panel_sha256": "fd4ed72d81c49ce8ea21b92a41f8b713ec44648dfd540ed61c9a8ba3116dd77e", + "tissue": { + "label": "tonsil", + "ontology_term_id": "UBERON:0002372", + "tissue_type": "tissue" + }, + "title": "Human tonsil T cells scRNA", + "url": "https://datasets.cellxgene.cziscience.com/033d8138-e31b-4e1d-9faf-539c65779a44.h5ad" + }, + { + "assay": [ + "10x 3' v2" + ], + "cell_count": 7803, + "clusters": 11, + "collection_doi": "10.1126/science.aat5031", + "collection_name": "Spatiotemporal immune zonation of the human kidney", + "dataset_id": "20d87640-4be8-487f-93d4-dce38378d00f", + "dataset_version_id": "281f6735-10c8-492e-be93-ccdc5b3d0170", + "group": "external", + "h5ad_sha256": "8dfd797cd2b668d4b2319284aa3c22a7d0ccbae4f11ec5fb32e541feeb0639fb", + "markers_sha256": "a84a86873fe12ce27f3c4215431c8cc3257bcfbe82829ba73dc0949ffcfbe89a", + "name": "kidney_immune", + "panel_sha256": "80c81979b9e39c50fc4545a810e88dd2b433a0c50171518ec9282aa40b7e6a79", + "tissue": { + "label": "cortex of kidney", + "ontology_term_id": "UBERON:0001225", + "tissue_type": "tissue" + }, + "title": "Mature kidney dataset: immune", + "url": "https://datasets.cellxgene.cziscience.com/281f6735-10c8-492e-be93-ccdc5b3d0170.h5ad" + }, + { + "assay": [ + "10x 3' v3" + ], + "cell_count": 8653, + "clusters": 13, + "collection_doi": "10.1073/pnas.2404775121", + "collection_name": "Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women", + "dataset_id": "7a419302-772d-4534-bffe-763c95b8c63d", + "dataset_version_id": "1ff5b228-befb-4160-a4e3-d672eeae9d8b", + "group": "external", + "h5ad_sha256": "a60d7963da9ed256114e9f3cba980d4a2527be7328a139f79fb7ee252f6f4bd5", + "markers_sha256": "fd69b9fe25b83db0d10a734a3636f2993d36bfcbefe3fced2ac170e0406dd93a", + "name": "endometrium_immune", + "panel_sha256": "22569977ce45b676cc24c16e90ef1ac0b33b8ce4da4c3c982ca5777cdb0e7fd3", + "tissue": { + "label": "endometrium", + "ontology_term_id": "UBERON:0001295", + "tissue_type": "tissue" + }, + "title": "Immune cells from five healthy donors", + "url": "https://datasets.cellxgene.cziscience.com/1ff5b228-befb-4160-a4e3-d672eeae9d8b.h5ad" + }, + { + "assay": [ + "10x 3' v3" + ], + "cell_count": 2094, + "clusters": 9, + "collection_doi": "10.1016/j.isci.2024.111628", + "collection_name": "Exploring the Utility of snRNA-seq in Profiling Human Bladder Tissue: A Comprehensive Comparison with scRNA-seq", + "dataset_id": "601c7454-17ff-432c-8e0d-902bfddb8013", + "dataset_version_id": "24f3b529-a9d2-4396-8173-2f8198d8a8d4", + "group": "external", + "h5ad_sha256": "dbb22a4116d1a5297e1d134d62a3155c6d998d5fee33449e31f172ec89a3033d", + "markers_sha256": "afca338b79b8fffe869dddf85032ef60f71d9e7eb59f70fed900f915139ab023", + "name": "bladder_immune", + "panel_sha256": "c47c21f94dd924f0bb4bffd2bf6f03f0a366dee60a88398a234bb304f681e147", + "tissue": { + "label": "dome of urinary bladder", + "ontology_term_id": "UBERON:8600049", + "tissue_type": "tissue" + }, + "title": "Adult bladder immune subset", + "url": "https://datasets.cellxgene.cziscience.com/24f3b529-a9d2-4396-8173-2f8198d8a8d4.h5ad" + }, + { + "assay": [ + "10x 3' v3" + ], + "cell_count": 2199, + "clusters": 11, + "collection_doi": "10.1016/j.cell.2020.12.016", + "collection_name": "Spatiotemporal analysis of human intestinal development at single-cell resolution", + "dataset_id": "4269074c-f2c1-4d88-b2c3-0946f59d5449", + "dataset_version_id": "bbf977be-6c4f-4e38-bff6-045962afb641", + "group": "external", + "h5ad_sha256": "2a93a5ed182b1260da0405199b6fb7a3ec9bf3e836c831032d63a5b046a4060f", + "markers_sha256": "e67f10f82e2ad33b5d8a35038c6e04ced40647dedaeb58737a6a9832f111f59d", + "name": "fetal_intestine", + "panel_sha256": "b64a7d6344ebe60625f50f51677f11c712e5257bf183c7e37f67e36e7730f84b", + "tissue": { + "label": "colon", + "ontology_term_id": "UBERON:0001155", + "tissue_type": "tissue" + }, + "title": "Spatiotemporal analysis of human intestinal development at single-cell resolution: Immune", + "url": "https://datasets.cellxgene.cziscience.com/bbf977be-6c4f-4e38-bff6-045962afb641.h5ad" } ], "hgnc": { @@ -150,6 +301,7 @@ }, "key": "bioai-singlecell-celltype-v1", "parameters": { + "definition_panel_genes": 144, 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"0.710", "pct_out": "0.148"}, {"gene": "PRR5", "logfc": "1.057", "pct_in": "0.689", "pct_out": "0.151"}, {"gene": "NFKBIA", "logfc": "1.007", "pct_in": "0.945", "pct_out": "0.814"}, {"gene": "TNFAIP3", "logfc": "0.997", "pct_in": "0.874", "pct_out": "0.653"}, {"gene": "JMY", "logfc": "0.983", "pct_in": "0.716", "pct_out": "0.350"}], "markers_sha256": "e67f10f82e2ad33b5d8a35038c6e04ced40647dedaeb58737a6a9832f111f59d", "species": "Homo sapiens", "split": "external", "task_id": "ct-227cbde019", "tissue": "colon"} diff --git a/examples/singlecell_celltype/sources/truth.jsonl b/examples/singlecell_celltype/sources/truth.jsonl index 74f1b25..a1ffff5 100644 --- a/examples/singlecell_celltype/sources/truth.jsonl +++ b/examples/singlecell_celltype/sources/truth.jsonl @@ -68,3 +68,84 @@ {"author_label": "group 2 innate lymphoid cell", "author_term": "CL:0001069", "cells": 149, "cluster": "c11", "dataset": "lung_t_nk_ilc", "label": "group 2 innate lymphoid cell", "note": "", "task_id": "ct-a53a01a447", "term": "CL:0001069"} {"author_label": "group 3 innate lymphoid cell", "author_term": "CL:0001071", "cells": 135, "cluster": "c12", "dataset": "lung_t_nk_ilc", "label": "group 3 innate lymphoid cell", "note": "", "task_id": "ct-3ec5acbb2d", "term": "CL:0001071"} {"author_label": "CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human", "author_term": "CL:0001074", "cells": 80, "cluster": "c13", "dataset": "lung_t_nk_ilc", "label": "CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human", "note": "", "task_id": "ct-307f739343", "term": "CL:0001074"} +{"author_label": "erythroid progenitor cell", "author_term": "CL:0000038", "cells": 390, "cluster": "c01", "dataset": "blood_bone_marrow", "label": "erythroid progenitor cell", "note": "", "task_id": "ct-f5e849f6ff", "term": "CL:0000038"} +{"author_label": "megakaryocyte-erythroid progenitor cell", "author_term": "CL:0000050", "cells": 35, "cluster": "c02", "dataset": "blood_bone_marrow", "label": "megakaryocyte-erythroid progenitor cell", "note": "", "task_id": "ct-3b8c7f5246", "term": "CL:0000050"} +{"author_label": "megakaryocyte progenitor cell", "author_term": "CL:0000553", "cells": 57, "cluster": "c03", "dataset": "blood_bone_marrow", "label": "megakaryocyte progenitor cell", "note": "", "task_id": "ct-3775a26491", "term": "CL:0000553"} +{"author_label": "plasmacytoid dendritic cell", "author_term": "CL:0000784", "cells": 46, "cluster": "c04", "dataset": "blood_bone_marrow", "label": "plasmacytoid dendritic cell", "note": "", "task_id": "ct-26fda93c9c", "term": "CL:0000784"} +{"author_label": "plasma cell", "author_term": "CL:0000786", "cells": 40, "cluster": "c05", "dataset": "blood_bone_marrow", "label": "plasma cell", "note": "", "task_id": "ct-62995bbc69", "term": "CL:0000786"} +{"author_label": "naive B cell", "author_term": "CL:0000788", "cells": 974, "cluster": "c06", "dataset": "blood_bone_marrow", "label": "naive B cell", "note": "", "task_id": "ct-d44564d7f6", "term": "CL:0000788"} +{"author_label": "gamma-delta T cell", "author_term": "CL:0000798", "cells": 109, "cluster": "c07", "dataset": "blood_bone_marrow", "label": "gamma-delta T cell", "note": "", "task_id": "ct-56d8f3ebbf", "term": "CL:0000798"} +{"author_label": "immature B cell", "author_term": "CL:0000816", "cells": 62, "cluster": "c08", "dataset": "blood_bone_marrow", "label": "immature B cell", "note": "", "task_id": "ct-1fdfebb69c", "term": "CL:0000816"} +{"author_label": "hematopoietic multipotent progenitor cell", "author_term": "CL:0000837", "cells": 171, "cluster": "c09", "dataset": "blood_bone_marrow", "label": "hematopoietic multipotent progenitor cell", "note": "", "task_id": "ct-75adde23f7", "term": "CL:0000837"} +{"author_label": "lymphoid lineage restricted progenitor cell", "author_term": "CL:0000838", "cells": 156, "cluster": "c10", "dataset": "blood_bone_marrow", "label": "lymphoid lineage restricted progenitor cell", "note": "", "task_id": "ct-7a81a9a19f", "term": "CL:0000838"} +{"author_label": "classical monocyte", "author_term": "CL:0000860", "cells": 4815, "cluster": "c11", "dataset": "blood_bone_marrow", "label": "classical monocyte", "note": "", "task_id": "ct-0094010baa", "term": "CL:0000860"} +{"author_label": "non-classical monocyte", "author_term": "CL:0000875", "cells": 1590, "cluster": "c12", "dataset": "blood_bone_marrow", "label": "non-classical monocyte", "note": "", "task_id": "ct-8c07cf76ca", "term": "CL:0000875"} +{"author_label": "naive thymus-derived CD4-positive, alpha-beta T cell", "author_term": "CL:0000895", "cells": 188, "cluster": "c13", "dataset": "blood_bone_marrow", "label": "naive thymus-derived CD4-positive, alpha-beta T cell", "note": "", "task_id": "ct-e1bfaa2341", "term": "CL:0000895"} +{"author_label": "CD4-positive, alpha-beta memory T cell", "author_term": "CL:0000897", "cells": 1645, "cluster": "c14", "dataset": "blood_bone_marrow", "label": "CD4-positive, alpha-beta memory T cell", "note": "", "task_id": "ct-ff19304f5c", "term": "CL:0000897"} +{"author_label": "naive thymus-derived CD8-positive, alpha-beta T cell", "author_term": "CL:0000900", "cells": 165, "cluster": "c15", "dataset": "blood_bone_marrow", "label": "naive thymus-derived CD8-positive, alpha-beta T cell", "note": "", "task_id": "ct-28eb7ea379", "term": "CL:0000900"} +{"author_label": "central memory CD8-positive, alpha-beta T cell", "author_term": "CL:0000907", "cells": 187, "cluster": "c16", "dataset": "blood_bone_marrow", "label": "central memory CD8-positive, alpha-beta T cell", "note": "", "task_id": "ct-95367720e6", "term": "CL:0000907"} +{"author_label": "CD8-positive, alpha-beta memory T cell", "author_term": "CL:0000909", "cells": 600, "cluster": "c17", "dataset": "blood_bone_marrow", "label": "CD8-positive, alpha-beta memory T cell", "note": "", "task_id": "ct-15649bcc33", "term": "CL:0000909"} +{"author_label": "effector memory CD8-positive, alpha-beta T cell", "author_term": "CL:0000913", "cells": 623, "cluster": "c18", "dataset": "blood_bone_marrow", "label": "effector memory CD8-positive, alpha-beta T cell", "note": "", "task_id": "ct-4b8439fcc9", "term": "CL:0000913"} +{"author_label": "CD16-negative, CD56-bright natural killer cell, human", "author_term": "CL:0000938", "cells": 77, "cluster": "c19", "dataset": "blood_bone_marrow", "label": "CD16-negative, CD56-bright natural killer cell, human", "note": "", "task_id": "ct-b95794dcf3", "term": "CL:0000938"} +{"author_label": "CD16-positive, CD56-dim natural killer cell, human", "author_term": "CL:0000939", "cells": 1721, "cluster": "c20", "dataset": "blood_bone_marrow", "label": "CD16-positive, CD56-dim natural killer cell, human", "note": "", "task_id": "ct-21afd5c734", "term": "CL:0000939"} +{"author_label": "unswitched memory B cell", "author_term": "CL:0000970", "cells": 596, "cluster": "c21", "dataset": "blood_bone_marrow", "label": "unswitched memory B cell", "note": "", "task_id": "ct-e7ae6683c5", "term": "CL:0000970"} +{"author_label": "class switched memory B cell", "author_term": "CL:0000972", "cells": 330, "cluster": "c22", "dataset": "blood_bone_marrow", "label": "class switched memory B cell", "note": "", "task_id": "ct-ccd8ad8cc1", "term": "CL:0000972"} +{"author_label": "conventional dendritic cell", "author_term": "CL:0000990", "cells": 352, "cluster": "c23", "dataset": "blood_bone_marrow", "label": "conventional dendritic cell", "note": "", "task_id": "ct-9e8b98aab5", "term": "CL:0000990"} +{"author_label": "basophil mast progenitor cell", "author_term": "CL:0002028", "cells": 33, "cluster": "c24", "dataset": "blood_bone_marrow", "label": "basophil mast progenitor cell", "note": "", "task_id": "ct-0224ef5d63", "term": "CL:0002028"} +{"author_label": "late promyelocyte", "author_term": "CL:0002151", "cells": 54, "cluster": "c25", "dataset": "blood_bone_marrow", "label": "late promyelocyte", "note": "", "task_id": "ct-9d2a6afe3f", "term": "CL:0002151"} +{"author_label": "early promyelocyte", "author_term": "CL:0002154", "cells": 106, "cluster": "c26", "dataset": "blood_bone_marrow", "label": "early promyelocyte", "note": "", "task_id": "ct-4e9d71ecad", "term": "CL:0002154"} +{"author_label": "myelocyte", "author_term": "CL:0002193", "cells": 324, "cluster": "c27", "dataset": "blood_bone_marrow", "label": "myelocyte", "note": "", "task_id": "ct-b7c75983d8", "term": "CL:0002193"} +{"author_label": "T cell", "author_term": "CL:0000084", "cells": 268, "cluster": "c01", "dataset": "tonsil_t", "label": "T cell", "note": "", "task_id": "ct-3daee1395a", "term": "CL:0000084"} +{"author_label": "CD4-positive helper T cell", "author_term": "CL:0000492", "cells": 839, "cluster": "c02", "dataset": "tonsil_t", "label": "CD4-positive helper T cell", "note": "", "task_id": "ct-f5551fdf21", "term": "CL:0000492"} +{"author_label": "natural killer cell", "author_term": "CL:0000623", "cells": 59, "cluster": "c03", "dataset": "tonsil_t", "label": "natural killer cell", "note": "", "task_id": "ct-8d82b1a772", "term": "CL:0000623"} +{"author_label": "CD8-positive, alpha-beta cytotoxic T cell", "author_term": "CL:0000794", "cells": 1119, "cluster": "c04", "dataset": "tonsil_t", "label": "CD8-positive, alpha-beta cytotoxic T cell", "note": "", "task_id": "ct-ec5325a064", "term": "CL:0000794"} +{"author_label": "regulatory T cell", "author_term": "CL:0000815", "cells": 612, "cluster": "c05", "dataset": "tonsil_t", "label": "regulatory T cell", "note": "", "task_id": "ct-62ef0fd4ba", "term": "CL:0000815"} +{"author_label": "central memory CD4-positive, alpha-beta T cell", "author_term": "CL:0000904", "cells": 1462, "cluster": "c06", "dataset": "tonsil_t", "label": "central memory CD4-positive, alpha-beta T cell", "note": "", "task_id": "ct-b322bece33", "term": "CL:0000904"} +{"author_label": "central memory CD8-positive, alpha-beta T cell", "author_term": "CL:0000907", "cells": 547, "cluster": "c07", "dataset": "tonsil_t", "label": 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"CL:0000097"} +{"author_label": "B cell", "author_term": "CL:0000236", "cells": 975, "cluster": "c02", "dataset": "kidney_immune", "label": "B cell", "note": "", "task_id": "ct-04f3e6a976", "term": "CL:0000236"} +{"author_label": "dendritic cell", "author_term": "CL:0000451", "cells": 220, "cluster": "c03", "dataset": "kidney_immune", "label": "dendritic cell", "note": "", "task_id": "ct-b864a5744b", "term": "CL:0000451"} +{"author_label": "natural killer cell", "author_term": "CL:0000623", "cells": 1322, "cluster": "c04", "dataset": "kidney_immune", "label": "natural killer cell", "note": "", "task_id": "ct-98402e60db", "term": "CL:0000623"} +{"author_label": "CD4-positive, alpha-beta T cell", "author_term": "CL:0000624", "cells": 2435, "cluster": "c05", "dataset": "kidney_immune", "label": "CD4-positive, alpha-beta T cell", "note": "", "task_id": "ct-8ab1b5fbd8", "term": "CL:0000624"} +{"author_label": "CD8-positive, alpha-beta T cell", "author_term": "CL:0000625", "cells": 991, "cluster": "c06", "dataset": "kidney_immune", "label": "CD8-positive, alpha-beta T cell", "note": "", "task_id": "ct-1c3cf91fbc", "term": "CL:0000625"} +{"author_label": "neutrophil", "author_term": "CL:0000775", "cells": 46, "cluster": "c07", "dataset": "kidney_immune", "label": "neutrophil", "note": "", "task_id": "ct-f2e4fa20cc", "term": "CL:0000775"} +{"author_label": "mature NK T cell", "author_term": "CL:0000814", "cells": 733, "cluster": "c08", "dataset": "kidney_immune", "label": "mature NK T cell", "note": "", "task_id": "ct-b51a9f2d53", "term": "CL:0000814"} +{"author_label": "classical monocyte", "author_term": "CL:0000860", "cells": 555, "cluster": "c09", "dataset": "kidney_immune", "label": "classical monocyte", "note": "", "task_id": "ct-d7d3163b78", "term": "CL:0000860"} +{"author_label": "non-classical monocyte", "author_term": "CL:0000875", "cells": 375, "cluster": "c10", "dataset": "kidney_immune", "label": "non-classical monocyte", "note": "", "task_id": "ct-c5e3a0ec1f", "term": "CL:0000875"} +{"author_label": "kidney resident macrophage", "author_term": "CL:1000698", "cells": 87, "cluster": "c11", "dataset": "kidney_immune", "label": "kidney resident macrophage", "note": "", "task_id": "ct-819cfbd986", "term": "CL:1000698"} +{"author_label": "fibroblast", "author_term": "CL:0000057", "cells": 40, "cluster": "c01", "dataset": "endometrium_immune", "label": "fibroblast", "note": "", "task_id": "ct-d929ec7963", "term": "CL:0000057"} +{"author_label": "mast cell", "author_term": "CL:0000097", "cells": 691, "cluster": "c02", "dataset": "endometrium_immune", "label": "mast cell", "note": "", "task_id": "ct-68351aaa63", "term": "CL:0000097"} +{"author_label": "circulating fibrocyte", "author_term": "CL:0000135", "cells": 247, "cluster": "c03", "dataset": "endometrium_immune", "label": "circulating fibrocyte", "note": "", "task_id": "ct-0919bb7151", "term": "CL:0000135"} +{"author_label": "glandular secretory epithelial cell", "author_term": "CL:0000150", "cells": 49, "cluster": "c04", "dataset": "endometrium_immune", "label": "glandular secretory epithelial cell", "note": "", "task_id": "ct-ad2d591627", "term": "CL:0000150"} +{"author_label": "macrophage", "author_term": "CL:0000235", "cells": 2187, "cluster": "c05", "dataset": "endometrium_immune", "label": "macrophage", "note": "", "task_id": "ct-89c1241fbf", "term": "CL:0000235"} +{"author_label": "B cell", "author_term": "CL:0000236", "cells": 84, "cluster": "c06", "dataset": "endometrium_immune", "label": "B cell", "note": "", "task_id": "ct-879d085000", "term": "CL:0000236"} +{"author_label": "natural killer cell", "author_term": "CL:0000623", "cells": 2861, "cluster": "c07", "dataset": "endometrium_immune", "label": "natural killer cell", "note": "", "task_id": "ct-ae89c1380f", "term": "CL:0000623"} +{"author_label": "leukocyte", "author_term": "CL:0000738", "cells": 140, "cluster": "c08", "dataset": "endometrium_immune", "label": "leukocyte", "note": "", "task_id": "ct-027de551e6", "term": "CL:0000738"} +{"author_label": "regulatory T cell", "author_term": "CL:0000815", "cells": 85, "cluster": "c09", "dataset": "endometrium_immune", "label": "regulatory T cell", "note": "", "task_id": "ct-c99aec2a45", "term": "CL:0000815"} +{"author_label": "CD4-positive, alpha-beta memory T cell", "author_term": "CL:0000897", "cells": 592, "cluster": "c10", "dataset": "endometrium_immune", "label": "CD4-positive, alpha-beta memory T cell", "note": "", "task_id": "ct-72757d8950", "term": "CL:0000897"} +{"author_label": "CD8-positive, alpha-beta memory T cell", "author_term": "CL:0000909", "cells": 893, "cluster": "c11", "dataset": "endometrium_immune", "label": "CD8-positive, alpha-beta memory T cell", "note": "", "task_id": "ct-7c21a7ad85", "term": "CL:0000909"} +{"author_label": "innate lymphoid cell", "author_term": "CL:0001065", "cells": 417, "cluster": "c12", "dataset": "endometrium_immune", "label": "innate lymphoid cell", "note": "", "task_id": "ct-76fa626271", "term": "CL:0001065"} +{"author_label": "hematopoietic precursor cell", "author_term": "CL:0008001", "cells": 235, "cluster": "c13", "dataset": "endometrium_immune", "label": "hematopoietic precursor cell", "note": "", "task_id": "ct-f7efaf4b7a", "term": "CL:0008001"} +{"author_label": "T cell", "author_term": "CL:0000084", "cells": 736, "cluster": "c01", "dataset": "bladder_immune", "label": "T cell", "note": "", "task_id": "ct-72dfb189c0", "term": "CL:0000084"} +{"author_label": "granulocyte", "author_term": "CL:0000094", "cells": 37, "cluster": "c02", "dataset": "bladder_immune", "label": "granulocyte", "note": "", "task_id": "ct-5169234be6", "term": "CL:0000094"} +{"author_label": "mast cell", "author_term": "CL:0000097", "cells": 55, "cluster": "c03", "dataset": "bladder_immune", "label": "mast cell", "note": "", "task_id": "ct-3959f97db0", "term": "CL:0000097"} +{"author_label": "macrophage", "author_term": "CL:0000235", "cells": 405, "cluster": "c04", "dataset": "bladder_immune", "label": "macrophage", "note": "", "task_id": "ct-302af8ae13", "term": "CL:0000235"} +{"author_label": "B cell", "author_term": "CL:0000236", "cells": 70, "cluster": "c05", "dataset": "bladder_immune", "label": "B cell", "note": "", "task_id": "ct-9814423bdc", "term": "CL:0000236"} +{"author_label": "dendritic cell", "author_term": "CL:0000451", "cells": 239, "cluster": "c06", "dataset": "bladder_immune", "label": "dendritic cell", "note": "", "task_id": "ct-9d243229e7", "term": "CL:0000451"} +{"author_label": "monocyte", "author_term": "CL:0000576", "cells": 442, "cluster": "c07", "dataset": "bladder_immune", "label": "monocyte", "note": "", "task_id": "ct-b269766ee9", "term": "CL:0000576"} +{"author_label": "plasma cell", "author_term": "CL:0000786", "cells": 31, "cluster": "c08", "dataset": "bladder_immune", "label": "plasma cell", "note": "", "task_id": "ct-ba5f0288e7", "term": "CL:0000786"} +{"author_label": "mature NK T cell", "author_term": "CL:0000814", "cells": 79, "cluster": "c09", "dataset": "bladder_immune", "label": "mature NK T cell", "note": "", "task_id": "ct-ed05c45d83", "term": "CL:0000814"} +{"author_label": "mast cell", "author_term": "CL:0000097", "cells": 40, "cluster": "c01", "dataset": "fetal_intestine", "label": "mast cell", "note": "", "task_id": "ct-ceffe8616a", "term": "CL:0000097"} +{"author_label": "macrophage", "author_term": "CL:0000235", "cells": 692, "cluster": "c02", "dataset": "fetal_intestine", "label": "macrophage", "note": "", "task_id": "ct-6dacd7effa", "term": "CL:0000235"} +{"author_label": "B cell", "author_term": "CL:0000236", "cells": 167, "cluster": "c03", "dataset": "fetal_intestine", "label": "B cell", "note": "", "task_id": "ct-ac7ec2b016", "term": "CL:0000236"} +{"author_label": "dendritic cell", "author_term": "CL:0000451", "cells": 128, "cluster": "c04", "dataset": "fetal_intestine", "label": "dendritic cell", "note": "", "task_id": "ct-18bf2c5651", "term": "CL:0000451"} +{"author_label": "monocyte", "author_term": "CL:0000576", "cells": 119, "cluster": "c05", "dataset": "fetal_intestine", "label": "monocyte", "note": "", "task_id": "ct-1dc66b7bae", "term": "CL:0000576"} +{"author_label": "natural killer cell", "author_term": "CL:0000623", "cells": 76, "cluster": "c06", "dataset": "fetal_intestine", "label": "natural killer cell", "note": "", "task_id": "ct-e712a5eb84", "term": "CL:0000623"} +{"author_label": "leukocyte", "author_term": "CL:0000738", "cells": 165, "cluster": "c07", "dataset": "fetal_intestine", "label": "leukocyte", "note": "", "task_id": "ct-a321096724", "term": "CL:0000738"} +{"author_label": "plasmacytoid dendritic cell", "author_term": "CL:0000784", "cells": 45, "cluster": "c08", "dataset": "fetal_intestine", "label": "plasmacytoid dendritic cell", "note": "", "task_id": "ct-0460394dc8", "term": "CL:0000784"} +{"author_label": "precursor B cell", "author_term": "CL:0000817", "cells": 76, "cluster": "c09", "dataset": "fetal_intestine", "label": "precursor B cell", "note": "", "task_id": "ct-a33f382e85", "term": "CL:0000817"} +{"author_label": "naive T cell", "author_term": "CL:0000898", "cells": 508, "cluster": "c10", "dataset": "fetal_intestine", "label": "naive T cell", "note": "", "task_id": "ct-be2c0ee626", "term": "CL:0000898"} +{"author_label": "group 3 innate lymphoid cell", "author_term": "CL:0001071", "cells": 183, "cluster": "c11", "dataset": "fetal_intestine", "label": "group 3 innate lymphoid cell", "note": "", "task_id": "ct-227cbde019", "term": "CL:0001071"} diff --git a/src/bioevidence_validator/definitions.py b/src/bioevidence_validator/definitions.py new file mode 100644 index 0000000..b94d3a3 --- /dev/null +++ b/src/bioevidence_validator/definitions.py @@ -0,0 +1,124 @@ +"""Ontology definitions as checks: what a claimed term is defined to have or lack, against what was measured. + +The Cell Ontology defines many cell types by marker proteins: a CD8-positive, alpha-beta T cell is a mature +alpha-beta T cell that `has plasma membrane part` the CD8 co-receptor and `lacks plasma membrane part` CD4; +a natural killer cell lacks CD3 epsilon. These axioms are part of a pinned release, not of anyone's +judgment about a dataset, so they can be checked against measurements without knowing the right answer: +when a record says a cluster is a CD8 T cell and CD4 is detected in most of its cells, the data contradict +the definition of the term it claims (BEV026). That is not proof the record is wrong (protein and transcript +differ, and some definitions are written for one species), so the finding sends the record to review; in a +feedback loop it goes back to the proposer with the measurement, which no omission can hide. + +**Experimental.** On transcript data the check did not transfer to new datasets: several protein definitions do +not hold for mRNA (mast cell CCR3, neutrophil CEACAM8, NK cells lacking CD3 epsilon), and it flagged correct +annotations as often as wrong ones. Fed back to models, its findings turned correct answers into wrong ones +(evaluation/llm_benchmark/README.md, external split). Use it on transcripts only with markers validated at the +mRNA level. + +`MarkerDefinitions` collects, for each term, its presence (`RO:0002104` has plasma membrane part) and absence +(`CL:4030046` lacks plasma membrane part) axioms, its own and inherited through `is_a`, and maps each protein +to genes: by its PRO short label or gene-based synonym (`CD4`, `HLA-DRA`; `Fcgr3` names the FCGR3A/FCGR3B +family), through the components of a +complex (`RO:0002180`, the CD8 co-receptor is CD8A and CD8B), or through its parent protein. Isoform-specific +markers (CD45RA) are left out: gene-level counts cannot see them. Relative axioms (high or low amounts) are +not checked; they compare with another cell type, not with the rest of a dataset. + +`DefinitionGrounder` reads the claimed term (the statement's object) and asks `measure(record)` for the +subject's measurements: gene -> (fraction of cells in which it is detected, log fold change against the other +cells). A presence axiom is contradicted when every measured gene of the protein is detected in fewer than +`present` of the cells; an absence axiom when some gene is detected in at least `absent` of them and is higher +than elsewhere (`absent_logfc`). Genes that were not measured are not judged. +""" +from __future__ import annotations + +import re +from collections.abc import Callable, Mapping +from functools import cache +from typing import Any + +from .engine import Finding +from .grounding import finding +from .identifiers import Genes, Ontology + +HAS, LACKS, COMPONENT = "RO:0002104", "CL:4030046", "RO:0002180" +KINDS = {HAS: "has", LACKS: "lacks"} + + +class MarkerDefinitions: + def __init__(self, ontology: Ontology, genes: Genes): + self.ontology, self.genes = ontology, genes + self.folded = {s.casefold(): s for s in genes.approved} + + def _symbols(self, label: str) -> tuple[str, ...]: + if label.casefold() in self.folded: + return (self.folded[label.casefold()],) + family = sorted(s for s in self.genes.approved if re.fullmatch(re.escape(label.upper()) + r"[A-Z]", s)) + return tuple(family) if 1 < len(family) <= 4 else () + + def protein_genes(self, protein: str) -> tuple[str, ...]: + return self._genes(protein, 0) + + @cache # noqa: B019 - one instance per pinned release, kept for the process + def _genes(self, protein: str, depth: int) -> tuple[str, ...]: + term = self.ontology.terms.get(protein) + if term is None or depth > 4 or (depth == 0 and "isoform" in term.name): + return () + for label in term.short_labels: + if found := self._symbols(label): + return found + parts = [target for relation, target in term.relations if relation == COMPONENT] + if parts: + return tuple(sorted({g for part in parts for g in self._genes(part, depth + 1)})) + if depth: # a modified or cleaved form: the gene of the protein it is a form of + return tuple(sorted({g for p in term.parents if p.startswith("PR:") for g in self._genes(p, depth + 1)})) + return () + + @cache # noqa: B019 + def of(self, curie: str) -> tuple[tuple[str, str, tuple[str, ...]], ...]: + """(kind, protein name, genes) for each testable presence or absence axiom, own and inherited.""" + found = [] + for ancestor in sorted(self.ontology.ancestors(curie)): + term = self.ontology.terms.get(ancestor) + for relation, target in term.relations if term else []: + if relation in KINDS and target.startswith("PR:") and (genes := self.protein_genes(target)): + protein = self.ontology.terms[target].name + found.append((KINDS[relation], protein, genes)) + return tuple(sorted(set(found))) + + +class DefinitionGrounder: + def __init__(self, definitions: MarkerDefinitions, + measure: Callable[[dict[str, Any]], Mapping[str, tuple[float, float]] | None], *, + present: float = 0.10, absent: float = 0.50, absent_logfc: float = 0.25): + self.definitions, self.measure = definitions, measure + self.present, self.absent, self.absent_logfc = present, absent, absent_logfc + ontology = definitions.ontology + self.name = f"definitions:{ontology.prefix}@{ontology.version}" + + def check(self, record: dict[str, Any]) -> list[Finding]: + claimed = record["statement"]["object"]["id"] + axioms = self.definitions.of(claimed) + stats = self.measure(record) if axioms else None + if not stats: + return [] + out = [] + described = self.definitions.ontology.describe(claimed) + for kind, protein, genes in axioms: + measured = [g for g in genes if g in stats] + if not measured: + continue + names = "/".join(measured) + if kind == "has" and all(stats[g][0] < self.present for g in measured): + seen = max(stats[g][0] for g in measured) + out.append(finding(record, "BEV026", f"{described} is defined as having {protein} ({names}) on the " + f"membrane, but {names} is detected in only {seen:.0%} of the " + "cluster's cells.", "$.statement.object.id")) + if kind == "lacks": + high = [g for g in measured if stats[g][0] >= self.absent and stats[g][1] > self.absent_logfc] + if high: + g = max(high, key=lambda x: stats[x][0]) + out.append(finding(record, "BEV026", f"{described} is defined as lacking {protein} ({g}), but {g} " + f"is detected in {stats[g][0]:.0%} of the cluster's cells, more " + f"than in the others (logfc {stats[g][1]:.2f}).", + "$.statement.object.id")) + return out diff --git a/src/bioevidence_validator/grounding.py b/src/bioevidence_validator/grounding.py index 89169b0..c70485e 100644 --- a/src/bioevidence_validator/grounding.py +++ b/src/bioevidence_validator/grounding.py @@ -16,6 +16,7 @@ BEV023 error a cited identifier is obsolete, withdrawn or not its current name (see `identifiers`) BEV024 error a cited identifier is malformed, or of the wrong kind for its place (see `identifiers`) BEV025 review a pinned reference resource contradicts the claim or its evidence (see `crosscheck`) + BEV026 review measurements contradict the ontology definition of the claimed term (see `definitions`) A grounder may also offer `verified_items(record)`: the evidence items it confirmed against their source. Only those count for evidence types a profile lists under `verified_evidence_types` (BEV020 otherwise). @@ -35,7 +36,8 @@ from .engine import Finding SEVERITY = {"BEV014": "error", "BEV015": "review", "BEV016": "error", "BEV017": "error", "BEV018": "review", - "BEV019": "error", "BEV022": "review", "BEV023": "error", "BEV024": "error", "BEV025": "review"} + "BEV019": "error", "BEV022": "review", "BEV023": "error", "BEV024": "error", "BEV025": "review", + "BEV026": "review"} class Grounder(Protocol): diff --git a/src/bioevidence_validator/identifiers.py b/src/bioevidence_validator/identifiers.py index 50934c6..2483e10 100644 --- a/src/bioevidence_validator/identifiers.py +++ b/src/bioevidence_validator/identifiers.py @@ -75,10 +75,13 @@ class Term: replaced_by: list[str] = field(default_factory=list) consider: list[str] = field(default_factory=list) disjoint: list[str] = field(default_factory=list) + relations: list[tuple[str, str]] = field(default_factory=list) # (relation, target): relationship, intersection_of + short_labels: list[str] = field(default_factory=list) # gene names of a protein term: PRO short labels, gene-based synonyms class Ontology: - """The terms of one pinned OBO release: names, exact synonyms, `is_a` parents, obsoletion, disjointness.""" + """The terms of one pinned OBO release: names, exact synonyms, `is_a` parents, obsoletion, disjointness, and + the relations that logical definitions use (e.g. `has plasma membrane part` a protein).""" def __init__(self, terms: dict[str, Term], prefix: str, version: str): self.terms, self.prefix, self.version = terms, prefix, version @@ -112,8 +115,12 @@ def from_obo(cls, data: bytes) -> Ontology: terms[value] = term elif tag == "name": term.name = value - elif tag == "synonym" and (match := re.match(r'"((?:[^"\\]|\\.)*)" EXACT\b', value)): - term.synonyms.append(match.group(1).replace('\\"', '"')) + elif tag == "synonym" and (match := re.match(r'"((?:[^"\\]|\\.)*)" (\w+)', value)): + text = match.group(1).replace('\\"', '"') + if match.group(2) == "EXACT": + term.synonyms.append(text) + if "PRO-short-label" in value or "Gene-based" in value: + term.short_labels.append(text) elif tag == "is_a": term.parents.append(value.split()[0]) elif tag == "is_obsolete": @@ -124,6 +131,10 @@ def from_obo(cls, data: bytes) -> Ontology: term.consider.append(value) elif tag == "disjoint_from": term.disjoint.append(value) + elif tag in ("relationship", "intersection_of") and len(value.split()) == 2: + pair = (value.split()[0], value.split()[1]) + if pair not in term.relations: + term.relations.append(pair) # `ontology: cl` or `ontology: cl/cl-basic`; a release file may also hold a few terms of other ontologies prefix = header.get("ontology", "").split("/")[0].upper() version = header.get("data-version", "") or header.get("date", "") diff --git a/tests/test_definitions.py b/tests/test_definitions.py new file mode 100644 index 0000000..cd8252c --- /dev/null +++ b/tests/test_definitions.py @@ -0,0 +1,147 @@ +"""Ontology marker definitions checked against measurements.""" +from test_reference_grounders import base + +from bioevidence_validator.definitions import DefinitionGrounder, MarkerDefinitions +from bioevidence_validator.engine import validate_record +from bioevidence_validator.identifiers import Genes, Ontology + +OBO = b"""format-version: 1.2 +data-version: cl/releases/2026-01-01/cl.obo +ontology: cl + +[Term] +id: CL:0000000 +name: cell + +[Term] +id: CL:0000084 +name: T cell +is_a: CL:0000000 ! cell + +[Term] +id: CL:0000623 +name: natural killer cell +is_a: CL:0000000 ! cell +intersection_of: CL:0000000 ! cell +intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon + +[Term] +id: CL:0000625 +name: CD8-positive, alpha-beta T cell +is_a: CL:0000084 ! T cell +intersection_of: CL:0000084 ! T cell +intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule +intersection_of: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 +relationship: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 + +[Term] +id: CL:0000939 +name: CD16-positive, CD56-dim natural killer cell, human +is_a: CL:0000623 ! natural killer cell +intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part Fc receptor III +intersection_of: CL:4030046 PR:000002015 ! lacks MHC class II DRA +intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part CD45RA +intersection_of: RO:0015016 PR:000001024 ! has low plasma membrane amount NCAM1 + +[Term] +id: PR:000001004 +name: CD4 molecule +synonym: "CD4" EXACT PRO-short-label [PRO:DNx] + +[Term] +id: PR:000001020 +name: CD3 epsilon +synonym: "CD3E" EXACT PRO-short-label [PRO:DNx] + +[Term] +id: PR:000001084 +name: T-cell surface glycoprotein CD8 alpha chain +synonym: "CD8A" EXACT PRO-short-label [PRO:DNx] + +[Term] +id: PR:000025408 +name: T-cell surface glycoprotein CD8 alpha chain isoform 1, glycosylated form +is_a: PR:000001084 ! CD8 alpha chain + +[Term] +id: PR:000001085 +name: T-cell surface glycoprotein CD8 beta chain +synonym: "CD8B" EXACT PRO-short-label [PRO:DNx] + +[Term] +id: PR:000025402 +name: T cell receptor co-receptor CD8 +relationship: RO:0002180 PR:000025408 ! has component CD8 alpha chain form +relationship: RO:0002180 PR:000001085 ! has component CD8 beta chain + +[Term] +id: PR:000001483 +name: low affinity immunoglobulin gamma Fc region receptor III +synonym: "Fcgr3" EXACT PRO-short-label [PRO:DNx] + +[Term] +id: PR:000002015 +name: MHC class II histocompatibility antigen alpha chain DRA +synonym: "HLA-DRA" RELATED Gene-based [] +synonym: "MHCcIIalpha_DRA" EXACT PRO-short-label [PRO:DAN] + +[Term] +id: PR:000001015 +name: receptor-type tyrosine-protein phosphatase C isoform CD45RA +synonym: "PTPRC" EXACT PRO-short-label [PRO:DNx] + +[Term] +id: PR:000001024 +name: neural cell adhesion molecule 1 +synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] +""" +SYMBOLS = ["CD4", "CD3E", "CD8A", "CD8B", "FCGR3A", "FCGR3B", "HLA-DRA", "PTPRC", "NCAM1"] +GENES = Genes([{"hgnc_id": f"HGNC:{n}", "symbol": s} for n, s in enumerate(SYMBOLS, start=1)], "test") +DEFINITIONS = MarkerDefinitions(Ontology.from_obo(OBO), GENES) + + +def test_protein_genes_follow_labels_families_components_and_forms(): + assert DEFINITIONS.protein_genes("PR:000001004") == ("CD4",) + assert DEFINITIONS.protein_genes("PR:000001483") == ("FCGR3A", "FCGR3B") # a family + assert DEFINITIONS.protein_genes("PR:000025402") == ("CD8A", "CD8B") # a complex, one part a modified form + assert DEFINITIONS.protein_genes("PR:000002015") == ("HLA-DRA",) # a gene-based synonym + assert DEFINITIONS.protein_genes("PR:000001015") == () # an isoform marker cannot be measured by gene counts + assert DEFINITIONS.protein_genes("PR:999") == () + + +def test_definitions_are_inherited_and_only_presence_or_absence(): + assert DEFINITIONS.of("CL:0000625") == (("has", "T cell receptor co-receptor CD8", ("CD8A", "CD8B")), + ("lacks", "CD4 molecule", ("CD4",))) + kinds = DEFINITIONS.of("CL:0000939") + assert ("lacks", "CD3 epsilon", ("CD3E",)) in kinds # from natural killer cell + assert all(genes != ("NCAM1",) for _, _, genes in kinds) # a relative amount is not checked + assert DEFINITIONS.of("CL:0000084") == () + + +def record(term, label): + return base(object={"id": term, "label": label, "entity_type": "cell_type"}) + + +def grounder(stats): + return DefinitionGrounder(DEFINITIONS, lambda record: stats) + + +def test_presence_and_absence_against_measurements(): + cd8 = record("CL:0000625", "CD8-positive, alpha-beta T cell") + fine = {"CD8A": (0.8, 2.0), "CD8B": (0.6, 1.5), "CD4": (0.05, -0.2)} + assert grounder(fine).check(cd8) == [] + no_cd8 = grounder({**fine, "CD8A": (0.02, -0.5), "CD8B": (0.04, -0.3)}).check(cd8) + assert [f.rule_id for f in no_cd8] == ["BEV026"] and "detected in only 4%" in no_cd8[0].message + assert grounder({**fine, "CD8A": (0.02, -0.5)}).check(cd8) == [] # one part of the complex is enough + cd4 = grounder({**fine, "CD4": (0.7, 1.1)}).check(cd8) + assert [f.rule_id for f in cd4] == ["BEV026"] and "lacking CD4 molecule (CD4), but CD4 is detected in 70%" in cd4[0].message + assert grounder({**fine, "CD4": (0.7, 0.1)}).check(cd8) == [] # not higher than elsewhere + assert grounder({"CD4": (0.9, 2.0)}).check(record("CL:0000084", "T cell")) == [] # nothing defined + assert grounder({}).check(cd8) == [] and grounder(None).check(cd8) == [] # nothing measured + assert grounder({"CD8A": (0.01, 0.0)}).name == "definitions:CL@cl/releases/2026-01-01/cl.obo" + + +def test_definition_findings_send_a_record_to_review(): + cd8 = record("CL:0000625", "CD8-positive, alpha-beta T cell") + report = validate_record(cd8, grounders=[grounder({"CD8A": (0.8, 2.0), "CD4": (0.9, 1.5)})]) + assert report["overall_status"] == "review_required" and {f["rule_id"] for f in report["findings"]} == {"BEV026"} diff --git a/tests/test_singlecell_case.py b/tests/test_singlecell_case.py index dc7eee3..c46b072 100644 --- a/tests/test_singlecell_case.py +++ b/tests/test_singlecell_case.py @@ -111,7 +111,7 @@ def test_problems_are_looked_up_directly(case): assert loop.gene_token(" CD3E;x=1 ") == "CD3E_x_1" -@pytest.mark.parametrize("folder", ["celltype-pilot", "celltype-test"]) +@pytest.mark.parametrize("folder", ["celltype-pilot", "celltype-test", "celltype-external"]) def test_scores_replay_from_committed_episodes(folder, tmp_path): committed = ROOT / "evaluation" / "llm_benchmark" / "results" / folder (tmp_path / "episodes.jsonl").write_bytes((committed / "episodes.jsonl").read_bytes()) @@ -136,3 +136,28 @@ def test_protocol_2_drops_the_reference_check_and_narrows_contradicting_markers( assert not any(g.name.startswith("reference:") for g in case.validator().grounders) assert "any that argue against it" in loop.prompt(task, 1) and "Only if some of its markers" in loop.prompt(task) assert loop.prompt(task, 1).split("Which cell type")[0] == loop.prompt(task).split("Which cell type")[0] + + +def test_protocol_3_adds_the_definition_check(case): + assert case.validator(protocol=3).grounders[-1].name.startswith("definitions:CL@") + assert not any(g.name.startswith("definitions:") for g in case.validator(protocol=2).grounders) + task = hepatocytes(case) + record = loop.record(case, task, answer("CL:0000182", "hepatocyte", "APOC3")) + panel = case.measure(record) + assert panel and all(0 <= pct <= 1 for pct, _ in panel.values()) + t_cell = loop.record(case, task, answer("CL:0000625", "CD8-positive, alpha-beta T cell", "APOC3")) + findings = case.validator(protocol=3).grounders[-1].check(t_cell) + assert [f.rule_id for f in findings] == ["BEV026"] and "CD8" in findings[0].message # no CD8 in hepatocytes + assert {t["split"] for t in case.tasks.values()} == {"pilot", "test", "external"} + assert loop.prompt(task, 3) == loop.prompt(task, 2) + + +def test_gate_without_definitions_admits_what_only_the_definition_check_stopped(): + row = {"calls": [{"answer": answer("CL:0000625", "CD8-positive, alpha-beta T cell", "CD8A")}], + "attempts": [{"status": "review_required", "codes": ["BEV026"], "to_expert": False}]} + assert loop.view(row, "gate")["answer"] is None + assert loop.view(row, "gate_without_definitions")["answer"]["cell_type_id"] == "CL:0000625" + row["attempts"][0]["codes"] = ["BEV017", "BEV026"] + assert loop.view(row, "gate_without_definitions")["answer"] is None + assert [n for n, _ in loop.views_for(3)] == ["model", "gate", "gate_without_definitions", "loop"] + assert loop.views_for(2) == loop.VIEWS