diff --git a/CHANGELOG.md b/CHANGELOG.md index 3495ff3..64f7744 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,16 @@ ## Unreleased +- 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 + answers gave a Cell Ontology ID that belongs to another term; none was admitted. Wrong or invalid + annotations fell from 43% of answers to 18% of those admitted behind the gate, at the cost of half + the annotations going to a person. The ASCT+B cross-check proved to be noise as a conflict source. + Protocol 2 (contradicting markers only for mixed clusters, no ASCT+B), frozen before the 46 held-out + clusters were run: identifier errors in 62 of 276 answers, none admitted; in the feedback loop, + answers compatible with the authors' term rose from 176 to 205, wrong or invalid fell from 36% of + answers to 20% of those admitted, and 8% of annotations went to a person. - Add generic grounders that check what a record cites against pinned reference releases, with messages that say what to fix: `OntologyGrounder` (ontology terms: existence, obsoletion, label, kind), `GeneGrounder` (HGNC symbols, previous symbols and aliases), `VariantGrounder` (HGVS form, diff --git a/evaluation/llm_benchmark/README.md b/evaluation/llm_benchmark/README.md index 7244023..e071365 100644 --- a/evaluation/llm_benchmark/README.md +++ b/evaluation/llm_benchmark/README.md @@ -235,6 +235,116 @@ What this shows: - One run, 18 tasks and a changed prompt: model-level numbers move between runs (GPT-5.6-Luna's first submissions went from 0 to 3 invalid citations), so read these as directions, not rates. +## Scenario 3: single-cell cell-type annotation + +The same loop outside the literature: each model annotates a cluster of a real single-cell dataset from +its top 20 marker genes, giving a Cell Ontology term and the markers that support it or argue against it +([case](../../examples/singlecell_celltype/README.md), [celltype_loop.py](celltype_loop.py), +[results](results/celltype-pilot/summary.md)). The reference is each study's own author annotation. +Answers are compared with it through the ontology: exact, coarser (an ancestor), finer (a descendant) or +wrong; an identifier that is not a current cell-type term is invalid. + +Bioevidence checks each answer with generic grounders: +- each cited marker must be one of the cluster's markers in the pinned table; +- the Cell Ontology term must exist, be current, be a cell type and match its label; +- gene symbols must be approved HGNC symbols; +- ASCT+B markers are cross-checked against the Cell Ontology's disjoint lineages. + +Fixable findings go back to the model, at most three answers. A record with the model's own contradicting +markers (BEV004) or an ASCT+B conflict (BEV025) goes to a person. Pilot, 24 clusters from six datasets, six +models: + +| Configuration | Annotated | Exact | Coarser | Finer | Wrong or invalid | Answers with an identifier or marker error | Routed to a person | +|---|---:|---:|---:|---:|---:|---:|---:| +| Model alone | 138/144 | 41 | 21 | 17 | 59 | 38/138 | 0 | +| Model + bioevidence gate | 56/144 | 32 | 13 | 1 | 10 | 0/56 | 82 | +| Model + bioevidence feedback loop | 67/144 | 35 | 13 | 4 | 15 | 0/67 | 71 | + +What this shows: + +- **Identifiers.** Models write Cell Ontology identifiers that belong to other terms. In 35 of 138 first + answers the ID and the label disagreed, e.g.: + - "Paneth cell" under CL:0000147 (pigment cell); + - "hepatic sinusoidal endothelial cell" under CL:0000639 (a basophil of the pituitary); + - "intestinal crypt stem cell" under CL:0002089 (a mouse ILC term). + + By model: Claude Haiku 4.5 and GPT-5.6-Luna each 12 of 23 answers with an identifier or marker error, + Gemini 3.8 Flash 7, Gemini 3.1 Pro 4, GPT-6-Astra 2, Claude Opus 5.5 1. A knowledge base stores the ID, + so these errors would enter it silently. + + None was admitted. The fix does not depend on the model: the finding names the term the label belongs + to. In the loop 11 were fixed and admitted; 26 went to a person, most because the revised answer still + carried its own contradicting markers. +- **Cell types.** Bioevidence cannot tell whether a cluster is an ILC2 or a Th2 cell. What its routing did + was concentrate wrong answers: 59 of 138 first answers were wrong or invalid (43%), against 10 of 56 + admitted behind the gate (18%) and 15 of 67 in the loop (22%). +- **Model-declared conflict is the strongest signal.** Answers in which the model cited a marker against + its own answer were wrong 63% of the time (39 of 62), against 26% (20 of 76) without. One example: + - Claude Haiku 4.5 called a pericyte cluster smooth muscle; + - it added that CCL2 and IGFBP7 suggest pericytes; + - that record went to a person. +- **The ASCT+B cross-check was mostly noise.** It fired on 23 first answers, 13 of them wrong, but for + reasons that do not hold. For example, CD44 cited for pancreatic ductal cells was flagged because + ASCT+B happens to list CD44 only for a lung T cell. FCER1G for NK cells was flagged because it is listed + for basophils and neutrophils. ASCT+B biomarker lists say where a gene is a marker, not that it is + specific. Disjointness removed the within-lineage alarms, but a partial reference still cannot support + "only". This protocol should not use it as a conflict source; the generic grounder stays, for + references that state specificity or exclusion. +- **The cost is the review load:** half of the annotations went to a person. Models cited markers against + their own answer in 64 of 144 first answers, because the prompt asked for "any that argue against it". + That is honest, and it carries the signal above, but it is more than a curation team can review. + +### Held-out test split (protocol 2) + +Two lessons from the pilot became protocol 2, committed before the 46 held-out clusters were run: + +- contradicting markers are asked for only when some clearly point to another cell type (a mixed cluster, + doublets); +- the ASCT+B cross-check is left out. + +Nothing was changed after the results were seen ([results](results/celltype-test/summary.md)). Six models, +46 clusters: + +| Configuration | Annotated | Exact | Coarser | Finer | Wrong or invalid | Answers with an identifier or marker error | Routed to a person | +|---|---:|---:|---:|---:|---:|---:|---:| +| Model alone | 276/276 | 117 | 33 | 26 | 100 | 63/276 | 0 | +| Model + bioevidence gate | 198/276 | 113 | 27 | 21 | 37 | 0/198 | 78 | +| Model + bioevidence feedback loop | 255/276 | 138 | 31 | 36 | 50 | 0/255 | 21 | + +What this shows: + +- **The loop makes the annotations better, not only safer.** + - Answers compatible with the authors' term (exact, coarser or finer) rose from 176 to 205. + - Exact matches rose from 117 to 138. + - Wrong or invalid fell from 100 (36% of answers) to 50 admitted (20% of what was admitted). + - Only 21 of 276 (8%) went to a person, against 71 of 144 (49%) in the pilot. +- **Most of the gain is identifiers.** + - 62 first answers gave a Cell Ontology ID that does not match its label, or is not a current cell type. + - By model: Claude Haiku 4.5 had 23 of 46 answers with an identifier or marker error, GPT-5.6-Luna 16, + Gemini 3.1 Pro 10, Gemini 3.8 Flash 9, Claude Opus 5.5 4, GPT-6-Astra 1. + - The finding names the term the label belongs to, so the model can correct the ID to what it meant. + - Outcome: 56 of the 62 were fixed and admitted (25 exact, 14 finer, 4 coarser, 13 wrong); 3 went to a + person and 3 were still rejected after three answers. + - None of these identifier errors depends on which model made it, and none was admitted. +- **The model's own conflict is now a sharp signal.** + - Only 17 first answers cited markers against their own answer (protocol 1: 64 of 144). + - 14 of those 17 were wrong (82%), against 33% of the rest. + - In the loop, 13 of the 18 records sent to an expert were wrong. +- **What remains is semantic, and much of it is the reference.** 50 admitted answers disagree with the + authors' term with valid identifiers and real markers. + - 7 called the duodenal cluster the authors label "B cell" a plasma cell. Its top markers are JCHAIN and + MZB1, so the models are probably right, but in the Cell Ontology a plasma cell is not a B cell. + - 11 called a "mesenchymal cell" a fibroblast or pancreatic stellate cell. + - Others are real fine-grained confusions: NK T cells called gamma-delta T cells (5), memory CD4 T cells + called naive (5), an ILC3 called a Th17 cell. + + Bioevidence cannot see these; expert labels and an audit of admitted records (#23, #24) can. + +Limits: +- Author labels are the reference. Some are coarse ("stem cell", "precursor cell") and some debatable, so + "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. + ## Semantic checks (#31) Grounding cannot tell whether a verbatim quote supports the claim, so two semantic layers were diff --git a/evaluation/llm_benchmark/agent_loop.py b/evaluation/llm_benchmark/agent_loop.py index 22635c2..8027d00 100644 --- a/evaluation/llm_benchmark/agent_loop.py +++ b/evaluation/llm_benchmark/agent_loop.py @@ -94,26 +94,26 @@ def wsl_path(path: Path) -> str: return f"/mnt/{text[0].lower()}{text[2:]}" if re.match(r"^[A-Za-z]:/", text) else text -def call_model(key: str, prompt: str, timeout: int = 600) -> tuple[dict, list[str]]: - """One fresh CLI call answering STEP_SCHEMA, through the WSL installs of Claude Code, Codex and Antigravity.""" +def call_model(key: str, prompt: str, timeout: int = 600, schema: dict | None = None) -> tuple[dict, list[str]]: + """One fresh CLI call answering `schema` (default STEP_SCHEMA), through the WSL installs of Claude Code, Codex and Antigravity.""" spec = run_models.MODELS[key] with tempfile.TemporaryDirectory(prefix="agent-", dir=Path("C:/t/agent-work")) as directory: work = Path(directory) - (work / "schema.json").write_text(json.dumps(STEP_SCHEMA), encoding="utf-8") + (work / "schema.json").write_text(json.dumps(schema or STEP_SCHEMA), encoding="utf-8") (work / "prompt.txt").write_text(prompt, encoding="utf-8") - schema, folder = wsl_path(work / "schema.json"), wsl_path(work) + schema_file, folder = wsl_path(work / "schema.json"), wsl_path(work) if spec["cli"] == "claude": # the WSL install; the Windows CLI's login can expire mid-run command = ("PATH=$(ls -d ~/.nvm/versions/node/*/bin | tail -1):$PATH claude -p --model " f"{spec['model']} --tools '' --strict-mcp-config --no-session-persistence --output-format json " - f"--json-schema \"$(cat {schema})\" < prompt.txt") + f"--json-schema \"$(cat {schema_file})\" < prompt.txt") parse = run_models.claude_parse elif spec["cli"] == "codex": disable = " ".join(f"--disable {f}" for f in run_models.CODEX_DISABLED) command = (f"codex exec -m {spec['model']} --ignore-user-config {disable} --sandbox read-only " - f"--skip-git-repo-check --ephemeral --json --output-schema {schema} -o last.json - < prompt.txt") + f"--skip-git-repo-check --ephemeral --json --output-schema {schema_file} -o last.json - < prompt.txt") parse = run_models.codex_parse else: - command = (f"agy --model {spec['model']} --output-format stream-json --json-schema {schema} --sandbox " + command = (f"agy --model {spec['model']} --output-format stream-json --json-schema {schema_file} --sandbox " f"--print-timeout {timeout}s --print \"$(cat prompt.txt)\"") parse = run_models.gemini_parse done = subprocess.run(["wsl.exe", "-e", "bash", "-lc", f"export PATH=$HOME/.local/bin:$PATH; cd {folder} && {command}"], diff --git a/evaluation/llm_benchmark/celltype_loop.py b/evaluation/llm_benchmark/celltype_loop.py new file mode 100644 index 0000000..ecd68fa --- /dev/null +++ b/evaluation/llm_benchmark/celltype_loop.py @@ -0,0 +1,409 @@ +"""Single-cell cell-type annotation by six models, alone and in bioevidence's feedback loop. + + uv run --frozen python evaluation/llm_benchmark/celltype_loop.py run --split pilot --output C:/t/celltype-pilot + uv run --frozen python evaluation/llm_benchmark/celltype_loop.py collect --output C:/t/celltype-pilot \ + --results evaluation/llm_benchmark/results/celltype-pilot + uv run --frozen python evaluation/llm_benchmark/celltype_loop.py score --results evaluation/llm_benchmark/results/celltype-pilot + +Each task shows a model the top 20 marker genes of one cluster of a real single-cell dataset (the cell types +its authors annotated, from `examples/singlecell_celltype`) and asks for the cluster's Cell Ontology term and +the marker genes that support or argue against it. The answer is built into an evidence record and validated +with five grounders: the pinned marker table (a cited marker must be one of this cluster's), the Cell Ontology +release (the term exists, is current, is a cell type and matches its label), HGNC (approved symbols), the +source bytes, and HuBMAP ASCT+B (a supporting marker that the reference assigns only to unrelated cell +types sends the record to an expert). The episode is `bioevidence_validator.feedback.revise`: fixable +findings go back to the model, at most three answers; conflicts go to an expert unchanged. + +Two protocols, each fixed before the split it was run on. Protocol 1 (the pilot) asked for markers that argue +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. + +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 +grounders: each answer is compared with the authors' term using the ontology (exact, coarser, finer or +wrong), and its identifiers and markers are looked up directly. +""" +from __future__ import annotations + +import argparse +import concurrent.futures +import datetime as dt +import hashlib +import json +import subprocess +import sys +import threading +import time +from pathlib import Path +from typing import Any + +from bioevidence_validator import feedback +from bioevidence_validator.crosscheck import ReferenceGrounder +from bioevidence_validator.engine import RecordValidator +from bioevidence_validator.grounding import SnapshotStore, SourceBytesGrounder +from bioevidence_validator.identifiers import GeneGrounder, Genes, Ontology, OntologyGrounder, _label_key +from bioevidence_validator.tables import TableGrounder, parse_table + +ROOT = Path(__file__).resolve().parent +sys.path.insert(0, str(ROOT)) +import agent_loop # noqa: E402 +import run_models # noqa: E402 +import score_claims # noqa: E402 + +CASE = ROOT.parents[1] / "examples" / "singlecell_celltype" +SOURCES = CASE / "sources" +ROUNDS = 3 +DECISIONS, STANCES = ["annotate", "uncertain"], ["supports", "contradicts"] +FIELDS = ["decision", "cell_type_id", "cell_type_label", "markers", "rationale"] +SCHEMA = { + "type": "object", "additionalProperties": False, "required": FIELDS, + "properties": { + "decision": {"type": "string", "enum": DECISIONS}, + "cell_type_id": {"type": "string"}, "cell_type_label": {"type": "string"}, + "markers": {"type": "array", "items": {"type": "object", "additionalProperties": False, + "required": ["gene", "stance"], + "properties": {"gene": {"type": "string"}, + "stance": {"type": "string", "enum": STANCES}}}}, + "rationale": {"type": "string"}, + }, +} +PROMPT_V1 = """This cluster comes from a single-cell RNA-seq dataset of {species} {tissue} ({assay}). Its top marker \ +genes, ranked by log fold change against all other cells of the dataset (logfc: difference of mean log-normalised \ +expression; pct_in and pct_out: fraction of cells expressing the gene inside and outside the cluster): + +gene\tlogfc\tpct_in\tpct_out +{table} + +Which cell type is this cluster? Give its Cell Ontology term (the CL identifier and the term's name) and the \ +marker genes of this cluster that support it, and any that argue against it. 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.""" +PROMPT = """This cluster comes from a single-cell RNA-seq dataset of {species} {tissue} ({assay}). Its top marker \ +genes, ranked by log fold change against all other cells of the dataset (logfc: difference of mean log-normalised \ +expression; pct_in and pct_out: fraction of cells expressing the gene inside and outside the cluster): + +gene\tlogfc\tpct_in\tpct_out +{table} + +Which cell type is this cluster? Give its Cell Ontology term (the CL identifier and the term's name) and the \ +marker genes of this cluster that support it (stance "supports"). Only if some of its markers clearly point to a \ +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} +REVISION = """{prompt} + +Your previous answer: +{previous} + +A validator checked it against the pinned Cell Ontology release, the HGNC gene symbols and this cluster's marker \ +table, and did not accept it: +{reasons} + +Revise your answer.""" + + +def load_jsonl(path: Path) -> list[dict]: + return [json.loads(line) for line in path.read_text(encoding="utf-8").splitlines() if line.strip()] + + +class Case: + """The pinned case: tasks, snapshots, and the references the grounders and the scorer read.""" + + def __init__(self) -> None: + self.manifest = json.loads((SOURCES / "manifest.json").read_text(encoding="utf-8")) + self.store = SnapshotStore.from_directory(SOURCES / "snapshots") + self.ontology = Ontology.from_obo(self.store.get(self.manifest["cell_ontology"]["sha256"]) or b"") + self.genes = Genes.from_hgnc(self.store.get(self.manifest["hgnc"]["sha256"]) or b"", + self.manifest["hgnc"]["retrieved"]) + self.reference = self.store.get(self.manifest["asctb"]["sha256"]) or b"" + 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} + + def validator(self, protocol: int = 2) -> RecordValidator: + grounders: list = [SourceBytesGrounder(self.store), TableGrounder(self.store, ["marker_gene"]), + OntologyGrounder([self.ontology], roots={"cell_type": ["CL:0000000"]}), GeneGrounder(self.genes)] + if protocol == 1: + grounders.append(ReferenceGrounder.from_table(self.reference, label="ASCT+B", evidence_key="gene", + relation="marker_of", ontology=self.ontology, + conflict="disjoint")) + return RecordValidator(profile=CASE / "profile.yaml", grounders=grounders) + + def markers(self, task: dict) -> set[str]: + return {r["gene"] for r in self.tables[task["markers_sha256"]] if r["cluster"] == task["cluster"]} + + +def prompt(task: dict, protocol: int = 2) -> str: + table = "\n".join(f"{m['gene']}\t{m['logfc']}\t{m['pct_in']}\t{m['pct_out']}" for m in task["markers"]) + return PROMPTS[protocol].format(species=task["species"], tissue=task["tissue"], assay=task["assay"], table=table) + + +def check_answer(answer: Any) -> dict: + if not isinstance(answer, dict) or set(answer) != set(FIELDS) or answer["decision"] not in DECISIONS: + raise ValueError("invalid answer") + if not isinstance(answer["markers"], list) or not all( + isinstance(m, dict) and set(m) == {"gene", "stance"} and isinstance(m["gene"], str) and m["stance"] in STANCES + for m in answer["markers"]): + raise ValueError("invalid markers") + return answer + + +def gene_token(text: str) -> str: + return text.strip().replace(";", "_").replace("=", "_") or "_" + + +def record(case: Case, task: dict, answer: dict) -> dict | None: + """The answer as an evidence record, or None when the model does not annotate.""" + if answer["decision"] != "annotate" or not answer["cell_type_id"].strip(): + return None + sha = task["markers_sha256"] + items, lines = [], {} + for n, marker in enumerate(answer["markers"], start=1): + items.append({"id": f"bioev:marker-{n}", "source_artifact_id": "bioev:markers", + "locator": f"cluster={task['cluster']};gene={gene_token(marker['gene'])}", + "evidence_type": "marker_gene", "extraction_method": "llm_extraction", "scope": ["NCBITaxon:9606"]}) + lines.setdefault(marker["stance"], []).append(items[-1]["id"]) + return { + "record_id": f"bioev:celltype-{task['task_id']}", "profile_id": "singlecell-celltype", + "statement": {"id": f"bioev:celltype-statement-{task['task_id']}", + "subject": {"id": f"cluster:{task['dataset']}/{task['cluster']}", + "label": f"cluster {task['cluster']} of the {task['tissue']} dataset", + "entity_type": "cell_cluster"}, + "predicate": "has_cell_type", + "object": {"id": answer["cell_type_id"].strip(), "label": answer["cell_type_label"].strip(), + "entity_type": "cell_type"}, + "scope": ["NCBITaxon:9606"], "statement_status": "proposed", + "evidence_lines": [{"id": f"bioev:line-{d}", "direction": d, "evidence_item_ids": ids} + for d, ids in lines.items()]}, + "source_artifacts": [{"id": "bioev:markers", "title": f"Marker table of the {task['dataset']} dataset", + "source_type": "dataset_snapshot", "uri": f"urn:sha256:{sha}", + "version": case.versions[sha], "retrieved_at": "2026-09-30T00:00:00Z", + "sha256": sha, "observed_sha256": sha}], + "evidence_items": items, "adjudications": [], "requested_uses": ["research_summary"], + } + + +def episode(key: str, task: dict, case: Case, protocol: int = 2) -> dict: + validator, calls, last = case.validator(protocol), [], {} + + def propose(reasons: list[str]) -> dict | None: + text = prompt(task, protocol) if not reasons else REVISION.format( + prompt=prompt(task, protocol), previous=json.dumps(last["answer"], ensure_ascii=False), + reasons="\n".join(f"- {r}" for r in reasons)) + started, answer, error, tools = time.monotonic(), None, None, [] + for _ in range(2): # one retry on an invalid answer or a tool call of the CLI's own + try: + answer, tools = agent_loop.call_model(key, text, schema=SCHEMA) + answer = check_answer(answer) + if not tools: + break + except (ValueError, KeyError, OSError, subprocess.TimeoutExpired, json.JSONDecodeError) as exc: + answer, error = None, f"{type(exc).__name__}: {exc}"[:300] + calls.append({"answer": answer, "error": error if answer is None else None, "cli_tools": tools, + "feedback": reasons, "seconds": round(time.monotonic() - started, 1)}) + if answer is None: + return None + last["answer"] = answer + return record(case, task, answer) + + attempts = feedback.revise(propose, validator, rounds=ROUNDS) + return {"model": key, "task_id": task["task_id"], **({"protocol": protocol} if protocol != 1 else {}), "calls": calls, + "attempts": [{"status": a.report["overall_status"], + "codes": sorted({f["rule_id"] for f in a.report["findings"]}), + "to_expert": feedback.to_expert(a.report), + "findings": [{"rule_id": f["rule_id"], "where": feedback.where(a.record, f["field_path"]), + "message": f["message"]} for f in a.report["findings"]], + "evidence": len(a.record["evidence_items"])} for a in attempts], + "finished_at": dt.datetime.now(dt.UTC).isoformat()} + + +def run(output: Path, split: str, models: list[str], workers: int, limit: int | None, protocol: int = 2) -> int: + case = Case() + tasks = [t for t in case.tasks.values() if t["split"] == split][:limit] + Path("C:/t/agent-work").mkdir(parents=True, exist_ok=True) + jobs = [(key, task, output / "episodes" / key / f"{task['task_id']}.json") for task in tasks for key in models] + jobs = [job for job in jobs if not job[2].exists()] + print(f"{len(jobs)} episode(s) to run", flush=True) + # Claude models share the operator's Claude usage limit: one episode at a time. + slots = {key: threading.Semaphore(1 if run_models.MODELS[key]["cli"] == "claude" else workers) for key in models} + + def work(job): + key, task, path = job + with slots[key]: + result = episode(key, task, case, protocol) + path.parent.mkdir(parents=True, exist_ok=True) + path.write_text(json.dumps(result, indent=2, ensure_ascii=False) + "\n", encoding="utf-8") + return result + + with concurrent.futures.ThreadPoolExecutor(max_workers=workers * len(models)) as pool: + for n, result in enumerate(pool.map(work, jobs), start=1): + final = result["attempts"][-1]["status"] if result["attempts"] else "no record" + errors = sum(c["error"] is not None for c in result["calls"]) + print(f"[{n}/{len(jobs)}] {result['model']} {result['task_id']}: {len(result['calls'])} call(s), " + f"{len(result['attempts'])} record(s), final {final}, {errors} error(s)", flush=True) + return 0 + + +def collect(output: Path, results: Path) -> None: + rows = [json.loads(p.read_text(encoding="utf-8")) for p in sorted((output / "episodes").glob("*/*.json"))] + for row in rows: + row.pop("finished_at", None) + results.mkdir(parents=True, exist_ok=True) + score_claims.write_jsonl(results / "episodes.jsonl", rows) + score(results) + + +# Scoring, independent of the grounders: direct lookups in the pinned releases and the marker table. + +def outcome(case: Case, truth: str, answer: dict) -> str: + term = case.ontology.terms.get(answer["cell_type_id"].strip()) + if term is None or term.obsolete or "CL:0000000" not in case.ontology.ancestors(term.id): + return "invalid" + if term.id == truth: + return "exact" + if term.id in case.ontology.ancestors(truth): + return "coarser" + if truth in case.ontology.ancestors(term.id): + return "finer" + return "wrong" + + +def problems(case: Case, task: dict, answer: dict) -> list[str]: + found = [] + term = case.ontology.terms.get(answer["cell_type_id"].strip()) + if term is None: + found.append("unknown_id") + elif term.obsolete: + found.append("obsolete_id") + elif "CL:0000000" not in case.ontology.ancestors(term.id): + found.append("not_a_cell_type") + elif _label_key(answer["cell_type_label"]) not in {_label_key(t) for t in [term.name, *term.synonyms]}: + found.append("label_mismatch") + markers = case.markers(task) + genes = [m["gene"].strip() for m in answer["markers"]] + if any(g not in case.genes.approved for g in genes): + found.append("unapproved_symbol") + if any(g not in markers for g in genes): + found.append("marker_not_in_data") + if not genes: + found.append("no_markers") + return found + + +VIEWS = [("model", "Model alone (first answer)"), ("gate", "Model + bioevidence gate (first answer)"), + ("loop", "Model + bioevidence feedback loop (last answer)")] + + +def view(row: dict, name: str) -> dict: + """What a view delivers: an answer (or none), and whether it went to a person.""" + calls, attempts = row["calls"], row["attempts"] + answered = [c["answer"] for c in calls if c["answer"] is not None] + if name == "model": + first = calls[0]["answer"] if calls else None + 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 + annotating = [a for a in answered if a["decision"] == "annotate" and a["cell_type_id"].strip()] + if chosen["status"] == "admitted": + return {"answer": annotating[index], "routed": False, "expert": False} + return {"answer": None, "routed": True, "expert": chosen["to_expert"]} + + +def score(results: Path) -> dict: + case = Case() + truth = {t["task_id"]: t for t in load_jsonl(SOURCES / "truth.jsonl")} + rows = load_jsonl(results / "episodes.jsonl") + models = [m for m in score_claims.MODEL_NAMES if any(r["model"] == m for r in rows)] + + def metrics(mine: list[dict], name: str) -> dict: + views = [(r, view(r, name)) for r in mine] + delivered = [(r, v) for r, v in views if v["answer"] is not None] + kinds = [outcome(case, truth[r["task_id"]]["term"], v["answer"]) for r, v in delivered] + issues = [problems(case, case.tasks[r["task_id"]], v["answer"]) for r, v in delivered] + rate = score_claims.rate + return {"tasks": len(mine), "answered": rate(len(delivered), len(mine)), + **{k: rate(kinds.count(k), len(mine)) for k in ("exact", "coarser", "finer", "wrong", "invalid")}, + "compatible": rate(sum(k in ("exact", "coarser", "finer") for k in kinds), len(mine)), + "with_identifier_or_marker_error": rate(sum(bool(i) for i in issues), len(delivered)), + **{f"error_{p}": rate(sum(p in i for i in issues), len(delivered)) + for p in ("unknown_id", "obsolete_id", "not_a_cell_type", "label_mismatch", "unapproved_symbol", + "marker_not_in_data", "no_markers")}, + "routed_to_a_person": rate(sum(v["routed"] for _, v in views), len(mine)), + "to_an_expert_as_conflict": rate(sum(v["expert"] for _, v in views), len(mine))} + + split = case.tasks[rows[0]["task_id"]]["split"] if rows else "pilot" + protocol = rows[0].get("protocol", 1) if rows else 2 + 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), + "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()} + (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") + print(render(summary)) + return summary + + +def render(summary: dict) -> str: + f = score_claims.fraction + protocol = int(summary["benchmark"].rsplit("v", 1)[1]) + lines = [f"# Single-cell cell-type annotation ({summary['split']} set" + + (f", protocol {protocol})" if protocol != 1 else ")"), "", + "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 |", "|---|---|---:|---:|---:|---:|---:|---:|---:|---:|"] + 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: + 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'])} | " + f"{f(m['with_identifier_or_marker_error'])} | {f(m['routed_to_a_person'])} |") + p = summary["pooled"]["model"] + lines += ["", "Errors in the models' first answers (all models): " + + ", ".join(f"{k.removeprefix('error_').replace('_', ' ')} {f(p[k])}" for k in sorted(p) + if k.startswith("error_")) + ".", + "", 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()) + ".", ""] + return "\n".join(lines) + + +def main(argv: list[str] | None = None) -> int: + parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) + 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("--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) + c = steps.add_parser("collect") + c.add_argument("--output", type=Path, required=True) + c.add_argument("--results", type=Path, required=True) + s = steps.add_parser("score") + s.add_argument("--results", type=Path, required=True) + args = parser.parse_args(argv) + if args.step == "collect": + collect(args.output, args.results) + return 0 + if args.step == "score": + score(args.results) + return 0 + return run(args.output, args.split, args.models, args.workers, args.limit, args.protocol) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/evaluation/llm_benchmark/results/celltype-pilot/episodes.jsonl b/evaluation/llm_benchmark/results/celltype-pilot/episodes.jsonl new file mode 100644 index 0000000..21b2628 --- /dev/null +++ b/evaluation/llm_benchmark/results/celltype-pilot/episodes.jsonl @@ -0,0 +1,144 @@ +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'liver sinusoidal endothelial cell' is not the name of CL:0002138 ('endothelial cell of lymphatic vessel'). 'liver sinusoidal endothelial cell' is the name of CL:1000398 (endothelial cell of hepatic sinusoid).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0002138", "cell_type_label": "liver sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "CLDN5", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "IL6ST", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TIMP1", "stance": "contradicts"}, {"gene": "TIMP3", "stance": "contradicts"}, {"gene": "FCN2", "stance": "contradicts"}, {"gene": "FCN3", "stance": "contradicts"}, {"gene": "IFI27", "stance": "contradicts"}], "rationale": "The cluster shows strong endothelial cell markers, particularly CLDN5 (claudin-5, tight junction protein with very high specificity: 0.713 in-cluster vs 0.020 out-of-cluster) and TFPI (tissue factor pathway inhibitor), which are canonical endothelial markers. Additional supporting markers include TM4SF1 (tetraspanin involved in endothelial function), HSPG2 (perlecan, a key ECM component of endothelial basement membrane), IL6ST, and GNG11. In the liver context (caudate lobe), this profile is consistent with liver sinusoidal endothelial cells (LSECs), which form the specialized fenestrated endothelium of hepatic sinusoids. The angiogenesis-related markers ID1 and ID3 further support endothelial identity. However, TIMP1 and TIMP3 (tissue inhibitors of metalloproteinases) are more typical of fibroblasts, and FCN2/FCN3 (ficolins) and IFI27 (interferon-induced) are more characteristic of monocytes/macrophages or immune activation. These contradicting markers may reflect either mixed populations or LSECs' known immune surveillance functions, but the preponderance of endothelial-specific markers strongly supports the endothelial classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.9}, {"answer": {"cell_type_id": "CL:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "CLDN5", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "IL6ST", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TIMP1", "stance": "contradicts"}, {"gene": "TIMP3", "stance": "contradicts"}, {"gene": "FCN2", "stance": "contradicts"}, {"gene": "FCN3", "stance": "contradicts"}, {"gene": "IFI27", "stance": "contradicts"}], "rationale": "The cluster shows strong endothelial cell markers, particularly CLDN5 (claudin-5, tight junction protein with high specificity: 0.713 in-cluster vs 0.020 out-of-cluster) and TFPI (tissue factor pathway inhibitor), which are canonical endothelial markers. Additional supporting markers include TM4SF1 (tetraspanin involved in endothelial function), HSPG2 (perlecan, a key ECM component of endothelial basement membrane), IL6ST, and GNG11. In the liver context (caudate lobe), this profile is consistent with hepatic sinusoidal endothelial cells (HSECs), which form the specialized fenestrated endothelium of hepatic sinusoids. The angiogenesis-related markers ID1 and ID3 further support endothelial identity. However, TIMP1 and TIMP3 are more typical of fibroblasts, and FCN2/FCN3 and IFI27 are more characteristic of immune cells, likely reflecting HSECs' known immune surveillance functions."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'liver sinusoidal endothelial cell' is not the name of CL:0002138 ('endothelial cell of lymphatic vessel'). 'liver sinusoidal endothelial cell' is the name of CL:1000398 (endothelial cell of hepatic sinusoid)."], "seconds": 11.7}], "model": "claude-haiku", "task_id": "ct-04aaea9940"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "FABP2", "stance": "supports"}, {"gene": "SI", "stance": "supports"}, {"gene": "SLC5A1", "stance": "supports"}, {"gene": "SLC26A3", "stance": "supports"}, {"gene": "ANPEP", "stance": "supports"}, {"gene": "ALDOB", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "APOA4", "stance": "supports"}, {"gene": "APOB", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "CES2", "stance": "supports"}, {"gene": "TMPRSS15", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "CDHR5", "stance": "supports"}], "rationale": "The marker profile is highly consistent with enterocytes. High-confidence brush border markers (FABP2, SI, SLC5A1, ANPEP) combined with elevated apolipoproteins and lipid metabolism genes reflect the enterocyte's roles in nutrient absorption and lipoprotein synthesis. Expression in essentially all cells in the cluster (pct_in ≈ 0.99-1.0) and much lower expression outside (pct_out typically 0.3-0.9) indicates strong cluster enrichment. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.2}], "model": "claude-haiku", "task_id": "ct-085bedbfa5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'Paneth cell' is not the name of CL:0000147 ('pigment cell'). 'Paneth cell' is the name of CL:0000510 (paneth 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:0000147", "cell_type_label": "Paneth cell", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "OLFM4", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}], "rationale": "REG1A, OLFM4, DMBT1, SPINK1, and REG3A are canonical Paneth cell markers expressed at very high logfc with high specificity (low pct_out relative to their high pct_in). These genes encode antimicrobial peptides and secretory proteins characteristic of Paneth cells, the specialized secretory cells at the base of intestinal crypts. AGR2 supports this profile as a protein disulfide isomerase involved in secretory cell function. The metallothionein genes are consistent with the oxidative environment of highly active secretory cells. No contradictory markers are present.\""}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.6}, {"answer": {"cell_type_id": "CL:0000510", "cell_type_label": "paneth cell", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "OLFM4", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}], "rationale": "REG1A, OLFM4, DMBT1, SPINK1, and REG3A are canonical Paneth cell markers expressed at very high logfc with high specificity (low pct_out relative to their high pct_in). These genes encode antimicrobial peptides and secretory proteins characteristic of Paneth cells, the specialized secretory cells at the base of intestinal crypts. AGR2 supports this profile as a protein disulfide isomerase involved in secretory cell function. The metallothionein genes are consistent with the oxidative environment of highly active secretory cells. No contradictory markers are present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'Paneth cell' is not the name of CL:0000147 ('pigment cell'). 'Paneth cell' is the name of CL:0000510 (paneth cell)."], "seconds": 9.3}], "model": "claude-haiku", "task_id": "ct-0f769ebe10"} +{"attempts": [{"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:0000148", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "GPNMB", "stance": "supports"}, {"gene": "PLP1", "stance": "contradicts"}], "rationale": "This cluster has a strong, unambiguous melanocyte signature. DCT, TYRP1, MLANA, PMEL, and MITF are canonical melanocyte markers: DCT and TYRP1 encode proteins in the melanin synthesis pathway; MLANA (Melan-A) is a well-characterized melanocyte antigen; PMEL is a major premelanosomal protein; MITF is the master transcription factor for melanocyte differentiation. All five show high fold-change and high selectivity (pct_in >> pct_out). GPNMB is another melanosomal protein supporting this assignment. The only contradictory marker is PLP1, a myelin protein more characteristic of oligodendrocytes; its presence here is anomalous but does not override the overwhelming melanocyte-specific signature from the top markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.2}], "model": "claude-haiku", "task_id": "ct-1445edf08f"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 16, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'intestinal epithelial cell' is not the name of CL:0000584 ('enterocyte'). 'intestinal epithelial cell' is the name of CL:0002563 (intestinal epithelial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"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:0000584", "cell_type_label": "intestinal epithelial cell", "decision": "annotate", "markers": [{"gene": "KRT8", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "CPS1", "stance": "contradicts"}, {"gene": "MT1G", "stance": "contradicts"}, {"gene": "MT1E", "stance": "contradicts"}, {"gene": "MT1X", "stance": "contradicts"}, {"gene": "MT2A", "stance": "contradicts"}], "rationale": "The marker signature is highly consistent with intestinal epithelial cells from duodenal tissue. Cytokeratins (KRT8/19/18) and EPCAM are core epithelial identity markers. PIGR (secretory IgA receptor), FABP1 (intestinal fatty acid binding protein), and RBP2 (retinol metabolism) are characteristic of absorptive intestinal epithelium. DMBT1, LGALS4, REG1A, and AGR2 further support epithelial identity. CPS1 (urea cycle enzyme, primarily hepatic) is unexpected and suggests possible contamination or non-canonical expression. Metallothioneins are ubiquitous stress/storage proteins not cell-type specific, though their high ranking suggests some metabolic activity in these cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.3}, {"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "KRT8", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "CPS1", "stance": "contradicts"}, {"gene": "MT1G", "stance": "contradicts"}, {"gene": "MT1E", "stance": "contradicts"}, {"gene": "MT1X", "stance": "contradicts"}, {"gene": "MT2A", "stance": "contradicts"}], "rationale": "The marker signature is highly consistent with enterocytes from duodenal tissue. Cytokeratins (KRT8/19/18) and EPCAM are core epithelial identity markers. PIGR (secretory IgA receptor), FABP1 (intestinal fatty acid binding protein), and RBP2 (retinol metabolism) are characteristic of absorptive intestinal epithelium. DMBT1, LGALS4, REG1A, and AGR2 further support enterocyte identity. CPS1 (urea cycle enzyme, primarily hepatic) is unexpected and suggests possible contamination or non-canonical expression. Metallothioneins are ubiquitous stress/storage proteins not cell-type specific, though their high ranking suggests some metabolic activity in these cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'intestinal epithelial cell' is not the name of CL:0000584 ('enterocyte'). 'intestinal epithelial cell' is the name of CL:0002563 (intestinal epithelial cell)."], "seconds": 14.8}], "model": "claude-haiku", "task_id": "ct-1fed4d68f2"} +{"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": "ACTA2", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "CCL2", "stance": "contradicts"}, {"gene": "IGFBP7", "stance": "contradicts"}], "rationale": "Strong ensemble of contractile proteins (ACTA2, MYL9, MYH11, TAGLN, TPM2, CALD1) definitively indicates smooth muscle differentiation. CCL2 and IGFBP7 suggest possible myofibroblast features (activated fibroblasts with smooth muscle characteristics), but the contractile gene signature is dominant and diagnostic."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.8}], "model": "claude-haiku", "task_id": "ct-22fc152fbd"} +{"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:0000624", "cell_type_label": "CD4-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LTA", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "ZBTB16", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "KIT", "stance": "contradicts"}], "rationale": "Strong concordance of T cell lineage markers (IL7R, CD52, LST1), CD4+ subset markers (IL7R especially), T cell development factors (TOX2), and T cell-produced cytokines (LTA, LTB). RORC indicates Th17 polarization. KIT expression is atypical for T cells but not prohibitive in activated populations. This is a confident CD4-positive helper T cell annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.6}], "model": "claude-haiku", "task_id": "ct-307f739343"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "pancreatic alpha cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "VGF", "stance": "supports"}, {"gene": "SLC30A8", "stance": "supports"}, {"gene": "SLC7A2", "stance": "supports"}], "rationale": "This cluster is definitively a pancreatic alpha cell based on GCG (glucagon) as the top marker with the highest logfc (5.1), the hormone specifically produced by alpha cells. Supporting markers include TTR (transthyretin, highly alpha-specific), PCSK2 (prohormone convertase for glucagon processing), and the chromogranins CHGA/CHGB which are characteristic of secretory endocrine cells. Secretogranins (SCG2, SCG5, VGF) and zinc transporter SLC30A8 are all consistent with pancreatic alpha cell identity. The cationic amino acid transporter SLC7A2 is relevant to arginine metabolism in glucagon synthesis. No markers strongly contradict this identity—all are consistent with endocrine/neuroendocrine cell biology.\n"}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.2}], "model": "claude-haiku", "task_id": "ct-32e6a3a16d"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'capillary endothelial cell' is not the name of CL:0002541 ('chorionic membrane mesenchymal stem cell'). 'capillary endothelial cell' is the name of CL:0002144 (capillary endothelial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"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:0002541", "cell_type_label": "capillary endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-E", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-B", "stance": "supports"}, {"gene": "IFI27", "stance": "contradicts"}, {"gene": "IFITM3", "stance": "contradicts"}, {"gene": "HSPA1A", "stance": "contradicts"}], "rationale": "PLVAP (plasmalemma vesicle-associated protein) is a highly specific and dominant marker (logfc 1.996, 87.9% expression in-cluster vs 3.7% out) for fenestrated endothelium, which is the primary endothelial type found in kidney glomerular capillaries. Supporting markers include TM4SF1 and CAVIN2 (endothelial cytoskeletal proteins), RAMP3 (endothelial receptor), and HLA genes reflecting MHC expression typical of endothelium. CD74 further supports endothelial identity. The major contradicting markers are IFI27, IFITM3, and HSPA1A—interferon-stimulated and stress response genes rarely prominent in resting endothelium. This likely reflects activated or inflammatory endothelium, possibly from immune stimulation or infection in the tissue sample at time of collection, but the endothelial identity is unambiguous."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.8}, {"answer": {"cell_type_id": "CL:0002144", "cell_type_label": "capillary endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-E", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-B", "stance": "supports"}, {"gene": "IFI27", "stance": "contradicts"}, {"gene": "IFITM3", "stance": "contradicts"}, {"gene": "HSPA1A", "stance": "contradicts"}], "rationale": "PLVAP (plasmalemma vesicle-associated protein) is a highly specific marker (logfc 1.996, 87.9% expression in-cluster vs 3.7% out) for fenestrated endothelium, characteristic of kidney glomerular capillaries. Supporting markers include TM4SF1 and CAVIN2 (endothelial cytoskeletal proteins), RAMP3 (endothelial receptor), and HLA genes reflecting MHC expression typical of endothelium. CD74 further supports endothelial identity. The contradicting markers (IFI27, IFITM3, HSPA1A) are interferon-stimulated and stress response genes, likely reflecting activated or inflammatory endothelium, but the endothelial identity is unambiguous."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'capillary endothelial cell' is not the name of CL:0002541 ('chorionic membrane mesenchymal stem cell'). 'capillary endothelial cell' is the name of CL:0002144 (capillary endothelial cell)."], "seconds": 11.0}], "model": "claude-haiku", "task_id": "ct-32f05dbab5"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV025"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'Langerhans cell' is not the name of CL:0000906 ('activated CD8-positive, alpha-beta T cell'). 'Langerhans cell' is the name of CL:0000453 (Langerhans cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "The ASCT+B reference lists HLA-DRA as a marker of CL:0000236 (B cell); CL:0000576 (monocyte); CL:0000875 (non-classical monocyte) and 2 more, cell types disjoint from CL:0000906.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c04;gene=HLA-DRA)"}, {"message": "The ASCT+B reference lists FCER1A as a marker of CL:0001056 (dendritic cell, human), cell types disjoint from CL:0000906.", "rule_id": "BEV025", "where": "evidence 8 (cluster=c04;gene=FCER1A)"}, {"message": "The ASCT+B reference lists AIF1 as a marker of CL:0000235 (macrophage), cell types disjoint from CL:0000906.", "rule_id": "BEV025", "where": "evidence 10 (cluster=c04;gene=AIF1)"}], "status": "rejected", "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:0000906", "cell_type_label": "Langerhans cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "SAT1", "stance": "contradicts"}, {"gene": "CST3", "stance": "contradicts"}], "rationale": "The combination of high MHC class II expression (HLA-DR, HLA-DP, HLA-DQ genes), CD74 (the invariant chain required for MHC class II assembly), and FCER1A (high-affinity IgE receptor) strongly identifies Langerhans cells. These are antigen-presenting dendritic cells resident in skin epidermis. Additional myeloid markers (LYZ, AIF1, TYROBP) and immune signaling genes support this identification. SAT1 and CST3 show elevated expression but are ubiquitously expressed across cell types and are less specific. The skin tissue source and the specific combination of markers—particularly FCER1A with high HLA-DR/MHC class II expression—is characteristic of Langerhans cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.7}, {"answer": {"cell_type_id": "CL:0000453", "cell_type_label": "Langerhans cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "SAT1", "stance": "contradicts"}, {"gene": "CST3", "stance": "contradicts"}], "rationale": "The combination of high MHC class II expression (HLA-DR, HLA-DP, HLA-DQ genes), CD74 (the invariant chain required for MHC class II assembly), and FCER1A (high-affinity IgE receptor) strongly identifies Langerhans cells. These are antigen-presenting dendritic cells resident in skin epidermis. Additional myeloid markers (LYZ, AIF1, TYROBP) and immune signaling genes support this identification. SAT1 and CST3 show elevated expression but are ubiquitously expressed across cell types and are less specific. The skin tissue source and the specific combination of markers—particularly FCER1A with high HLA-DR/MHC class II expression—is characteristic of Langerhans cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'Langerhans cell' is not the name of CL:0000906 ('activated CD8-positive, alpha-beta T cell'). 'Langerhans cell' is the name of CL:0000453 (Langerhans cell)."], "seconds": 12.8}], "model": "claude-haiku", "task_id": "ct-3385c5a4a1"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'acinar cell of pancreas' is not the name of CL:0000622 ('acinar cell'). 'acinar cell of pancreas' is the name of CL:0002064 (pancreatic acinar cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0000622", "cell_type_label": "acinar cell of pancreas", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PRSS1", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "CD24", "stance": "contradicts"}], "rationale": "The cluster expresses the complete set of pancreatic digestive enzymes: serine proteases (PRSS1, CTRB2, CPB1), carboxypeptidases (CPA1, CPA2), lipase (PNLIP), phospholipase (PLA2G1B), and elastase (CEL). These are all hallmarks of acinar cell secretory granules. REG1A/REG3A/REG1B (regenerating proteins) are classic pancreatic acinar cell markers involved in cell proliferation and survival. SPINK1 (serine protease inhibitor) is the pancreatic trypsin inhibitor, essential for preventing premature enzyme activation. CD24 is broadly expressed across the tissue (pct_out=0.893) and thus argues against acinar cell specificity, though it may be present in these cells as well."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.7}, {"answer": {"cell_type_id": "CL:0002064", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PRSS1", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "CD24", "stance": "contradicts"}], "rationale": "The cluster expresses the complete set of pancreatic digestive enzymes: serine proteases (PRSS1, CTRB2, CPB1), carboxypeptidases (CPA1, CPA2), lipase (PNLIP), phospholipase (PLA2G1B), and elastase (CEL). These are all hallmarks of pancreatic acinar cell secretory granules. REG1A/REG3A/REG1B (regenerating proteins) are classic pancreatic acinar cell markers involved in cell proliferation and survival. SPINK1 (serine protease inhibitor Kazal type 1) is the pancreatic trypsin inhibitor, essential for preventing premature enzyme activation. CD24 is broadly expressed across the tissue (pct_out=0.893) and thus argues against pancreatic acinar cell specificity, though it may be present in these cells as well."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'acinar cell of pancreas' is not the name of CL:0000622 ('acinar cell'). 'acinar cell of pancreas' is the name of CL:0002064 (pancreatic acinar cell)."], "seconds": 13.6}], "model": "claude-haiku", "task_id": "ct-36d56001f7"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'collecting duct principal cell' is not the name of CL:0002191 ('granulocytopoietic cell'). Closest names: CL:1001431 (kidney collecting duct principal cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000454 (kidney collecting duct epithelial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0002191", "cell_type_label": "collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "HSD11B2", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "contradicts"}, {"gene": "SPINK1", "stance": "contradicts"}], "rationale": "This cluster exhibits the characteristic marker gene profile of kidney collecting duct principal cells. HSD11B2 is a highly specific marker for these cells, involved in corticosteroid regulation in the cortical collecting duct. The co-expression of CALB1 (calbindin), SLC4A1, CA12, and ATP1B1 strongly supports principal cell identity, with these genes mediating calcium handling, anion transport, pH regulation, and sodium reabsorption respectively. The exceptionally high expression of mitochondrial genes reflects the high ATP demand of active ion transport in these cells. RHCG expression is atypical for principal cells (more characteristic of collecting duct intercalated cells) and SPINK1 is not a standard kidney marker, introducing minor contradictions in the profile."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.5}, {"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "HSD11B2", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "contradicts"}, {"gene": "SPINK1", "stance": "contradicts"}], "rationale": "This cluster exhibits the characteristic marker gene profile of kidney collecting duct principal cells. HSD11B2 is a highly specific marker for these cells, involved in corticosteroid regulation in the cortical collecting duct. The co-expression of CALB1 (calbindin), SLC4A1, CA12, and ATP1B1 strongly supports principal cell identity, with these genes mediating calcium handling, anion transport, pH regulation, and sodium reabsorption respectively. The exceptionally high expression of mitochondrial genes reflects the high ATP demand of active ion transport in these cells. RHCG expression is atypical for principal cells (more characteristic of collecting duct intercalated cells) and SPINK1 is not a standard kidney marker, introducing minor contradictions in the profile."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'collecting duct principal cell' is not the name of CL:0002191 ('granulocytopoietic cell'). Closest names: CL:1001431 (kidney collecting duct principal cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000454 (kidney collecting duct epithelial cell)."], "seconds": 13.2}], "model": "claude-haiku", "task_id": "ct-3cbc7c57fd"} +{"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": "CD3D", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "MALAT1", "stance": "contradicts"}, {"gene": "TMSB4X", "stance": "contradicts"}, {"gene": "RPS3", "stance": "contradicts"}, {"gene": "S100A4", "stance": "contradicts"}], "rationale": "The cluster is identified as CD8+ T cells based on strong expression of core T cell markers (CD3D, TRAC, CD52) combined with cytotoxic effector markers (NKG7, granzyme A). CD3D and TRAC are definitional for T cells; their high logfc values (1.68 and 1.46) and high pct_in (79.5% and 72.6%) confirm T cell identity. The presence of NKG7 and GZMA in the top 20 markers indicates cytotoxic function characteristic of CD8+ T cells or activated effector T cells. IL32, CCL5, and CXCR4 support T cell activation and trafficking. Housekeeping genes (MALAT1, TMSB4X, RPS3) are broadly expressed and don't support specific cell type identity; S100A4 is a general immune activation marker without T cell specificity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.2}], "model": "claude-haiku", "task_id": "ct-3f2898af5e"} +{"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:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL6A2", "stance": "supports"}, {"gene": "DCN", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "FBLN1", "stance": "supports"}, {"gene": "GSN", "stance": "supports"}, {"gene": "MMP2", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "SERPINF1", "stance": "supports"}, {"gene": "APOD", "stance": "supports"}, {"gene": "CTSK", "stance": "contradicts"}], "rationale": "The cluster shows the prototypical fibroblast signature: high expression of collagen genes (COL1A1, COL1A2, COL3A1, COL6A2) and extracellular matrix-associated proteins (DCN, LUM, FBLN1, GSN, SFRP2, IGFBP5, SERPINF1, APOD), plus MMP2 for ECM remodeling. This is consistent with dermal fibroblasts from skin. CTSK (cathepsin K) is atypical as it's primarily associated with osteoclasts and bone-resident cells, making it contradictory to fibroblast identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.1}], "model": "claude-haiku", "task_id": "ct-5e18af843a"} +{"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:0000169", "cell_type_label": "pancreatic beta cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "HADH", "stance": "supports"}, {"gene": "RBP4", "stance": "contradicts"}, {"gene": "UCHL1", "stance": "contradicts"}], "rationale": "This cluster is a pancreatic beta cell population. The top markers include the defining beta cell genes: INS (insulin), IAPP (islet amyloid polypeptide), and PDX1 (pancreatic transcription factor). Supporting markers include PCSK1 (prohormone convertase essential for insulin maturation), ABCC8 (ATP-sensitive K+ channel subunit critical for glucose-stimulated insulin secretion), G6PC2 (glucose sensor), SCGN (secretagogin, involved in insulin granule dynamics), and HADH (fatty acid oxidation in beta cells). RBP4 and UCHL1 are less typical of beta cells—RBP4 is more associated with hepatocytes and adipocytes, and UCHL1 is a known neuronal marker—suggesting possible technical artifact or biological heterogeneity, but the overwhelming consensus strongly indicates a beta cell cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.9}], "model": "claude-haiku", "task_id": "ct-6ea69bcccb"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'enteroendocrine cell' is not the name of CL:0000150 ('glandular secretory epithelial cell'). 'enteroendocrine cell' is the name of CL:0000164 (enteroendocrine cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0000150", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "NEUROD1", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "MDK", "stance": "contradicts"}, {"gene": "SOX4", "stance": "contradicts"}], "rationale": "This cluster shows a strong neuroendocrine signature characteristic of enteroendocrine cells in the duodenum. Supporting markers include: NEUROD1 (essential transcription factor for endocrine differentiation with high specificity), chromogranins A and B (universal neuroendocrine markers), FEV (specific to enteroendocrine development), INSM1 (neuroendocrine differentiation factor), and secretogranins (SCG2, SCG5, SCGN) involved in peptide hormone granule formation. The presence of specific peptide hormones SCT (secretin, S cell marker) and MLN (motilin, Mo cell marker) further supports enteroendocrine identity. CPE is essential for neuropeptide processing. Contradicting markers include MDK, which is more typical of mesenchymal and immune cells (high pct_out: 0.708), and SOX4, a transcription factor more commonly associated with neural/mesenchymal differentiation rather than mature endocrine specification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.0}, {"answer": {"cell_type_id": "CL:0000164", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "NEUROD1", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "MDK", "stance": "contradicts"}, {"gene": "SOX4", "stance": "contradicts"}], "rationale": "This cluster shows a strong neuroendocrine signature characteristic of enteroendocrine cells in the duodenum. Supporting markers include: NEUROD1 (essential transcription factor for endocrine differentiation with high specificity), chromogranins A and B (universal neuroendocrine markers), FEV (specific to enteroendocrine development), INSM1 (neuroendocrine differentiation factor), and secretogranins (SCG2, SCG5, SCGN) involved in peptide hormone granule formation. The presence of specific peptide hormones SCT (secretin, S cell marker) and MLN (motilin, Mo cell marker) further supports enteroendocrine identity. CPE is essential for neuropeptide processing. Contradicting markers include MDK, which is more typical of mesenchymal and immune cells (high pct_out: 0.708), and SOX4, a transcription factor more commonly associated with neural/mesenchymal differentiation rather than mature endocrine specification."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'enteroendocrine cell' is not the name of CL:0000150 ('glandular secretory epithelial cell'). 'enteroendocrine cell' is the name of CL:0000164 (enteroendocrine cell)."], "seconds": 10.0}], "model": "claude-haiku", "task_id": "ct-76f0318d60"} +{"attempts": [{"codes": ["BEV025"], "evidence": 13, "findings": [{"message": "The ASCT+B reference lists FCER1G as a marker of CL:0000767 (basophil); CL:0000775 (neutrophil); CL:0000784 (plasmacytoid dendritic cell) and 5 more, cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 10 (cluster=c09;gene=FCER1G)"}, {"message": "The ASCT+B reference lists CCL3 as a marker of CL:4033041 (CCL3-positive alveolar macrophage), cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 11 (cluster=c09;gene=CCL3)"}], "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": "KLRB1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "The cluster is identified as natural killer cells based on high expression of canonical NK cell markers (NKG7, KLRB1, KLRD1, KLRF1), cytotoxic granule proteins (GZMA), NK signaling adapters (TYROBP/DAP12, HCST/DAP10, FCER1G), and NK-associated chemokines (CCL3, CCL4, CCL5). No contradictory markers are present in the top 20."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.7}], "model": "claude-haiku", "task_id": "ct-992627e517"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV025"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'T helper cell (Th2)' is not the name of CL:0000912 ('helper T cell'). Closest names: CL:0002061 (T-helper 9 cell); CL:0000546 (T-helper 2 cell); CL:0000545 (T-helper 1 cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0000912.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=GATA3)"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0000912.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=HPGDS)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV025"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0000546.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=GATA3)"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0000546.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=HPGDS)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000912", "cell_type_label": "T helper cell (Th2)", "decision": "annotate", "markers": [{"gene": "GATA3", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL10RA", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "The cluster is dominated by GATA3 (Th2 master regulator) and PTGDR2/HPGDS (Th2-specific prostaglandin pathway), strongly indicating T helper cells with Th2 differentiation. Supporting markers include T cell surface proteins (TESPA1, KLRB1), T cell cytokines (IL32, LTB), and IL10RA consistent with Th2 IL-10 responsiveness. KRT1 (epithelial keratin) is anomalous and contradicts a pure lymphoid identity—likely represents contamination or measurement artifact. The overall signature is definitively helper T cell with Th2 polarization."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.1}, {"answer": {"cell_type_id": "CL:0000546", "cell_type_label": "T-helper 2 cell", "decision": "annotate", "markers": [{"gene": "GATA3", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL10RA", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "The cluster is dominated by GATA3 (Th2 master transcription factor) and PTGDR2/HPGDS (prostaglandin D2 pathway, highly specific to Th2 cells). Supporting markers include T cell surface proteins (TESPA1, KLRB1), T cell cytokines (IL32, LTB), and IL10RA consistent with Th2 IL-10 responsiveness. KRT1 (epithelial keratin) contradicts lymphoid identity and likely represents contamination or artifact. The signature is definitively Th2."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'T helper cell (Th2)' is not the name of CL:0000912 ('helper T cell'). Closest names: CL:0002061 (T-helper 9 cell); CL:0000546 (T-helper 2 cell); CL:0000545 (T-helper 1 cell)."], "seconds": 9.9}], "model": "claude-haiku", "task_id": "ct-a53a01a447"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'blood vessel endothelial cell' is not the name of CL:0000017 ('spermatocyte'). 'blood vessel endothelial cell' is the name of CL:0000071 (blood vessel endothelial cell).", "rule_id": "BEV017", "where": "object label"}], "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:0000017", "cell_type_label": "blood vessel endothelial cell", "decision": "annotate", "markers": [{"gene": "AQP1", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "S100A4", "stance": "contradicts"}], "rationale": "Strong endothelial marker signature driven by canonical markers AQP1, TM4SF1, and RAMP2, with supporting evidence from TIMP3 (vascular remodeling) and VIM (mesenchymal lineage). S100A4 is more typical of fibroblasts but appears as minor marker. IFI27, IFITM3, and immediate early genes reflect endothelial activation state rather than contradicting identity. Kidney context consistent with peritubular or glomerular endothelium."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.5}, {"answer": {"cell_type_id": "CL:0000071", "cell_type_label": "blood vessel endothelial cell", "decision": "annotate", "markers": [{"gene": "AQP1", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "VIM", "stance": "contradicts"}, {"gene": "S100A4", "stance": "contradicts"}], "rationale": "Strong endothelial marker signature driven by canonical markers AQP1, TM4SF1, and RAMP2, with supporting TIMP3 (vascular remodeling). The interferon-stimulated genes (IFI27, IFITM3) and immediate early genes (JUNB, FOS, EGR1, ZFP36) reflect endothelial activation state consistent with inflammatory or wound-response context rather than contradicting the endothelial identity. VIM and S100A4 are mesenchymal markers more typical of fibroblasts, suggesting some heterogeneity or endothelial-mesenchymal transition, but the dominant signature is clearly endothelial. Kidney context is consistent with peritubular or glomerular capillary endothelium."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'blood vessel endothelial cell' is not the name of CL:0000017 ('spermatocyte'). 'blood vessel endothelial cell' is the name of CL:0000071 (blood vessel endothelial cell)."], "seconds": 12.9}], "model": "claude-haiku", "task_id": "ct-c22bc01239"} +{"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:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "TRDV2", "stance": "supports"}, {"gene": "NCR3", "stance": "contradicts"}, {"gene": "BLK", "stance": "contradicts"}], "rationale": "CD3E is expressed in 93.4% of cells in this cluster, making it diagnostic for T lymphocytes. IL7R is similarly highly expressed (96.4%), indicating IL-7-responsive T cells, typically naive or IL-7-dependent subsets. Additional support comes from CD52 and LTB, both T cell-associated markers. The presence of KLRB1 and TRDV2 suggests these may be innate-like T cells or gamma-delta T cells. However, NCR3 (NK marker) and BLK (B cell kinase) expression are contradictory and unusual in T cells, possibly indicating either a contaminating minor population or rare multipotent precursor features. The overwhelming signal from CD3E and IL7R confidently identifies this cluster as T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.7}], "model": "claude-haiku", "task_id": "ct-c84f57496a"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "CL:1000010", "cell_type_label": "cycling/proliferating epithelial cell", "decision": "uncertain", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "SFTPA1", "stance": "contradicts"}, {"gene": "SFTPB", "stance": "contradicts"}, {"gene": "SFTPC", "stance": "contradicts"}], "rationale": "The cluster is dominated by S/G2/M phase markers (MKI67, TOP2A, CDK1, NUSAP1, CENPF) with extremely restricted expression outside the cluster, indicating active proliferation. However, the complete absence of surfactant genes (which would identify type II pneumocytes) and other lung cell-type-specific markers makes definitive cell type assignment uncertain. This could represent cycling pneumocytes, airway progenitors, or general proliferating epithelial cells. The proliferative state is unambiguous; the specific cell type is not."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.1}], "model": "claude-haiku", "task_id": "ct-c8e68f267e"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'collecting duct principal cell' is not the name of CL:0002251 ('epithelial cell of alimentary canal'). Closest names: CL:1001431 (kidney collecting duct principal cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000454 (kidney collecting duct epithelial cell).", "rule_id": "BEV017", "where": "object label"}], "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:0002251", "cell_type_label": "collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "contradicts"}], "rationale": "Strong expression of DEFB1, HSD11B2, and KLK1—canonical principal cell markers—combined with high ATP1B1 (active transport) and CALB1 (calcium handling) clearly identifies collecting duct principal cells. RHCG's presence is somewhat contradictory as it preferentially marks intercalated cells, suggesting possible minor intercalated cell contribution or that cell-type boundaries are less distinct than the canonical assignments."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.2}, {"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "contradicts"}], "rationale": "Strong expression of DEFB1, HSD11B2, and KLK1—canonical principal cell markers—combined with high ATP1B1 (active transport) and CALB1 (calcium handling) clearly identifies kidney collecting duct principal cells. RHCG's presence is contradictory as it preferentially marks intercalated cells, suggesting possible minor intercalated cell contribution or incomplete cell-type separation."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'collecting duct principal cell' is not the name of CL:0002251 ('epithelial cell of alimentary canal'). Closest names: CL:1001431 (kidney collecting duct principal cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000454 (kidney collecting duct epithelial cell)."], "seconds": 12.5}], "model": "claude-haiku", "task_id": "ct-e7cab67ae5"} +{"attempts": [{"codes": ["BEV017", "BEV025"], "evidence": 9, "findings": [{"message": "The label 'pancreatic duct cell' is not the name of CL:0002079 ('pancreatic ductal cell'). Closest names: CL:0002079 (pancreatic ductal cell); CL:0000173 (pancreatic D cell); CL:0000171 (pancreatic A cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "The ASCT+B reference lists CD44 as a marker of CL:4033038 (lung resident memory CD4-positive, alpha-beta T cell), cell types disjoint from CL:0002079.", "rule_id": "BEV025", "where": "evidence 7 (cluster=c05;gene=CD44)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV025"], "evidence": 9, "findings": [{"message": "The ASCT+B reference lists CD44 as a marker of CL:4033038 (lung resident memory CD4-positive, alpha-beta T cell), cell types disjoint from CL:0002079.", "rule_id": "BEV025", "where": "evidence 7 (cluster=c05;gene=CD44)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic duct cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD44", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}], "rationale": "The distinctive upregulation of CFTR (logfc 2.555) and SLC4A4 (logfc 1.977) in pancreatic tissue is diagnostic for ductal cells, which require these genes for bicarbonate-rich fluid secretion. Supporting markers include epithelial and ductal-specific genes (TACSTD2/EpCAM, MMP7, SPP1). Ubiquitously expressed genes (HLA-B, TMSB4X) and general cell adhesion markers (CD44, CD24) are consistent with but not diagnostic for ductal identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.6}, {"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic ductal cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD44", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}], "rationale": "The distinctive upregulation of CFTR (logfc 2.555) and SLC4A4 (logfc 1.977) in pancreatic tissue is diagnostic for ductal cells, which require these genes for bicarbonate-rich fluid secretion. Supporting markers include epithelial and ductal-specific genes (TACSTD2/EpCAM, MMP7, SPP1). Ubiquitously expressed genes (HLA-B, TMSB4X) and general cell adhesion markers (CD44, CD24) are consistent with but not diagnostic for ductal identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic duct cell' is not the name of CL:0002079 ('pancreatic ductal cell'). Closest names: CL:0002079 (pancreatic ductal cell); CL:0000173 (pancreatic D cell); CL:0000171 (pancreatic A cell)."], "seconds": 8.9}], "model": "claude-haiku", "task_id": "ct-ee90c8cca6"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000182", "cell_type_label": "hepatocyte", "decision": "annotate", "markers": [{"gene": "ALB", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "APOA2", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "APOC1", "stance": "supports"}, {"gene": "APOH", "stance": "supports"}, {"gene": "FGA", "stance": "supports"}, {"gene": "FGB", "stance": "supports"}, {"gene": "FGG", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "TF", "stance": "supports"}, {"gene": "HP", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "AMBP", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "ORM1", "stance": "supports"}, {"gene": "ORM2", "stance": "supports"}, {"gene": "CYP2E1", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}], "rationale": "This cluster shows a dominant signature of serum/plasma proteins and hepatocyte-specific metabolic enzymes. The entire marker gene list consists of hepatocyte-specific products: major serum proteins (albumin, apolipoproteins, fibrinogen, transferrin, haptoglobin, alpha-1 antitrypsin), coagulation factors, transport proteins (retinol binding protein, transthyretin), and the hepatocyte-selective cytochrome P450 enzyme CYP2E1. The high expression and specificity of these markers (high pct_in, low pct_out for genes like TF, CYP2E1) is diagnostic of primary hepatocytes. No contradictory markers are present; all markers consistently support hepatocyte identity with no genes indicative of other liver cell types (cholangiocytes, stellate cells, immune cells, or endothelial cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.6}], "model": "claude-haiku", "task_id": "ct-fa6e0d282d"} +{"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:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "FCN3", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "CCL14", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "CLDN5", "stance": "contradicts"}], "rationale": "Several general endothelial genes are high in this cluster: GNG11, TM4SF1, IGFBP7, HSPG2, ID1/ID3, TFPI and TIMP3. On top of that, it expresses the classic human liver sinusoidal endothelial (LSEC) genes FCN3, FCN2, DNASE1L3, CRHBP, CCL14 and LIFR, as described in human liver atlases. CLDN5 is the one weak point. It is higher in macrovascular, periportal and central-vein endothelium than in true sinusoidal cells, so the cluster may include some of those vascular endothelial cells. Still, the sinusoid-specific scavenger and lectin genes dominate, so hepatic sinusoidal endothelial cell is the best single label."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.4}], "model": "claude-opus", "task_id": "ct-04aaea9940"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000334", "cell_type_label": "enterocyte of epithelium of small intestine", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "APOA4", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "APOB", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "FABP2", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "SI", "stance": "supports"}, {"gene": "ANPEP", "stance": "supports"}, {"gene": "TMPRSS15", "stance": "supports"}, {"gene": "SLC5A1", "stance": "supports"}, {"gene": "CDHR5", "stance": "supports"}, {"gene": "SLC26A3", "stance": "supports"}, {"gene": "PRAP1", "stance": "supports"}, {"gene": "CES2", "stance": "supports"}], "rationale": "These are absorptive enterocytes of the small intestine. The cluster shows high levels of brush-border enzymes and transporters: SI (sucrase-isomaltase), ANPEP, TMPRSS15 (enteropeptidase, which is specific to the duodenum), SLC5A1 (SGLT1), SLC26A3 and the microvillus protein CDHR5. It also expresses the machinery for packaging dietary fat into chylomicrons (APOB, APOA4, APOA1, APOC3), the lipid-binding proteins FABP1 and FABP2, the retinol-binding protein RBP2 and the fructose-metabolism enzyme ALDOB. Together this is the profile of a mature small-intestinal enterocyte. None of the top genes argue against it. PIGR and PHGR1 are general epithelial genes that are expressed widely across the epithelium, so they do not help tell cell types apart."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.0}], "model": "claude-opus", "task_id": "ct-085bedbfa5"} +{"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:0002250", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "SLC12A2", "stance": "supports"}, {"gene": "PPP1R1B", "stance": "supports"}, {"gene": "IGFBP2", "stance": "supports"}, {"gene": "HMGA1", "stance": "supports"}, {"gene": "RPS2", "stance": "supports"}, {"gene": "RPS3", "stance": "supports"}, {"gene": "PTMA", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "REG1A", "stance": "contradicts"}, {"gene": "REG3A", "stance": "contradicts"}, {"gene": "PIGR", "stance": "contradicts"}, {"gene": "DMBT1", "stance": "contradicts"}], "rationale": "The strongest evidence is the specific crypt stem cell markers OLFM4 (97% of cells in the cluster vs 31% outside) and SLC12A2 (93% vs 18%). PPP1R1B and IGFBP2, which are enriched in crypt base and progenitor cells, add to this. Undifferentiated cells show high HMGA1, PTMA and ribosomal protein genes (RPS2, RPS3), and these are all up here. KRT18 and AGR2 confirm the cells are epithelial. LGR5 and proliferation genes are not among the top markers, but LGR5 is often poorly detected with 10x 3' v2. High REG1A, REG3A, DMBT1, SPINK1 and PIGR point to some differentiation or antimicrobial crypt programmes, and may mean transit-amplifying or early progenitor cells are mixed in. They are also expressed widely outside the cluster, so they only weakly argue against this call. This is the general term. The small-intestine-specific CL term would be more precise, but I did not use it because I'm not sure of its exact ID."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.1}], "model": "claude-opus", "task_id": "ct-0f769ebe10"} +{"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:0000148", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "CAPN3", "stance": "supports"}, {"gene": "GPNMB", "stance": "supports"}, {"gene": "SNCA", "stance": "supports"}, {"gene": "QPCT", "stance": "supports"}, {"gene": "CD63", "stance": "supports"}, {"gene": "PLP1", "stance": "supports"}, {"gene": "GPM6B", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}, {"gene": "S100A2", "stance": "contradicts"}], "rationale": "The melanin-synthesis and melanosome genes are expressed in 78–92% of the cluster's cells and almost nowhere else (about 2–3% of other cells). These are DCT, TYRP1, MLANA and PMEL, together with MITF, the master regulator of melanocytes, and the melanocyte-enriched genes CAPN3, GPNMB, SNCA and QPCT. That pattern marks these cells as epidermal melanocytes. PLP1, GPM6B and NSG1 are neural-crest/glial-type genes that skin melanocytes commonly express, so they fit a neural-crest origin. Schwann cells can't be ruled out completely, but they would not express the pigmentation genes. KRT14 and S100A2 are keratinocyte genes, and they are also common in other cells (pct_out 0.69 and 0.50). They most likely come from ambient RNA or melanocyte–keratinocyte doublets, not from the melanocytes themselves."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}], "model": "claude-opus", "task_id": "ct-1445edf08f"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 18, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists MT1E as a marker of CL:4033042 (metallothionein-positive alveolar macrophage), cell types disjoint from CL:1000334.", "rule_id": "BEV025", "where": "evidence 9 (cluster=c09;gene=MT1E)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:1000334", "cell_type_label": "enterocyte of epithelium of small intestine", "decision": "annotate", "markers": [{"gene": "RBP2", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "CPS1", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1E", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}, {"gene": "MT2A", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "REG1A", "stance": "contradicts"}, {"gene": "DMBT1", "stance": "contradicts"}, {"gene": "AGR2", "stance": "contradicts"}], "rationale": "This is small-intestinal epithelium, as shown by EPCAM, KRT8, KRT18, KRT19 and LGALS4. The enterocyte absorptive/metabolic program is present: RBP2, FABP1, GSTA1 and CPS1. CCL25 is specific to small-intestinal enterocytes, and PIGR plus the metallothioneins (MT1G, MT1E, MT1X, MT2A) fit enterocytes. REG1A, DMBT1 and AGR2 point toward a crypt-proximal, immature or secretory-like state, possibly reflecting duodenal/Brunner's gland context. They argue mildly against fully mature villus enterocytes. Mature brush-border markers (APOA4, APOB, ALPI) are not among the top genes. The best-fitting term is small-intestinal enterocyte, probably an early or immature one."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.9}], "model": "claude-opus", "task_id": "ct-1fed4d68f2"} +{"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:0000359", "cell_type_label": "vascular associated smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "CRISPLD2", "stance": "supports"}, {"gene": "ID4", "stance": "supports"}, {"gene": "RGS5", "stance": "contradicts"}, {"gene": "IGFBP7", "stance": "supports"}], "rationale": "These are clearly mural (perivascular contractile) cells. The contractile genes TAGLN, MYL9, ACTA2, TPM2 and CALD1 are strongly enriched, and most cells in the cluster express them. MYH11 is a fairly specific smooth muscle marker, and it is found in 56% of cells here versus 3% elsewhere, which points to vascular smooth muscle rather than pure pericytes. RGS5 and IGFBP7 are also present, and together with MYH11 these suggest the cells sit along blood vessels, as opposed to the arrector pili muscle. However, RGS5 is a pericyte marker, found in about half the cells. That means the cluster likely includes some pericytes, so pericyte (CL:0000669) is the main alternative. I chose vascular smooth muscle because MYH11 and ACTA2 are strong and RGS5 is only moderate. CCL2, IL6 and GADD45B suggest the cells were activated or stressed, possibly during tissue dissociation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.2}], "model": "claude-opus", "task_id": "ct-22fc152fbd"} +{"attempts": [{"codes": ["BEV025"], "evidence": 14, "findings": [{"message": "The ASCT+B reference lists AQP3 as a marker of CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell); CL:1001431 (kidney collecting duct principal cell) and 1 more, cell types disjoint from CL:0001071.", "rule_id": "BEV025", "where": "evidence 13 (cluster=c13;gene=AQP3)"}], "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": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "HPN", "stance": "supports"}, {"gene": "SCN1B", "stance": "supports"}, {"gene": "LINC00299", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LTA", "stance": "supports"}, {"gene": "ZBTB16", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "IGFBP4", "stance": "supports"}], "rationale": "RORC with KIT and IL7R is the defining ILC3 phenotype. LST1, IL4I1, TOX2, HPN, SCN1B and LINC00299 are well-known human ILC3 signature genes, and HPN and SCN1B are nearly absent from other cells. Lymphotoxin (LTA/LTB) fits LTi-like ILC3. ILC2 markers (GATA3, KLRG1, PTGDR2), T-cell receptor/CD3 genes and cytotoxic NK genes are missing. No marker clearly contradicts ILC3; HSPB1, ITGB1, CD52 and SLA are broadly expressed and not specific."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.1}], "model": "claude-opus", "task_id": "ct-307f739343"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "pancreatic A cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "IRX2", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "LOXL4", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "RGS4", "stance": "supports"}, {"gene": "KCTD12", "stance": "supports"}, {"gene": "SLC7A2", "stance": "supports"}, {"gene": "ALDH1A1", "stance": "supports"}, {"gene": "TMEM176B", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}], "rationale": "GCG is the top marker by a wide margin (logFC 5.1). Its detection outside the cluster is probably background RNA contamination common in CEL-seq2 pancreas data. IRX2 (98% inside vs 11% outside) and LOXL4 are highly alpha-specific. TTR, GC, TM4SF4, RGS4, KCTD12, SLC7A2, ALDH1A1 and TMEM176B are known alpha-cell-enriched genes in human islets. PCSK2 processes proglucagon into glucagon. The chromogranins and secretogranins confirm the cells are endocrine. No beta (INS, IAPP), delta (SST), PP (PPY) or exocrine markers are among the top genes, so this is a pancreatic A (alpha) cell."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.1}], "model": "claude-opus", "task_id": "ct-32e6a3a16d"} +{"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:1000892", "cell_type_label": "kidney capillary endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "RGCC", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HSPA1A", "stance": "contradicts"}], "rationale": "This cluster matches endothelial cells. PLVAP is nearly specific to the cluster (pct_in 0.88 vs pct_out 0.04). Other endothelial genes are also high: CAVIN2, RAMP3, GNG11, TM4SF1, RGCC, IFI27 and RNASE1. PLVAP marks fenestrated endothelium, which fits the kidney's peritubular or vasa recta capillaries better than glomerular endothelium. RGCC and IGFBP5 further suggest capillaries. CD74 and HLA class II genes are commonly expressed by human microvascular endothelium. HSPA1A, JUNB and SOCS3 look like a stress response from tissue dissociation, not a cell-identity signal. I could not check the CL identifier and term name from memory. If the vascular bed is uncertain, the broader \"endothelial cell\" (CL:0000115) is a safe fallback."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.1}], "model": "claude-opus", "task_id": "ct-32f05dbab5"} +{"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:0000451", "cell_type_label": "dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CXCL8", "stance": "contradicts"}, {"gene": "G0S2", "stance": "contradicts"}], "rationale": "This is a myeloid antigen-presenting cell. It shows very high MHC class II expression (HLA-DR, -DP and -DQ, plus CD74) and the pan-myeloid genes TYROBP, FCER1G, AIF1 and LYZ. High CST3 together with FCER1A and GPR183 points most to conventional dendritic cells, most likely the cDC2 subtype, in dermis. Skin Langerhans markers (CD207, CD1A) are not among the top genes, so the broader term \"dendritic cell\" is used. CXCL8, G0S2 and LYZ suggest some monocyte-derived or inflammatory activation, so a mixture with mono-derived DCs or macrophages can't be ruled out."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.8}], "model": "claude-opus", "task_id": "ct-3385c5a4a1"} +{"attempts": [{"codes": ["BEV004"], "evidence": 18, "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:0002064", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "PRSS1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "GSTA2", "stance": "supports"}, {"gene": "ALDOB", "stance": "supports"}, {"gene": "OLFM4", "stance": "contradicts"}, {"gene": "DUOX2", "stance": "contradicts"}, {"gene": "SERPINA3", "stance": "contradicts"}, {"gene": "CFB", "stance": "contradicts"}], "rationale": "The cluster is dominated by acinar digestive enzymes (PRSS1, CTRB2, PNLIP, PLA2G1B, CPA1/2, CPB1, CEL), each expressed in about 99-100% of its cells and strongly enriched against other cells. SPINK1 and the REG family are also strongly up. Ductal or inflammatory genes (OLFM4, DUOX2, SERPINA3, CFB, CD24) suggest some acinar-ductal or inflammatory character, but they are secondary. The widespread REG and enzyme expression in other cells probably reflects ambient RNA in CEL-seq2 data."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.9}], "model": "claude-opus", "task_id": "ct-36d56001f7"} +{"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:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}, {"gene": "SPINK1", "stance": "contradicts"}], "rationale": "SLC4A1 (AE1; 93% in vs 8% out), SLC26A7 and ATP6V0D2 (V-ATPase) together are the defining signature of type A intercalated cells. RHCG and TMEM213 are shared intercalated-cell markers, and DEFB1, CA12 and ATP1B1 fit distal nephron/collecting duct cells. CALB1, HSD11B2 and SPINK1 are more typical of principal or connecting-tubule cells and probably reflect ambient RNA or connecting-tubule intercalated cells. Type B markers (SLC26A4, SLC4A9) are absent. Mitochondrial genes and MALAT1 are uninformative."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.5}], "model": "claude-opus", "task_id": "ct-3cbc7c57fd"} +{"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": "CD3D", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CORO1A", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "CD3D (79% of cells in the cluster vs 3% elsewhere) and TRAC (73% vs 4%) are highly specific to T cells, and TRAC points to alpha-beta T cells. IL32, CORO1A, CXCR4 and CD52 fit lymphocytes. CCL5, NKG7 and GZMA suggest a cytotoxic effector-memory state, which is common among T cells resident in the liver. CD8A/B and CD4 are not in the top markers, and NKG7/GZMA could come from some NK cells mixed into the cluster. So I chose the broad term \"T cell\" rather than a specific subset. No markers argue against it."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}], "model": "claude-opus", "task_id": "ct-3f2898af5e"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002620", "cell_type_label": "skin fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL6A2", "stance": "supports"}, {"gene": "FBLN1", "stance": "supports"}, {"gene": "MMP2", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "CTSK", "stance": "supports"}, {"gene": "CFD", "stance": "supports"}, {"gene": "APOD", "stance": "supports"}, {"gene": "CCDC80", "stance": "supports"}, {"gene": "PLAC9", "stance": "supports"}, {"gene": "SERPINF1", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}], "rationale": "The top markers are fibroblast extracellular-matrix genes: DCN, LUM, the collagens COL1A1, COL1A2, COL3A1 and COL6A2, FBLN1 and CCDC80. They come with genes typical of dermal fibroblasts: MMP2, CTSK, SFRP2, CFD, APOD, CXCL14, SOD3, PLAC9 and SERPINF1. Because the tissue is skin, the matching term is skin fibroblast. No keratinocyte, endothelial, immune or mural-cell markers are present. CEBPB is a general transcription factor and does not point to a specific cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.5}], "model": "claude-opus", "task_id": "ct-5e18af843a"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000169", "cell_type_label": "type B pancreatic cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "MAFA", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "ADCYAP1", "stance": "supports"}, {"gene": "NPTX2", "stance": "supports"}, {"gene": "HADH", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "MEG3", "stance": "supports"}, {"gene": "SYT13", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}], "rationale": "INS and IAPP are the top markers. MAFA, ADCYAP1 and NPTX2 are strongly specific to this cluster (pct_out 0.09–0.29). PDX1, HADH, G6PC2, PCSK1, MEG3 and SYT13 are typical of human beta cells. No markers for other cell types (GCG, SST, PPY, or exocrine genes) are enriched. The high pct_out for INS is expected because ambient hormone transcripts are common in CEL-seq2 islet data. Nothing in the list argues against beta cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.8}], "model": "claude-opus", "task_id": "ct-6ea69bcccb"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000164", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PCSK1N", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}], "rationale": "Strong, specific expression of general neuroendocrine and secretory-granule genes (CHGA, CHGB, PCSK1N, SCG2, SCG5, CPE, SCGN) and of the enteroendocrine lineage transcription factors NEUROD1, INSM1 and FEV identifies enteroendocrine cells. The duodenal hormones SCT (secretin) and MLN (motilin) are both present, along with FEV, so the cluster is a mix of enteroendocrine subtypes. MLN is also only partly specific. For these reasons the broad enteroendocrine cell term is used instead of a single subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.9}], "model": "claude-opus", "task_id": "ct-76f0318d60"} +{"attempts": [{"codes": ["BEV025"], "evidence": 15, "findings": [{"message": "The ASCT+B reference lists FCER1G as a marker of CL:0000767 (basophil); CL:0000775 (neutrophil); CL:0000784 (plasmacytoid dendritic cell) and 5 more, cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 7 (cluster=c09;gene=FCER1G)"}, {"message": "The ASCT+B reference lists CCL3 as a marker of CL:4033041 (CCL3-positive alveolar macrophage), cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 11 (cluster=c09;gene=CCL3)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "Core NK genes are expressed: KLRF1, KLRD1, NKG7 and IL2RB, with the adaptors TYROBP, FCER1G and HCST, and the cytotoxic/chemokine genes GZMA, CCL3, CCL4, CCL5 and XCL2. KLRF1, XCL2 and IL2RB are highly specific to this cluster. No T-cell genes (CD3, TRAC) appear among the top markers, which favours NK cells over T, MAIT or NKT cells. Strong KLRB1 and XCL2 suggest liver-resident CD56-bright NK cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.0}], "model": "claude-opus", "task_id": "ct-992627e517"} +{"attempts": [{"codes": ["BEV017", "BEV025"], "evidence": 10, "findings": [{"message": "The label 'group 2 innate lymphoid cell' is not the name of CL:0001081 ('group 2 innate lymphoid cell, human'). 'group 2 innate lymphoid cell' is the name of CL:0001069 (group 2 innate lymphoid cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0001081.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=HPGDS)"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0001081.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=GATA3)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV025"], "evidence": 10, "findings": [{"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0001081.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=HPGDS)"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0001081.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=GATA3)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0001081", "cell_type_label": "group 2 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "KRT1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "IL10RA", "stance": "supports"}, {"gene": "SAMSN1", "stance": "supports"}], "rationale": "HPGDS and PTGDR2 (CRTH2) are highly specific to this cluster (pct_out about 0.01), together with GATA3 and KRT1. This is the canonical ILC2 signature. KLRB1, IL32, LTB and TESPA1 fit a lymphocyte identity. T-cell genes (CD3, TRBC, CD4) are not among the top markers, which favours ILC2 over PTGDR2+ Th2 cells, although Th2 remains the main alternative."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.1}, {"answer": {"cell_type_id": "CL:0001081", "cell_type_label": "group 2 innate lymphoid cell, human", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "KRT1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "IL10RA", "stance": "supports"}, {"gene": "SAMSN1", "stance": "supports"}], "rationale": "HPGDS and PTGDR2 (CRTH2) are almost unique to this cluster (pct_out about 0.01). Together with GATA3 and KRT1, they form the canonical signature of human ILC2s. KLRB1 (CD161), IL32, LTB and TESPA1 fit a lymphocyte identity. T-cell genes (CD3, TRBC, CD4) are not among the top markers, which favours ILC2 over PTGDR2+ Th2 cells, although Th2 cells remain the main alternative. The dataset is human, so I used the human-specific term CL:0001081 ('group 2 innate lymphoid cell, human'). Its parent term is CL:0001069."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'group 2 innate lymphoid cell' is not the name of CL:0001081 ('group 2 innate lymphoid cell, human'). 'group 2 innate lymphoid cell' is the name of CL:0001069 (group 2 innate lymphoid cell)."], "seconds": 11.5}], "model": "claude-opus", "task_id": "ct-a53a01a447"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "RAMP2", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "NHERF2", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "IFITM3", "stance": "supports"}, {"gene": "HLA-B", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "GSN", "stance": "supports"}], "rationale": "RAMP2, NHERF2 (SLC9A3R2), TM4SF1, IFI27, ID1, TIMP3 and AQP1 together form a typical kidney endothelial signature. The combination of AQP1 with endothelial genes points to peritubular capillaries or descending vasa recta. VIM, S100A6 and high HLA-B fit a mesenchymal-like vascular cell rather than tubular epithelium. The immediate-early genes (FOS, JUNB, EGR1, ZFP36) are probably a stress response from dissociation. Classic pan-endothelial genes such as PECAM1, VWF, EMCN and PLVAP are not in the top 20, so I am annotating at the general endothelial cell level instead of a specific kidney vascular subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.7}], "model": "claude-opus", "task_id": "ct-c22bc01239"} +{"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:0000940", "cell_type_label": "mucosal invariant T cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "NCR3", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "ANXA1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TRDV2", "stance": "contradicts"}, {"gene": "BLK", "stance": "contradicts"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "These are T cells (CD3E, IL32) with a type-17, innate-like memory profile: KLRB1/CD161, CCR6, IL7R, NCR3, LTB, plus the memory/tissue genes S100A4, S100A6, ANXA1 and AQP3. That fits MAIT cells best. However, TRDV2 (35% in the cluster vs 4% elsewhere) and BLK point to Vd2/IL-17-type gamma-delta T cells mixed in, and LST1 hints at ILC3-like cells. The defining MAIT genes (TRAV1-2, SLC4A10, ZBTB16) are not among the top markers, so this may be a mixed innate-like type-17 T-cell cluster. Confidence is moderate."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.0}], "model": "claude-opus", "task_id": "ct-c84f57496a"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "CL:0000000", "cell_type_label": "cell (proliferating/cycling cell of undetermined lineage)", "decision": "uncertain", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "STMN1", "stance": "supports"}, {"gene": "HMGB2", "stance": "supports"}, {"gene": "H4C3", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}], "rationale": "Every top marker belongs to the cell-cycle/proliferation program (MKI67, TOP2A, UBE2C, NUSAP1, CENPF, CDK1, TYMS, histones, tubulins, STMN1, HMGB2). There are no lineage markers (no PTPRC, CD3E, NKG7, CD68, EPCAM, SFTPC, PECAM1 or COL1A2). VIM suggests a non-epithelial identity, possibly immune or stromal, but it is not specific enough. The cells are clearly cycling, but their type can't be determined from these markers. In lung, such clusters are often proliferating T/NK cells or macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.1}], "model": "claude-opus", "task_id": "ct-c8e68f267e"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000768", "cell_type_label": "kidney connecting tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "CALB1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}], "rationale": "CALB1 and KLK1 are highly specific (pct_out 0.064 and 0.041) and together define the connecting tubule; KLK1 is produced mainly by connecting tubule cells. HSD11B2 (aldosterone-sensitive distal nephron), DEFB1, TMEM52B, ATP1B1 and RHCG fit distal nephron epithelium. No DCT markers (SLC12A3, PVALB) or principal cell marker (AQP2) are among the top genes, so connecting tubule fits better than DCT2 or collecting duct, though some overlap with neighbouring cells is possible. GDF15, S100A2 and TNFRSF12A suggest a stress response, and the MT- genes and MALAT1 reflect cell quality rather than identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.7}], "model": "claude-opus", "task_id": "ct-e7cab67ae5"} +{"attempts": [{"codes": ["BEV025"], "evidence": 12, "findings": [{"message": "The ASCT+B reference lists CD44 as a marker of CL:4033038 (lung resident memory CD4-positive, alpha-beta T cell), cell types disjoint from CL:0002079.", "rule_id": "BEV025", "where": "evidence 8 (cluster=c05;gene=CD44)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic ductal cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}, {"gene": "ONECUT2", "stance": "supports"}, {"gene": "CD44", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "SOX4", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "SEL1L3", "stance": "supports"}], "rationale": "CFTR and SLC4A4 (bicarbonate secretion) plus SPP1, MMP7, TACSTD2, ANXA4, ONECUT2 and CD44 are the classic ductal markers in human pancreas single-cell data. None of the top genes points to endocrine, acinar or stromal cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.9}], "model": "claude-opus", "task_id": "ct-ee90c8cca6"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000182", "cell_type_label": "hepatocyte", "decision": "annotate", "markers": [{"gene": "ALB", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "APOA2", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "APOC1", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "FGA", "stance": "supports"}, {"gene": "FGB", "stance": "supports"}, {"gene": "FGG", "stance": "supports"}, {"gene": "TF", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "AMBP", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "HP", "stance": "supports"}, {"gene": "ORM1", "stance": "supports"}, {"gene": "ORM2", "stance": "supports"}, {"gene": "APOH", "stance": "supports"}, {"gene": "CYP2E1", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}], "rationale": "Nearly all cells in the cluster express, far above the rest of the dataset, the hepatocyte program: secreted plasma proteins (ALB, TTR, TF, RBP4, AMBP, HP, ORM1/2, SERPINA1, APOH), fibrinogen chains (FGA/FGB/FGG), apolipoproteins (APOA1/A2/C1/C3) and CYP2E1. No markers argue against it. Some of these genes are also detected in many cells outside the cluster, most likely ambient RNA from hepatocytes. CYP2E1 hints at pericentral hepatocytes, but without GLUL/CYP1A2 the general hepatocyte term is safer."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.4}], "model": "claude-opus", "task_id": "ct-fa6e0d282d"} +{"attempts": [{"codes": ["BEV017"], "evidence": 14, "findings": [{"message": "The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0000639 ('basophil cell of pars distalis of adenohypophysis').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 15, "findings": [{"message": "The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0002138 ('endothelial cell of lymphatic vessel').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 15, "findings": [{"message": "The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0000639 ('basophil cell of pars distalis of adenohypophysis').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000639", "cell_type_label": "hepatic sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "CCL14", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}], "rationale": "This cluster expresses canonical and highly specific markers of hepatic sinusoidal endothelial cells (LSECs), including CCL14, FCN3, FCN2, DNASE1L3, and CRHBP, along with general vascular endothelial markers such as CLDN5, TM4SF1, GNG11, and IGFBP7. There are no contradicting marker genes present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.2}, {"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "hepatic sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "CCL14", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}], "rationale": "This cluster from the human caudate lobe of liver exhibits strong and specific expression of canonical liver sinusoidal endothelial cell (LSEC) markers including CCL14, FCN3, FCN2, DNASE1L3, and CRHBP, alongside core vascular endothelial genes such as CLDN5, TM4SF1, GNG11, IGFBP7, ID1, and ID3. The correct Cell Ontology identifier for hepatic sinusoidal endothelial cell is CL:0002138 (replacing the incorrect identifier CL:0000639). There are no contradicting marker genes."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0000639 ('basophil cell of pars distalis of adenohypophysis')."], "seconds": 51.5}, {"answer": {"cell_type_id": "CL:0000639", "cell_type_label": "hepatic sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "CCL14", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}], "rationale": "This cluster from the human caudate lobe of liver shows strong, characteristic expression of canonical liver sinusoidal endothelial cell (LSEC) markers including CCL14, FCN3, FCN2, DNASE1L3, and CRHBP, together with general and sinusoidal endothelial markers such as CLDN5, TM4SF1, GNG11, IGFBP7, ID1, ID3, and TFPI. The valid Cell Ontology term for hepatic sinusoidal endothelial cell is CL:0000639. There are no contradicting marker genes."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0002138 ('endothelial cell of lymphatic vessel')."], "seconds": 13.5}], "model": "gemini-flash", "task_id": "ct-04aaea9940"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "APOA4", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "PRAP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "ANPEP", "stance": "supports"}, {"gene": "PHGR1", "stance": "supports"}, {"gene": "TMPRSS15", "stance": "supports"}, {"gene": "SMIM24", "stance": "supports"}, {"gene": "SLC26A3", "stance": "supports"}, {"gene": "FABP2", "stance": "supports"}, {"gene": "CDHR5", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "SI", "stance": "supports"}, {"gene": "APOB", "stance": "supports"}, {"gene": "CES2", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "SLC5A1", "stance": "supports"}], "rationale": "The marker gene profile demonstrates defining characteristics of mature small intestinal (duodenal) enterocytes. Canonical brush border digestive enzymes include SI (sucrase-isomaltase), ANPEP (alanyl aminopeptidase), and duodenal-specific TMPRSS15 (enteropeptidase/enterokinase). Key nutrient transport and lipid absorption machinery genes are strongly enriched, including FABP1, FABP2, RBP2, SLC5A1 (SGLT1), SLC26A3, and apolipoproteins (APOA1, APOA4, APOB, APOC3). CDHR5 is a component of the enterocyte brush border intermicrovillar adhesion complex. There are no contradictory markers among the top genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.5}], "model": "gemini-flash", "task_id": "ct-085bedbfa5"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'intestinal crypt stem cell' is not the name of CL:0002066 ('Feyrter cell'). '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": ["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:0002066", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "SLC12A2", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "HMGA1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "PIGR", "stance": "contradicts"}, {"gene": "REG3A", "stance": "contradicts"}], "rationale": "The cluster is characterized by high expression of OLFM4, the canonical marker for human intestinal crypt stem cells (crypt base columnar cells), along with SLC12A2, HMGA1, REG1A, and DMBT1, which are highly enriched in the intestinal stem and progenitor compartment. Markers of mature differentiated lineages (such as DEFA5/DEFA6 for Paneth cells, MUC2 for goblet cells, and APOA1/FABP1 for mature enterocytes) are absent, although general epithelial and mature secretory-associated genes like PIGR and REG3A show modest expression."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.2}, {"answer": {"cell_type_id": "CL:0002250", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "SLC12A2", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "HMGA1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "PIGR", "stance": "contradicts"}, {"gene": "REG3A", "stance": "contradicts"}], "rationale": "The cluster strongly expresses OLFM4, the canonical marker of human intestinal crypt stem cells (crypt base columnar cells), together with SLC12A2, HMGA1, REG1A, and DMBT1, which are enriched in the crypt stem/progenitor cell compartment. More differentiated lineage markers (such as Paneth or mature enterocyte markers) are absent, though general epithelial/secretory genes like PIGR and REG3A are detected at modest levels."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'intestinal crypt stem cell' is not the name of CL:0002066 ('Feyrter cell'). 'intestinal crypt stem cell' is the name of CL:0002250 (intestinal crypt stem cell)."], "seconds": 9.2}], "model": "gemini-flash", "task_id": "ct-0f769ebe10"} +{"attempts": [{"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:0000148", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "GPNMB", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}], "rationale": "This cluster distinctly expresses canonical melanocyte-specific markers, including DCT (dopachrome tautomerase), TYRP1 (tyrosinase-related protein 1), MLANA (melan-A / MART1), PMEL (premelanosome protein), and the lineage-defining transcription factor MITF. These genes are strongly upregulated with high log fold changes and very low expression outside the cluster (~2-9%). The presence of KRT14 likely reflects ambient RNA contamination from abundant epidermal keratinocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.6}], "model": "gemini-flash", "task_id": "ct-1445edf08f"} +{"attempts": [{"codes": ["BEV025"], "evidence": 17, "findings": [{"message": "The ASCT+B reference lists MT1E as a marker of CL:4033042 (metallothionein-positive alveolar macrophage), cell types disjoint from CL:0000584.", "rule_id": "BEV025", "where": "evidence 15 (cluster=c09;gene=MT1E)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "FABP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "CPS1", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1E", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}, {"gene": "MT2A", "stance": "supports"}], "rationale": "The cluster exhibits classic markers of duodenal enterocytes (CL:0000584). FABP1 and RBP2 are canonical markers of intestinal absorptive enterocytes responsible for lipid and retinoid handling. GSTA1 and CPS1 are enterocyte-enriched metabolic enzymes. Epithelial identity is confirmed by EPCAM, KRT8, KRT18, and KRT19. In the human duodenum, mature enterocytes characteristically express high levels of antimicrobial/mucosal factors (REG1A, DMBT1, PIGR), the gut-homing chemokine CCL25, and high levels of metallothioneins (MT1G, MT1E, MT1X, MT2A, MT1H). No top marker genes argue against enterocyte identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.6}], "model": "gemini-flash", "task_id": "ct-1fed4d68f2"} +{"attempts": [{"codes": [], "evidence": 9, "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": "MYL9", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}], "rationale": "The cluster shows strong, specific expression of canonical smooth muscle contractile machinery genes, including TAGLN (transgelin), ACTA2 (alpha smooth muscle actin), MYH11 (smooth muscle myosin heavy chain 11), MYL9, TPM2, and CALD1. The expression of MYH11 specifically identifies mature smooth muscle cells, distinguishing them from pericytes and fibroblasts. Concurrently, markers such as RGS5, ADIRF, and IGFBP7 confirm its vascular mural/vascular-associated identity in the skin, corresponding to vascular associated smooth muscle cells (CL:0000359)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.7}], "model": "gemini-flash", "task_id": "ct-22fc152fbd"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists AQP3 as a marker of CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell); CL:1001431 (kidney collecting duct principal cell) and 1 more, cell types disjoint from CL:0001071.", "rule_id": "BEV025", "where": "evidence 10 (cluster=c13;gene=AQP3)"}], "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": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LTA", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "HPN", "stance": "supports"}, {"gene": "SCN1B", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "ZBTB16", "stance": "supports"}, {"gene": "LINC00299", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "This cluster exhibits the canonical and highly specific transcriptional profile of human group 3 innate lymphoid cells (ILC3):\n1. Key lineage markers: RORC encodes RORγt, the master transcription factor defining ILC3s. KIT (CD117) and IL7R (CD127) are hallmark surface markers of helper-like ILCs and specifically ILC3s in human tissue.\n2. Canonical ILC3 effector and identity genes: High expression of lymphotoxin genes (LTB and LTA) is characteristic of ILC3s, which use LTα1β2 signaling for mucosal lymphoid tissue maintenance and epithelial defense.\n3. Specific human ILC3 signature genes: IL4I1, TOX2, HPN (hepsin), SCN1B, AQP3, and LINC00299 represent well-documented, highly specific markers of human ILC3s identified in single-cell transcriptomic atlases of human ILCs.\n4. ZBTB16 (PLZF) is involved in ILC development and effector differentiation.\n5. LST1 is primarily recognized as a myeloid-associated transcript, but its presence here does not outweigh the definitive combination of RORC, KIT, IL7R, IL4I1, LTB, and LTA in the absence of T cell receptor components (e.g. CD3)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 63.2}], "model": "gemini-flash", "task_id": "ct-307f739343"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "pancreatic A cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "IRX2", "stance": "supports"}, {"gene": "LOXL4", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "SLC30A8", "stance": "supports"}], "rationale": "The expression profile is uniquely characteristic of human pancreatic alpha cells (pancreatic A cells). Key supporting markers include GCG (glucagon, the primary hormone secreted by alpha cells), PCSK2 (proprotein convertase required for processing proglucagon to mature glucagon), IRX2 (alpha cell lineage transcription factor), and well-established human alpha cell markers including TTR, GC, TM4SF4, and LOXL4, alongside general endocrine/islet granule markers such as CHGA, CHGB, and SLC30A8. No marker genes argue against this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.2}], "model": "gemini-flash", "task_id": "ct-32e6a3a16d"} +{"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:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "CD74", "stance": "contradicts"}, {"gene": "HLA-DRB1", "stance": "contradicts"}], "rationale": "The cluster strongly and specifically expresses hallmark endothelial cell markers, most notably PLVAP (plasmalemma vesicle-associated protein, pct_in 0.879 vs pct_out 0.037), CAVIN2 (pct_in 0.907 vs pct_out 0.124), RNASE1 (pct_in 0.946 vs pct_out 0.139), RAMP3, TM4SF1, and GNG11. While CD74 and HLA-DRB1 are classical MHC class II markers typically found in professional antigen-presenting cells, renal microvascular endothelial cells in humans constitutively express MHC class II molecules. Thus, the profile unambiguously identifies this cluster as an endothelial cell (CL:0000115)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.5}], "model": "gemini-flash", "task_id": "ct-32f05dbab5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 16, "findings": [{"message": "The label 'CD1c-positive myeloid dendritic cell' is not the name of CL:0002396 ('CD14-low, CD16-positive monocyte'). '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": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002396", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "The expression profile strongly identifies this cluster as CD1c-positive myeloid dendritic cells (cDC2 / type 2 conventional dendritic cells; CL:0002396) in the skin dermis:\n1. Extremely high expression of MHC class II molecules and antigen presentation machinery: HLA-DRA, CD74, HLA-DRB1, HLA-DPB1, HLA-DPA1, HLA-DQA1, HLA-DQB1, HLA-DRB5, and CST3.\n2. Specific expression of FCER1A (Fc epsilon receptor Ia) alongside FCER1G, which in human myeloid and dendritic cell subsets uniquely distinguishes cDC2s from cDC1s and macrophages.\n3. Expression of GPR183 (EBI2), a key chemotactic receptor enriched in and essential for cDC2 tissue positioning.\n4. Co-expression of myeloid markers LYZ, TYROBP (DAP12), and AIF1, typical of dermal myeloid dendritic cells.\n5. Lack of Langerhans cell markers (CD207/langerin, CD1A), cDC1 markers (CLEC9A, XCR1), mature/migratory DC markers (LAMP3, CCR7), and macrophage-specific markers (CD163, CD68, MRC1, MERTK) argues against other skin myeloid cell types."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 57.1}, {"answer": {"cell_type_id": "CL:0002399", "cell_type_label": "CD1c-positive myeloid dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "The marker profile strongly identifies this cluster as CD1c-positive myeloid dendritic cells (cDC2 / type 2 conventional dendritic cells; CL:0002399) in human skin:\n1. High expression of MHC class II molecules and antigen processing/presentation machinery: HLA-DRA, CD74, HLA-DRB1, HLA-DPB1, HLA-DPA1, HLA-DQA1, HLA-DQB1, and CST3.\n2. Distinctive expression of FCER1A (Fc epsilon receptor Ia) and FCER1G, which in human myeloid/dendritic subsets specifically marks CD1c+ cDC2s and differentiates them from cDC1s and macrophages.\n3. Expression of GPR183 (EBI2), a key chemotactic receptor critical for cDC2 tissue localization.\n4. Expression of general myeloid/dendritic cell genes including LYZ, TYROBP (DAP12), and AIF1."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD1c-positive myeloid dendritic cell' is not the name of CL:0002396 ('CD14-low, CD16-positive monocyte'). 'CD1c-positive myeloid dendritic cell' is the name of CL:0002399 (CD1c-positive myeloid dendritic cell)."], "seconds": 12.6}], "model": "gemini-flash", "task_id": "ct-3385c5a4a1"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002064", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "PRSS1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}], "rationale": "This cluster exhibits high and specific expression of canonical pancreatic digestive enzymes and zymogens (PRSS1, CTRB2, PNLIP, PLA2G1B, CPB1, CPA1, CPA2, CEL), the trypsin inhibitor SPINK1, and regenerating islet-derived family members (REG1A, REG1B, REG3A). These are definitive markers of pancreatic acinar cells. No markers contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.8}], "model": "gemini-flash", "task_id": "ct-36d56001f7"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'type A intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). 'type A intercalated cell' is the name of CL:0005011 (renal alpha-intercalated 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:0005010", "cell_type_label": "type A intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}], "rationale": "The cluster is identified as a type A intercalated cell (CL:0005010) of the kidney collecting duct / distal nephron. It strongly expresses canonical type A intercalated cell markers responsible for proton secretion and bicarbonate reabsorption: SLC4A1 (AE1, basolateral Cl-/HCO3- exchanger), SLC26A7 (basolateral anion exchanger), ATP6V0D2 (vacuolar H+-ATPase subunit), and RHCG (ammonia transporter). It also displays high expression of TMEM213, CA12, DEFB1, and SPINK1, which are characteristic of human kidney intercalated cells. In contrast, CALB1 and HSD11B2 are traditionally canonical markers of the distal convoluted tubule, connecting tubule, and collecting duct principal cells, arguing against a classical intercalated cell profile (likely reflecting ambient RNA or expression in connecting tubule transitional cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.7}, {"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "type A intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}], "rationale": "The cluster is identified as a type A intercalated cell (CL:0005011) of the kidney collecting duct / distal nephron. It strongly expresses canonical type A intercalated cell markers responsible for proton secretion and bicarbonate reabsorption: SLC4A1 (AE1, basolateral Cl-/HCO3- exchanger), SLC26A7 (basolateral anion exchanger), ATP6V0D2 (vacuolar H+-ATPase subunit), and RHCG (ammonia transporter). It also displays high expression of TMEM213, CA12, DEFB1, and SPINK1, which are characteristic of human kidney intercalated cells. In contrast, CALB1 and HSD11B2 are canonical markers of distal convoluted tubule / connecting tubule / principal cells, arguing against a classical intercalated cell profile."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type A intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). 'type A intercalated cell' is the name of CL:0005011 (renal alpha-intercalated cell)."], "seconds": 11.4}], "model": "gemini-flash", "task_id": "ct-3cbc7c57fd"} +{"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": "TRAC", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CORO1A", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "The cluster shows strong and specific expression of canonical T cell lineage markers CD3D (79.5% in vs 3.0% out) and TRAC (72.6% in vs 3.7% out), which unequivocally identify this cluster as T cells. The high expression of CCL5, IL32, NKG7, GZMA, and HCST further indicates an effector / cytotoxic T cell phenotype commonly resident in human liver tissue. General lymphocyte and immune-associated genes like CD52, CORO1A, and CXCR4 also support this annotation. None of the top marker genes contradict a T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.7}], "model": "gemini-flash", "task_id": "ct-3f2898af5e"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "CFD", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "GSN", "stance": "supports"}, {"gene": "COL6A2", "stance": "supports"}, {"gene": "COL1A1", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "FBLN1", "stance": "supports"}, {"gene": "PLAC9", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "MMP2", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "SOD3", "stance": "supports"}, {"gene": "CCDC80", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "APOD", "stance": "supports"}, {"gene": "CTSK", "stance": "supports"}, {"gene": "CEBPB", "stance": "supports"}, {"gene": "SERPINF1", "stance": "supports"}], "rationale": "This cluster strongly and consistently expresses canonical markers of skin fibroblasts. The top enriched genes include core extracellular matrix (ECM) structural components such as collagens (COL1A1, COL1A2, COL3A1, COL6A2), proteoglycans (DCN, LUM), and ECM glycoproteins (FBLN1, CCDC80). It also highly expresses characteristic dermal fibroblast secreted factors, signaling proteins, and enzymes, including CFD, CXCL14, SFRP2, MMP2, SOD3, CTSK, IGFBP5, APOD, and SERPINF1. There are no conflicting lineage-specific markers (e.g., keratinocytes, melanocytes, endothelial, or immune cell markers). Therefore, this cluster is unambiguously identified as a fibroblast (CL:0000057)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.5}], "model": "gemini-flash", "task_id": "ct-5e18af843a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'type B pancreatic cell' is not the name of CL:0000166 ('chromaffin cell'). 'type B pancreatic cell' is the name of CL:0000169 (type B pancreatic 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:0000166", "cell_type_label": "type B pancreatic cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "MAFA", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "HADH", "stance": "supports"}, {"gene": "SYT13", "stance": "supports"}, {"gene": "NPTX2", "stance": "supports"}], "rationale": "The cluster strongly expresses classic, canonical marker genes of pancreatic beta cells (type B pancreatic cells), notably INS (insulin) and IAPP (islet amyloid polypeptide), alongside key beta-cell transcription factors (MAFA, PDX1), proinsulin processing enzymes (PCSK1), and beta-cell metabolic/secretion regulators (G6PC2, ABCC8, HADH, SYT13). No markers contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.8}, {"answer": {"cell_type_id": "CL:0000169", "cell_type_label": "type B pancreatic cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "MAFA", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "HADH", "stance": "supports"}, {"gene": "SYT13", "stance": "supports"}, {"gene": "NPTX2", "stance": "supports"}], "rationale": "The cluster exhibits high and specific expression of canonical marker genes of pancreatic beta cells (type B pancreatic cell, CL:0000169), including INS (insulin), IAPP (islet amyloid polypeptide), beta-cell transcription factors (PDX1, MAFA), prohormone processing enzyme PCSK1, and glucose-sensing/secretion machinery components (G6PC2, ABCC8, HADH, SYT13, NPTX2). No markers contradict this annotation."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type B pancreatic cell' is not the name of CL:0000166 ('chromaffin cell'). 'type B pancreatic cell' is the name of CL:0000169 (type B pancreatic cell)."], "seconds": 12.4}], "model": "gemini-flash", "task_id": "ct-6ea69bcccb"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'enteroendocrine cell' is not the name of CL:0000169 ('type B pancreatic cell'). 'enteroendocrine cell' is the name of CL:0000164 (enteroendocrine cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0000169", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "CHGA", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PCSK1N", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "TFF3", "stance": "contradicts"}], "rationale": "The cluster expresses classic pan-enteroendocrine / neuroendocrine markers including chromogranins (CHGA, CHGB), secretogranins (SCG2, SCG5, SCGN), prohormone processing and neuroendocrine peptides (PCSK1N, CPE), and lineage-determining transcription factors (NEUROD1, INSM1, FEV). In addition, gut hormone genes such as secretin (SCT) and motilin (MLN) are characteristic hormones produced by enteroendocrine cells in the duodenum. TFF3 is typically enriched in goblet cells and can be considered a marker that argues against this specific lineage, though low/moderate levels or ambient RNA from goblet cells are frequently seen in intestinal single-cell datasets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.4}, {"answer": {"cell_type_id": "CL:0000164", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "CHGA", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PCSK1N", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "TFF3", "stance": "contradicts"}], "rationale": "The cluster expresses classic pan-enteroendocrine markers including chromogranins (CHGA, CHGB), secretogranins (SCG2, SCG5, SCGN), neuroendocrine peptide/processing factors (PCSK1N, CPE), and key lineage transcription factors (NEUROD1, INSM1, FEV). In addition, enteroendocrine hormones characteristic of the duodenum such as secretin (SCT) and motilin (MLN) are distinctly expressed. TFF3 is a canonical goblet cell marker and argues against this lineage (likely present as ambient RNA or low-level co-expression). The correct Cell Ontology ID for enteroendocrine cell is CL:0000164."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'enteroendocrine cell' is not the name of CL:0000169 ('type B pancreatic cell'). 'enteroendocrine cell' is the name of CL:0000164 (enteroendocrine cell)."], "seconds": 9.1}], "model": "gemini-flash", "task_id": "ct-76f0318d60"} +{"attempts": [{"codes": ["BEV025"], "evidence": 15, "findings": [{"message": "The ASCT+B reference lists FCER1G as a marker of CL:0000767 (basophil); CL:0000775 (neutrophil); CL:0000784 (plasmacytoid dendritic cell) and 5 more, cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 6 (cluster=c09;gene=FCER1G)"}, {"message": "The ASCT+B reference lists CCL3 as a marker of CL:4033041 (CCL3-positive alveolar macrophage), cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 14 (cluster=c09;gene=CCL3)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "KLRF1", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "This cluster originates from a human liver caudate lobe scRNA-seq dataset (consistent with MacParland et al., 2018). It exhibits robust expression of natural killer (NK) cell-defining surface receptors, signaling adapters, and cytotoxic effector molecules. In particular, KLRF1 (NKp80) is a hallmark NK cell-specific marker, alongside KLRD1 (CD94), KLRB1 (CD161), and CD7. Intracellular signaling adapters essential for NK-activating receptors (TYROBP/DAP12, FCER1G, and HCST/DAP10), cytokine receptors (IL2RB/CD122), cytotoxicity/chemokine genes (NKG7, GZMA, XCL2, CCL3, CCL4, CCL5), and CMC1 further corroborate the natural killer cell identity. The absence of canonical T cell lineage markers (e.g., CD3 subunits) rules out T and NKT cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.7}], "model": "gemini-flash", "task_id": "ct-992627e517"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0000546.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=HPGDS)"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0000546.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=GATA3)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000546", "cell_type_label": "T-helper 2 cell", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "The marker gene expression profile strongly identifies this cluster as T-helper 2 cells (Th2 cells, CL:0000546). Key supporting evidence includes high and specific expression of PTGDR2 (CRTH2 / CD294, the canonical surface marker of Th2 cells) and HPGDS (hematopoietic prostaglandin D synthase), which function together in the PGD2 pathway characteristic of Th2 cells. Additionally, GATA3 is the lineage-defining master transcription factor for type 2 immunity, while IL32, LTB, and TESPA1 (involved in TCR signaling and enriched in Th2 cells) support the CD4+ T cell identity. KRT1 is normally an epithelial marker and is likely present due to ambient RNA contamination or technical artifact."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.7}], "model": "gemini-flash", "task_id": "ct-a53a01a447"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "TM4SF1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}], "rationale": "The cluster exhibits characteristic expression of canonical endothelial marker genes including TM4SF1, RAMP2 (a key component of the adrenomedullin receptor complex in vascular endothelium), TIMP3, IFI27, and ID1. In the kidney, AQP1 is highly expressed in descending vasa recta endothelial cells as well as proximal tubular and descending thin limb epithelial cells; here its high expression alongside prominent vascular/endothelial markers and the absence of tubular epithelial markers (such as LRP2, CUBN, or SLC12A1) firmly identifies this cluster as endothelial cells (CL:0000115)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.5}], "model": "gemini-flash", "task_id": "ct-c22bc01239"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists KLRB1 as a marker of CL:0000940 (mucosal invariant T cell), cell types disjoint from CL:0000798.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c06;gene=KLRB1)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "NCR3", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "BLK", "stance": "contradicts"}, {"gene": "LST1", "stance": "contradicts"}, {"gene": "CAPG", "stance": "contradicts"}], "rationale": "The cluster is identified as a gamma-delta T cell (CL:0000798). A definitive marker is TRDV2 (T cell receptor delta variable 2), which is captured in 10x 5' scRNA-seq and specifically forms the TCR delta chain of Vdelta2 gamma-delta T cells. The cluster also shows strong expression of the T-cell coreceptor CD3E, along with characteristic gamma-delta / cytotoxic T-cell markers such as KLRB1 (CD161), NCR3 (NKp30), CCR6, IL7R, and LTB. Canonical B-cell (BLK) or myeloid-associated genes (LST1, CAPG) appear at lower frequencies or represent known atypical transcripts in this lymphocyte lineage, arguing superficially against a pure T-cell phenotype but fully consistent overall with gamma-delta T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.0}], "model": "gemini-flash", "task_id": "ct-c84f57496a"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [{"gene": "TOP2A", "stance": "contradicts"}, {"gene": "MKI67", "stance": "contradicts"}, {"gene": "CDK1", "stance": "contradicts"}, {"gene": "UBE2C", "stance": "contradicts"}, {"gene": "CENPF", "stance": "contradicts"}, {"gene": "NUSAP1", "stance": "contradicts"}, {"gene": "TYMS", "stance": "contradicts"}, {"gene": "STMN1", "stance": "contradicts"}, {"gene": "HMGB2", "stance": "contradicts"}, {"gene": "H4C3", "stance": "contradicts"}], "rationale": "The top marker genes for this cluster (H4C3, STMN1, TUBA1B, TUBB, HMGB2, TOP2A, TYMS, MKI67, UBE2C, NUSAP1, CENPF, CDK1) are canonical hallmarks of cell cycle progression, DNA replication (S phase), and mitosis (G2/M phase). There are no lineage-specific marker genes present (e.g., epithelial, endothelial, mesenchymal, or immune markers) to resolve the underlying cell type of origin. In the Cell Ontology, proliferation/cycling is a cellular state/biological process rather than a distinct anatomical cell type. Because the cluster is defined solely by cell cycle signatures without lineage-defining markers, it cannot be assigned to a specific Cell Ontology cell type term."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.8}], "model": "gemini-flash", "task_id": "ct-c8e68f267e"} +{"attempts": [{"codes": ["BEV004", "BEV023"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0002371 (obsolete somatic cell) is obsolete in the pinned CL release. Use CL:0000000 (cell).", "rule_id": "BEV023", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV017"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'kidney collecting duct principal cell' is not the name of CL:1000714 ('kidney cortex collecting duct principal cell'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0002371", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "KLK1", "stance": "contradicts"}], "rationale": "The cluster strongly expresses canonical markers of human kidney collecting duct principal cells (CL:0002371), prominently led by DEFB1, HSD11B2 (11-beta-hydroxysteroid dehydrogenase type 2, crucial for aldosterone-regulated sodium transport in principal cells), TMEM52B, RHCG, and ATP1B1. CALB1 is also expressed in cortical collecting duct principal cells as well as connecting tubule (CNT) and distal convoluted tubule (DCT) cells. The presence of KLK1 (tissue kallikrein) reflects the transition/overlap with connecting tubule cells, but the overwhelming enrichment of DEFB1, HSD11B2, and TMEM52B decisively points to collecting duct principal cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.3}, {"answer": {"cell_type_id": "CL:1000714", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "KLK1", "stance": "contradicts"}], "rationale": "The cluster strongly expresses key marker genes characteristic of kidney collecting duct principal cells (CL:1000714), including DEFB1, HSD11B2 (11-beta-hydroxysteroid dehydrogenase type 2, essential for aldosterone specificity in principal cells), TMEM52B, RHCG, and ATP1B1. CALB1 is also expressed in cortical collecting duct principal cells as well as connecting tubule (CNT) and distal convoluted tubule (DCT) cells. KLK1 (tissue kallikrein) is predominantly a marker of the connecting tubule, reflecting the close developmental and transcriptional continuum between CNT and cortical collecting duct cells, but the high enrichment of DEFB1, HSD11B2, and TMEM52B confirms the cell type as kidney collecting duct principal cell."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0002371 (obsolete somatic cell) is obsolete in the pinned CL release. Use CL:0000000 (cell)."], "seconds": 25.1}, {"answer": {"cell_type_id": "CL:1000714", "cell_type_label": "kidney cortex collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "KLK1", "stance": "contradicts"}], "rationale": "The cluster displays high expression of canonical collecting duct principal cell markers, including DEFB1, HSD11B2 (11-beta-hydroxysteroid dehydrogenase type 2), TMEM52B, RHCG, and ATP1B1. Furthermore, CALB1 is strongly enriched (logfc 2.298, pct_in 0.856), which specifically distinguishes cortical collecting duct principal cells from medullary collecting duct principal cells. KLK1 is predominantly expressed in connecting tubule cells, reflecting the transcriptional proximity along the distal nephron/collecting system, but the overall marker profile definitively identifies this cluster as kidney cortex collecting duct principal cell (CL:1000714)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct principal cell' is not the name of CL:1000714 ('kidney cortex collecting duct principal cell'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal cell)."], "seconds": 28.7}], "model": "gemini-flash", "task_id": "ct-e7cab67ae5"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic ductal cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}, {"gene": "ONECUT2", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}], "rationale": "This cluster strongly and specifically expresses canonical marker genes of pancreatic ductal cells, notably CFTR (cystic fibrosis transmembrane conductance regulator), SLC4A4 (electrogenic sodium bicarbonate cotransporter), TACSTD2 (TROP2), MMP7, SPP1, ANXA4, and ONECUT2. There is no significant expression of acinar (e.g., PRSS1, CPA1) or endocrine islet markers (e.g., INS, GCG, SST)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.5}], "model": "gemini-flash", "task_id": "ct-ee90c8cca6"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000182", "cell_type_label": "hepatocyte", "decision": "annotate", "markers": [{"gene": "ALB", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "APOA2", "stance": "supports"}, {"gene": "APOC1", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "FGA", "stance": "supports"}, {"gene": "ORM1", "stance": "supports"}, {"gene": "HP", "stance": "supports"}, {"gene": "FGB", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "TF", "stance": "supports"}, {"gene": "AMBP", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "CYP2E1", "stance": "supports"}, {"gene": "FGG", "stance": "supports"}, {"gene": "APOH", "stance": "supports"}, {"gene": "ORM2", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}], "rationale": "The cluster originates from the liver and expresses canonical hepatocyte markers including serum albumin (ALB), apolipoproteins (APOC3, APOA2, APOC1, APOA1, APOH), coagulation factors/fibrinogen chains (FGA, FGB, FGG), carrier/acute-phase proteins (TTR, HP, ORM1, ORM2, TF, AMBP, SERPINA1, RBP4), and the metabolic cytochrome P450 enzyme CYP2E1. There are no conflicting lineage markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.9}], "model": "gemini-flash", "task_id": "ct-fa6e0d282d"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "IGFBP7", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "CCL14", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "IL6ST", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "HLA-E", "stance": "supports"}, {"gene": "IFITM3", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of general endothelial cell markers such as CLDN5, TM4SF1, GNG11, and IGFBP7. Furthermore, it specifically expresses established markers for liver sinusoidal endothelial cells (LSECs), particularly FCN3, FCN2, DNASE1L3, and CRHBP. This combination of generic endothelial and LSEC-specific markers identifies these cells as endothelial cells of the hepatic sinusoid."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.8}], "model": "gemini-pro", "task_id": "ct-04aaea9940"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "APOA4", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "PRAP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "ANPEP", "stance": "supports"}, {"gene": "PHGR1", "stance": "supports"}, {"gene": "TMPRSS15", "stance": "supports"}, {"gene": "SMIM24", "stance": "supports"}, {"gene": "SLC26A3", "stance": "supports"}, {"gene": "FABP2", "stance": "supports"}, {"gene": "CDHR5", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "SI", "stance": "supports"}, {"gene": "APOB", "stance": "supports"}, {"gene": "CES2", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "SLC5A1", "stance": "supports"}], "rationale": "The cluster expresses high levels of apolipoproteins (APOA4, APOA1, APOC3, APOB), fatty acid-binding proteins (FABP1, FABP2), and retinol-binding protein (RBP2), which are characteristic of lipid absorption and chylomicron formation. It also features typical intestinal brush border enzymes like sucrase-isomaltase (SI) and aminopeptidase N (ANPEP), as well as the duodenum-specific enteropeptidase (TMPRSS15). The presence of the sodium/glucose cotransporter (SLC5A1) and structural microvilli markers (CDHR5) further confirms that these are mature enterocytes (intestinal absorptive cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.6}], "model": "gemini-pro", "task_id": "ct-085bedbfa5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'intestinal stem cell' is not the name of CL:0011026 ('progenitor cell'). Closest names: CL:0002250 (intestinal crypt stem cell); CL:0019032 (intestinal tuft cell); CL:0000047 (neural stem 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:0011026", "cell_type_label": "intestinal stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "SLC12A2", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}], "rationale": "The cluster expresses extremely high levels of OLFM4, which is the canonical marker for human intestinal stem cells (specifically crypt base columnar cells). It also exhibits high expression of SLC12A2 and CCL25, which are characteristic of small intestinal crypt epithelial cells. The presence of secretory and antimicrobial factors such as REG1A, REG3A, AGR2, and DMBT1 is typical of the crypt base niche, while PTMA and ribosomal genes indicate an active, cycling cell population consistent with stem or early transit-amplifying cells. There are no top markers that strongly contradict this assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.7}, {"answer": {"cell_type_id": "CL:0002250", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "SLC12A2", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}], "rationale": "The cluster expresses high levels of OLFM4, which is the canonical marker for human intestinal crypt stem cells (specifically crypt base columnar cells). It also exhibits high expression of SLC12A2 and CCL25, which are characteristic of small intestinal crypt epithelial cells. The presence of factors such as REG1A, AGR2, and DMBT1 is typical of the crypt base niche. There are no top markers that strongly contradict this assignment."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'intestinal stem cell' is not the name of CL:0011026 ('progenitor cell'). Closest names: CL:0002250 (intestinal crypt stem cell); CL:0019032 (intestinal tuft cell); CL:0000047 (neural stem cell)."], "seconds": 16.8}], "model": "gemini-pro", "task_id": "ct-0f769ebe10"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'melanocyte' is not the name of CL:0000147 ('pigment cell'). 'melanocyte' is the name of CL:0000148 (melanocyte).", "rule_id": "BEV017", "where": "object label"}], "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:0000147", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}], "rationale": "The cluster exhibits high expression of classic, canonical melanocyte markers including DCT, TYRP1, MLANA, PMEL, and the master melanocyte transcription factor MITF, strongly indicating it is a melanocyte cluster. The expression of KRT14, a basal keratinocyte marker, is likely due to ambient RNA (which is very common in skin scRNA-seq data due to the abundance of keratinocytes), but it biologically contradicts a pure melanocyte identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.8}, {"answer": {"cell_type_id": "CL:0000148", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}], "rationale": "The cluster exhibits high expression of classic, canonical melanocyte markers including DCT, TYRP1, MLANA, PMEL, and the master melanocyte transcription factor MITF, strongly indicating it is a melanocyte cluster. The expression of KRT14, a basal keratinocyte marker, is likely due to ambient RNA (which is very common in skin scRNA-seq data due to the abundance of keratinocytes), but it biologically contradicts a pure melanocyte identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'melanocyte' is not the name of CL:0000147 ('pigment cell'). 'melanocyte' is the name of CL:0000148 (melanocyte)."], "seconds": 15.2}], "model": "gemini-pro", "task_id": "ct-1445edf08f"} +{"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:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "FABP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "CPS1", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "REG1A", "stance": "contradicts"}, {"gene": "AGR2", "stance": "contradicts"}], "rationale": "This cluster expresses canonical markers of the absorptive enterocyte lineage, including FABP1, RBP2, CPS1, and GSTA1. It also highly expresses general epithelial markers (EPCAM, KRT8, KRT18, KRT19) and functional markers of the small intestinal epithelium (PIGR for IgA transport, and the chemokine CCL25). The robust expression of multiple metallothioneins (MT1G, MT1E, MT1X, MT2A, MT1H) is also consistent with the active metabolic role of enterocytes. \n\nHowever, the top marker REG1A and the presence of AGR2—both of which are typically associated with secretory lineages in the intestine, such as Paneth or goblet cells—could argue against a pure mature absorptive enterocyte state. Still, the absence of classical definitive secretory markers like MUC2 (goblet cells) or DEFA5/DEFA6 (Paneth cells) makes enterocyte (CL:0000584) the most accurate classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.9}], "model": "gemini-pro", "task_id": "ct-1fed4d68f2"} +{"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": "MYL9", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}], "rationale": "This cluster highly expresses canonical markers of smooth muscle cells, particularly genes encoding contractile proteins such as ACTA2 (alpha-smooth muscle actin), MYH11 (smooth muscle myosin heavy chain), TAGLN (transgelin), MYL9 (myosin light chain 9), TPM2 (tropomyosin 2), and CALD1. Additionally, RGS5 is a well-known marker for mural cells (which encompass vascular smooth muscle cells and pericytes). The presence of MYH11 is particularly specific to smooth muscle cells and typically distinguishes them from pericytes, strongly supporting the smooth muscle cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.8}], "model": "gemini-pro", "task_id": "ct-22fc152fbd"} +{"attempts": [{"codes": ["BEV017"], "evidence": 5, "findings": [{"message": "The label 'type 3 innate lymphoid cell' is not the name of CL:0001071 ('group 3 innate lymphoid cell'). Closest names: CL:0001071 (group 3 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001069 (group 2 innate lymphoid 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:0001071", "cell_type_label": "type 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}], "rationale": "The cluster expresses IL7R (CD127), RORC (the master transcription factor for ILC3s), and KIT (CD117), which collectively form the canonical gene signature for type 3 innate lymphoid cells (ILC3s). The expression of genes such as LTB, LTA, TOX2, and IL4I1 is also characteristic of the ILC3 profile. The lack of standard T-cell markers (e.g., CD3 complex genes) among the top markers supports an innate lymphoid identity over Th17 cells, which would otherwise share the RORC+ signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.7}, {"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}], "rationale": "The cluster expresses IL7R (CD127), RORC (the master transcription factor for ILC3s), and KIT (CD117), which collectively form the canonical gene signature for group 3 innate lymphoid cells (ILC3s). The expression of genes such as LTB, LTA, TOX2, and IL4I1 is also characteristic of the ILC3 profile. The lack of standard T-cell markers (e.g., CD3 complex genes) among the top markers supports an innate lymphoid identity over Th17 cells, which would otherwise share the RORC+ signature."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type 3 innate lymphoid cell' is not the name of CL:0001071 ('group 3 innate lymphoid cell'). Closest names: CL:0001071 (group 3 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001069 (group 2 innate lymphoid cell)."], "seconds": 13.3}], "model": "gemini-pro", "task_id": "ct-307f739343"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "pancreatic A cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "IRX2", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}], "rationale": "The cluster exhibits extremely high expression of GCG (glucagon), the canonical and definitive marker for pancreatic alpha cells (pancreatic A cells). It also expresses IRX2, a transcription factor that is specifically enriched in alpha cells within the pancreatic islets. The presence of CHGA, CHGB, SCG2, SCG5, and PCSK2 confirms the general neuroendocrine identity of the cells. The absence of other major islet hormones like INS (beta cells) or SST (delta cells) among the top markers further solidifies the assignment as pancreatic alpha cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.7}], "model": "gemini-pro", "task_id": "ct-32e6a3a16d"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "RGCC", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical endothelial cell markers, including PLVAP, RNASE1, CAVIN2, TM4SF1, GNG11, RGCC, and RAMP3. Specifically, PLVAP is a well-known marker for fenestrated capillary endothelial cells, which are abundant in the kidney (e.g., peritubular capillaries and vasa recta). Additionally, renal microvascular endothelial cells are known to express high levels of MHC class II molecules, which accounts for the prominent appearance of CD74, HLA-DRB1, and other HLA genes among the top markers. None of the listed top markers contradict an endothelial identity in this context."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.0}], "model": "gemini-pro", "task_id": "ct-32f05dbab5"} +{"attempts": [{"codes": [], "evidence": 13, "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": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The cluster expresses very high levels of MHC class II genes (HLA-DRA, HLA-DRB1, HLA-DPB1, HLA-DPA1, HLA-DQA1, HLA-DQB1) and the invariant chain CD74, which are characteristic of professional antigen-presenting cells. The presence of FCER1A (a classic marker for cDC2 cells in human tissues), along with myeloid/DC markers LYZ, AIF1, TYROBP, FCER1G, and CST3, strongly identifies these cells as dendritic cells. There are no prominent markers suggesting an alternative identity such as B cells (which would express MS4A1/CD20) or mast cells (which would lack high MHC class II expression)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.4}], "model": "gemini-pro", "task_id": "ct-3385c5a4a1"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002064", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PRSS1", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}], "rationale": "The cluster exhibits robust expression of classical pancreatic acinar cell markers, including genes encoding for digestive enzymes (PRSS1, CTRB2, PNLIP, PLA2G1B, CPB1, CPA1, CPA2, CEL) and other characteristic acinar secretory proteins (REG1A, REG1B, REG3A, SPINK1). The marker profile strongly and unambiguously supports the identification of this cluster as pancreatic acinar cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.2}], "model": "gemini-pro", "task_id": "ct-36d56001f7"} +{"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:0005011", "cell_type_label": "type A intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}], "rationale": "The cluster expresses classic and highly specific markers for type A intercalated cells of the kidney collecting duct, including the basolateral chloride/bicarbonate exchangers SLC4A1 (AE1) and SLC26A7, the V-ATPase subunit ATP6V0D2, and the ammonia transporter RHCG. TMEM213 and CA12 further support the intercalated cell identity. However, the cluster also exhibits strong expression of CALB1 and HSD11B2, which are typically restricted to principal cells and connecting tubule (CNT) cells. This co-expression may represent a specific subpopulation (e.g., type A intercalated cells residing in the connecting tubule), transitional cells, or technical artifacts such as doublets or ambient RNA from neighboring principal cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.3}], "model": "gemini-pro", "task_id": "ct-3cbc7c57fd"} +{"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": "TRAC", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "The cluster expresses highly specific and definitive markers for T cells, notably CD3D (a component of the T-cell receptor-CD3 complex) and TRAC (T-cell receptor alpha constant). Additionally, the cluster expresses markers indicative of an effector or cytotoxic phenotype commonly seen in T cells (and NK cells), such as CCL5, IL32, NKG7, GZMA, and HCST. CD52 is also a classic lymphocyte antigen. There are no markers in the provided list that contradict this T cell annotation, as the remaining genes (like MALAT1, TMSB4X, RPS3, and HLA genes) are broadly expressed."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.8}], "model": "gemini-pro", "task_id": "ct-3f2898af5e"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL6A2", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "FBLN1", "stance": "supports"}, {"gene": "MMP2", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}], "rationale": "The cluster expresses canonical markers of fibroblasts, particularly extracellular matrix components heavily produced by these cells. These include collagens (COL1A1, COL1A2, COL3A1, COL6A2) and proteoglycans like decorin (DCN) and lumican (LUM). Additional expression of FBLN1, MMP2, and SFRP2 further strongly supports a fibroblast identity within the skin. There are no markers contradicting this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.7}], "model": "gemini-pro", "task_id": "ct-5e18af843a"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000169", "cell_type_label": "type B pancreatic cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "MAFA", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}], "rationale": "The cluster is defined by the very high expression of INS (Insulin), which is the canonical hormone uniquely produced by pancreatic beta cells. IAPP (Islet Amyloid Polypeptide) is co-secreted with insulin. Additionally, the cluster expresses critical beta-cell transcription factors such as PDX1 and MAFA, which are essential for beta cell maturation and insulin gene expression. Other supporting markers include ABCC8 (a subunit of the KATP channel regulating insulin secretion), G6PC2 (an islet-specific protein), and PCSK1 (an enzyme that processes proinsulin into mature insulin). There are no markers in the top list that contradict this assignment (such as GCG for alpha cells or SST for delta cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.2}], "model": "gemini-pro", "task_id": "ct-6ea69bcccb"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000164", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "PCSK1N", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}], "rationale": "The cluster exhibits high expression of canonical pan-enteroendocrine markers, including chromogranins (CHGA, CHGB) and secretogranins (SCG2, SCG5, SCGN). It also expresses essential neuroendocrine transcription factors like NEUROD1 and INSM1. The presence of specific hormones such as SCT (secretin) and MLN (motilin) further confirms the identity of these cells as enteroendocrine cells of the duodenum."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.1}], "model": "gemini-pro", "task_id": "ct-76f0318d60"} +{"attempts": [{"codes": ["BEV025"], "evidence": 15, "findings": [{"message": "The ASCT+B reference lists CCL3 as a marker of CL:4033041 (CCL3-positive alveolar macrophage), cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 7 (cluster=c09;gene=CCL3)"}, {"message": "The ASCT+B reference lists FCER1G as a marker of CL:0000767 (basophil); CL:0000775 (neutrophil); CL:0000784 (plasmacytoid dendritic cell) and 5 more, cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 11 (cluster=c09;gene=FCER1G)"}], "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": "KLRB1", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "KLRF1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}], "rationale": "The cluster's top differentially expressed genes clearly indicate a natural killer (NK) cell identity. It robustly expresses hallmark killer cell lectin-like receptors such as KLRB1 (CD161), KLRD1 (CD94), and especially KLRF1 (NKp80), which is highly specific to NK cells. The presence of cytotoxic effector molecules (GZMA, NKG7), characteristic chemokines secreted by activated NK cells (CCL3, CCL4, CCL5, XCL2), and essential signaling adapter proteins for NK activating receptors (TYROBP/DAP12, HCST/DAP10, FCER1G) further solidify this annotation. Additionally, IL2RB (CD122) is critical for NK cell development and responsiveness, and CD7 is typically present on both NK and T cells. No top marker genes argue against an NK cell assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.9}], "model": "gemini-pro", "task_id": "ct-992627e517"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0000546.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=GATA3)"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0000546.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=HPGDS)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000546", "cell_type_label": "T helper 2 cell", "decision": "annotate", "markers": [{"gene": "GATA3", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "HPGDS", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TESPA1", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "The cluster is defined by the classical Th2/ILC2 markers GATA3 (the master transcription factor for type 2 immunity) and PTGDR2 (also known as CRTH2, the canonical surface marker for these cells). HPGDS is also highly characteristic of type 2 lymphocytes. The distinction between ILC2s and Th2 cells is made clear by the ubiquitous expression of IL32 (a canonical T cell marker) and TESPA1 (a gene fundamentally involved in T cell receptor signaling), which strongly support a T helper 2 cell identity over an ILC2 identity. KRT1 is an epidermal/epithelial keratin and its presence contradicts a lymphoid identity, likely representing ambient RNA contamination or a doublet artifact."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.3}], "model": "gemini-pro", "task_id": "ct-a53a01a447"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "RAMP2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}], "rationale": "The cluster exhibits distinct expression of canonical endothelial markers such as RAMP2 and TM4SF1, along with the mesenchymal/endothelial marker VIM. The high expression of AQP1 (Aquaporin-1) is particularly informative; while it is widely known as a proximal tubule marker, it is also highly expressed in the descending vasa recta (DVR) endothelial cells in the kidney. The complete absence of standard proximal tubule markers (like LRP2 or CUBN) paired with endothelial gene expression confirms this cluster represents DVR endothelial cells. Furthermore, TIMP3 and IFI27 are enriched in renal endothelial subsets. Other genes like FOS, JUNB, and EGR1 are immediate early genes typically upregulated by the stress of single-cell dissociation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.0}], "model": "gemini-pro", "task_id": "ct-c22bc01239"} +{"attempts": [{"codes": ["BEV025"], "evidence": 5, "findings": [{"message": "The ASCT+B reference lists KLRB1 as a marker of CL:0000940 (mucosal invariant T cell), cell types disjoint from CL:0000798.", "rule_id": "BEV025", "where": "evidence 4 (cluster=c06;gene=KLRB1)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "NCR3", "stance": "supports"}], "rationale": "The expression of CD3E confirms this cluster represents a T cell population. The specific expression of TRDV2 (T cell receptor delta variable 2) is a defining marker for the Vgamma9Vdelta2 subset of gamma-delta T cells. High expression of IL7R, KLRB1 (CD161), NCR3 (NKp30), and CCR6 are all highly characteristic of gamma-delta T cell populations, particularly in mucosal or tissue environments like the lung."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.6}], "model": "gemini-pro", "task_id": "ct-c84f57496a"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "unknown", "cell_type_label": "unknown", "decision": "uncertain", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}], "rationale": "The provided top marker genes (including MKI67, TOP2A, TYMS, CDK1, UBE2C, and CENPF) are all canonical markers of the cell cycle, mitosis, and proliferation. There are no clear lineage-specific markers (e.g., canonical markers for epithelial, immune, endothelial, or mesenchymal lineages) present among the top differentially expressed genes. In single-cell RNA-seq data, actively dividing cells frequently group together into a distinct cluster driven by their shared, overwhelming proliferation transcriptional program, particularly if cell cycle effects are not regressed out. Because these markers indicate a cell state (proliferation) rather than identifying a specific cellular identity or lineage, the true cell type of this cluster cannot be determined from these markers alone."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.4}], "model": "gemini-pro", "task_id": "ct-c8e68f267e"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'kidney connecting tubule epithelial cell' is not the name of CL:1001431 ('kidney collecting duct principal cell'). 'kidney connecting tubule epithelial cell' is the name of CL:1000768 (kidney connecting tubule epithelial 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:1001431", "cell_type_label": "kidney connecting tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "CALB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of CALB1, HSD11B2, KLK1, and DEFB1, which together form a highly specific signature for connecting tubule (CNT) cells in the kidney. CALB1 is a classic marker for the distal convoluted tubule and connecting tubule, while HSD11B2 marks the aldosterone-sensitive distal nephron (connecting tubule and collecting duct principal cells). The combination of these two, along with KLK1 and TMEM52B, strongly identifies these cells as connecting tubule epithelial cells. (Note: CNT cells are functionally and developmentally closely related to collecting duct principal cells, and sometimes they share ontology nodes or are annotated similarly, but this specific marker profile is classically CNT)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 57.5}, {"answer": {"cell_type_id": "CL:1000768", "cell_type_label": "kidney connecting tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "CALB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of CALB1, HSD11B2, KLK1, and DEFB1, which together form a highly specific signature for connecting tubule (CNT) cells in the kidney. CALB1 is a classic marker for the distal convoluted tubule and connecting tubule, while HSD11B2 marks the aldosterone-sensitive distal nephron (connecting tubule and collecting duct principal cells). The combination of these two, along with KLK1 and TMEM52B, strongly identifies these cells as kidney connecting tubule epithelial cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney connecting tubule epithelial cell' is not the name of CL:1001431 ('kidney collecting duct principal cell'). 'kidney connecting tubule epithelial cell' is the name of CL:1000768 (kidney connecting tubule epithelial cell)."], "seconds": 18.9}], "model": "gemini-pro", "task_id": "ct-e7cab67ae5"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic ductal cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "ONECUT2", "stance": "supports"}], "rationale": "The cluster exhibits very strong and specific expression of canonical pancreatic ductal cell markers. Specifically, CFTR (cystic fibrosis transmembrane conductance regulator) and SLC4A4 (sodium bicarbonate cotransporter) are essential for the primary physiological function of pancreatic ductal cells, which is the secretion of bicarbonate-rich fluid. Furthermore, several well-known structural and surface markers highly enriched in the pancreatic ductal epithelium, such as SPP1, TACSTD2, MMP7, TM4SF1, and CD24, are among the top differentially expressed genes. There is a notable absence of markers corresponding to other pancreatic cell populations such as acinar (e.g., PRSS1, AMY2A) or endocrine cells (e.g., INS, GCG), solidly confirming the ductal cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.2}], "model": "gemini-pro", "task_id": "ct-ee90c8cca6"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000182", "cell_type_label": "hepatocyte", "decision": "annotate", "markers": [{"gene": "APOC3", "stance": "supports"}, {"gene": "APOA2", "stance": "supports"}, {"gene": "APOC1", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "FGA", "stance": "supports"}, {"gene": "ORM1", "stance": "supports"}, {"gene": "HP", "stance": "supports"}, {"gene": "ALB", "stance": "supports"}, {"gene": "FGB", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "TF", "stance": "supports"}, {"gene": "AMBP", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "ORM2", "stance": "supports"}, {"gene": "CYP2E1", "stance": "supports"}, {"gene": "FGG", "stance": "supports"}, {"gene": "APOH", "stance": "supports"}], "rationale": "The cluster's top marker genes are classically indicative of hepatocytes, the main parenchymal cells of the liver. The presence of genes encoding major blood plasma proteins (albumin [ALB], apolipoproteins [APOC3, APOA2, APOC1, APOA1, APOH], fibrinogen chains [FGA, FGB, FGG], transferrin [TF], and transthyretin [TTR]) strongly supports this annotation. Additionally, the cluster expresses hepatocyte-specific phase I drug metabolizing enzymes like CYP2E1. There are no notable contradicting markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.5}], "model": "gemini-pro", "task_id": "ct-fa6e0d282d"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "FCN3", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CCL14", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}], "rationale": "The endothelial signature (CLDN5, GNG11, TM4SF1, TFPI), combined with FCN2, FCN3, DNASE1L3, CCL14 and CRHBP, supports liver sinusoidal endothelial cells. No listed marker clearly contradicts this identity. Canonical sinusoidal markers CLEC4G, STAB2 and LYVE1 are not listed, but absence from a top-marker list does not establish lack of expression."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.5}], "model": "gpt-astra", "task_id": "ct-04aaea9940"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "APOA4", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "ANPEP", "stance": "supports"}, {"gene": "TMPRSS15", "stance": "supports"}, {"gene": "SLC26A3", "stance": "supports"}, {"gene": "FABP2", "stance": "supports"}, {"gene": "CDHR5", "stance": "supports"}, {"gene": "SI", "stance": "supports"}, {"gene": "APOB", "stance": "supports"}, {"gene": "SLC5A1", "stance": "supports"}], "rationale": "The markers strongly identify mature absorptive enterocytes: SI, ANPEP and TMPRSS15 support brush-border digestion; SLC5A1 supports glucose absorption; and FABP1, FABP2, RBP2 and apolipoproteins support intestinal lipid and retinoid handling. Their widespread expression within the cluster supports a coherent enterocyte identity consistent with duodenum. None of the listed markers clearly argues against this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.9}], "model": "gpt-astra", "task_id": "ct-085bedbfa5"} +{"attempts": [{"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:0002250", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "HMGA1", "stance": "supports"}, {"gene": "SLC12A2", "stance": "supports"}, {"gene": "IGFBP2", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "REG3A", "stance": "contradicts"}], "rationale": "The strong, nearly ubiquitous OLFM4 expression, together with HMGA1, SLC12A2 and IGFBP2, favors intestinal crypt stem/progenitor cells. REG1A supports a crypt-associated regenerative phenotype but is not stem-cell-specific. REG3A is a weak counter-indicator suggesting Paneth-like antimicrobial differentiation; however, canonical Paneth markers DEFA5, DEFA6 and LYZ are not among the supplied top markers. Confidence is moderate: this list cannot cleanly distinguish stem cells from their immediate progenitor descendants."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.0}], "model": "gpt-astra", "task_id": "ct-0f769ebe10"} +{"attempts": [{"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:0000148", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "GPNMB", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}], "rationale": "The coordinated enrichment of melanin-synthesis genes DCT and TYRP1, melanosome markers MLANA and PMEL, and the melanocyte regulator MITF strongly identifies melanocytes. KRT14 is a weak conflicting keratinocyte-associated signal, potentially reflecting ambient RNA or doublets; it does not outweigh the specific melanocyte signature. PLP1 expression alone does not establish a competing glial identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.1}], "model": "gpt-astra", "task_id": "ct-1445edf08f"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "RBP2", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "CPS1", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}], "rationale": "RBP2, FABP1, CPS1 and GSTA1 support a duodenal absorptive enterocyte identity; LGALS4 and epithelial markers reinforce it. REG1A, DMBT1 and AGR2 suggest a secretory or regenerative program but do not clearly contradict enterocyte identity. No listed marker strongly argues against this annotation; the precise maturation or functional subtype remains unresolved."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}], "model": "gpt-astra", "task_id": "ct-1fed4d68f2"} +{"attempts": [{"codes": [], "evidence": 6, "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": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}], "rationale": "The coordinated contractile program, particularly MYH11 together with strong TAGLN, ACTA2 and MYL9 enrichment, supports smooth muscle cells. RGS5 suggests a mural-cell identity and raises pericytes as an alternative, but does not contradict smooth muscle identity. No listed marker strongly argues against this annotation. These markers do not establish a specific anatomical smooth-muscle subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.3}], "model": "gpt-astra", "task_id": "ct-22fc152fbd"} +{"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:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "RORC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "ZBTB16", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "LTA", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "The combined RORC, IL7R and KIT signature strongly supports ILC3 identity, with ZBTB16 supporting an innate lymphoid program and LTA/LTB consistent with lymphoid tissue signaling. LST1 is a myeloid-associated caution, although not decisive against ILC3. IL4I1 also overlaps with antigen-presenting cells. These top markers support ILC3 annotation but do not establish a narrower subtype or exclude mixed cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 60.4}], "model": "gpt-astra", "task_id": "ct-307f739343"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "pancreatic A cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "IRX2", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}], "rationale": "This is a pancreatic alpha (A) cell cluster. Strong GCG enrichment, together with GC, IRX2, TTR and TM4SF4, supports alpha-cell identity; PCSK2 and chromogranins support endocrine secretory function. No listed marker clearly contradicts this annotation. GCG detection outside the cluster does not negate its strong expression enrichment within it."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.9}], "model": "gpt-astra", "task_id": "ct-32e6a3a16d"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "RGCC", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}], "rationale": "The coherent vascular endothelial signature strongly supports endothelial cells. PLVAP suggests fenestrated renal microvascular endothelium, potentially peritubular capillaries, but the precise subtype is less certain. No listed marker clearly contradicts this identity. CD74 and HLA-DRB1 indicate antigen-presentation activity and can occur in activated endothelial cells; they do not outweigh the endothelial signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.0}], "model": "gpt-astra", "task_id": "ct-32f05dbab5"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000451", "cell_type_label": "dendritic cell", "decision": "annotate", "markers": [{"gene": "FCER1A", "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": "GPR183", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "FCER1A together with strong MHC class II/CD74 expression and myeloid markers supports dendritic cells, likely a conventional DC2-like population. These markers overlap with other myeloid antigen-presenting cells, so a narrower subtype is not established. CXCL8 suggests inflammatory activation rather than contradicting the annotation. No listed marker clearly argues against dendritic cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 120.8}], "model": "gpt-astra", "task_id": "ct-3385c5a4a1"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002064", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "PRSS1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}], "rationale": "The coordinated enrichment of pancreatic digestive enzymes, expressed in nearly all cluster cells, strongly identifies pancreatic acinar cells. REG genes and SPINK1 reinforce this assignment. OLFM4, DUOX2 and CD24 may reflect epithelial activation or a regenerative state, but do not outweigh the acinar program. None of the supplied markers clearly contradict this identity; a more specific cell state cannot be established from this list alone."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.6}], "model": "gpt-astra", "task_id": "ct-36d56001f7"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'type A intercalated cell of collecting duct of renal tubule' is not the name of CL:0002200 ('oxyphil cell of thyroid').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV017"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'renal alpha-intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). 'renal alpha-intercalated cell' is the name of CL:0005011 (renal alpha-intercalated cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0002200", "cell_type_label": "type A intercalated cell of collecting duct of renal tubule", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}], "rationale": "SLC4A1 and SLC26A7 strongly identify type A (alpha) intercalated cells, supported by the proton-pump component ATP6V0D2 and ammonia transporter RHCG. These markers occur in 93–99% of cluster cells, indicating a coherent acid-secreting phenotype. CALB1 and HSD11B2 are more typical of other distal-nephron epithelial populations and provide mild conflicting evidence, but do not outweigh the type A marker combination. Mitochondrial genes are not cell-type-specific."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 60.3}, {"answer": {"cell_type_id": "CL:0005010", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}], "rationale": "SLC4A1 and SLC26A7 identify acid-secreting alpha-intercalated cells, supported by ATP6V0D2, RHCG and CA12. CALB1 and HSD11B2 favor other distal-nephron populations and constitute mild conflicting evidence, but the strong, widespread alpha-intercalated marker combination supports annotation. The previous ontology identifier was incorrect."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type A intercalated cell of collecting duct of renal tubule' is not the name of CL:0002200 ('oxyphil cell of thyroid')."], "seconds": 33.5}, {"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "CALB1", "stance": "contradicts"}, {"gene": "HSD11B2", "stance": "contradicts"}], "rationale": "Strong, widespread SLC4A1 and SLC26A7 expression supports acid-secreting renal alpha-intercalated cells, reinforced by ATP6V0D2, RHCG and CA12. CALB1 and HSD11B2 favor other distal-nephron populations and provide mild conflicting evidence, but do not outweigh the alpha-intercalated signature. The corrected Cell Ontology identifier is CL:0005011."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'renal alpha-intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). 'renal alpha-intercalated cell' is the name of CL:0005011 (renal alpha-intercalated cell)."], "seconds": 35.4}], "model": "gpt-astra", "task_id": "ct-3cbc7c57fd"} +{"attempts": [{"codes": [], "evidence": 6, "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": "TRAC", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "CD3D and TRAC strongly support T-cell identity, while CCL5, NKG7 and GZMA support a cytotoxic phenotype. NKG7 is also expressed by NK cells, but the strong T-cell receptor signature favors cytotoxic T cells. No listed marker clearly contradicts this annotation. The supplied markers do not establish CD8 expression or a finer subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.2}], "model": "gpt-astra", "task_id": "ct-3f2898af5e"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL6A2", "stance": "supports"}, {"gene": "FBLN1", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "CFD", "stance": "supports"}, {"gene": "SERPINF1", "stance": "supports"}], "rationale": "Strong, coordinated expression of extracellular-matrix genes DCN, LUM, and multiple collagens identifies dermal fibroblasts. SFRP2, CXCL14, CFD, and SERPINF1 reinforce this interpretation in human skin. No supplied markers clearly contradict it. A finer fibroblast subtype cannot be assigned confidently from this list alone."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.0}], "model": "gpt-astra", "task_id": "ct-5e18af843a"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000169", "cell_type_label": "type B pancreatic cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "MAFA", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "HADH", "stance": "supports"}], "rationale": "This is a pancreatic beta-cell cluster. Strong INS and IAPP enrichment, together with PDX1, MAFA and G6PC2, supports beta-cell identity. PCSK1, ABCC8 and HADH reinforce the insulin-processing and secretion program. No listed marker clearly contradicts this annotation; less specific markers do not argue against it."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.1}], "model": "gpt-astra", "task_id": "ct-6ea69bcccb"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000164", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "PCSK1N", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "FEV", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}], "rationale": "The coordinated endocrine differentiation markers NEUROD1 and INSM1, together with chromogranins and secretory-processing genes, strongly support enteroendocrine identity. SCT and MLN support intestinal hormone secretion. SCT enrichment suggests an S-cell-like population, but the supplied markers do not establish a single hormone-defined subtype. No listed marker clearly contradicts enteroendocrine identity; TFF3 also occurs in intestinal secretory cells and alone does not establish goblet-cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.6}], "model": "gpt-astra", "task_id": "ct-76f0318d60"} +{"attempts": [{"codes": ["BEV025"], "evidence": 11, "findings": [{"message": "The ASCT+B reference lists FCER1G as a marker of CL:0000767 (basophil); CL:0000775 (neutrophil); CL:0000784 (plasmacytoid dendritic cell) and 5 more, cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 5 (cluster=c09;gene=FCER1G)"}], "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": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The combined NK-receptor signature (KLRD1, KLRF1), signaling adaptors (TYROBP, FCER1G, HCST), and cytotoxic/chemokine markers (NKG7, GZMA, XCL2) strongly supports natural killer cells. KLRB1 is compatible with NK cells but also occurs in some T-cell populations. No listed marker clearly contradicts this annotation. The markers do not establish a specific NK-cell subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.6}], "model": "gpt-astra", "task_id": "ct-992627e517"} +{"attempts": [{"codes": ["BEV004", "BEV016"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "CL:0001117 is not in the pinned CL release (releases/2026-06-08). 'group 2 innate lymphoid cell' is the name of CL:0001069 (group 2 innate lymphoid cell).", "rule_id": "BEV016", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV025"], "evidence": 5, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0001069.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=HPGDS)"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0001069.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=GATA3)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0001117", "cell_type_label": "group 2 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "The strong, widespread HPGDS–PTGDR2 (CRTH2)–GATA3 signature, together with KLRB1 (CD161), strongly favors ILC2. KRT1 is an atypical epithelial keratin signal and could reflect contamination or doublets. Th2 cells share several markers; definitive separation requires checking T-cell receptor/CD3 expression, which this top-marker list does not establish."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.1}, {"answer": {"cell_type_id": "CL:0001069", "cell_type_label": "group 2 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "Strong, widespread HPGDS, PTGDR2 (CRTH2), GATA3 and KLRB1 expression supports group 2 innate lymphoid cells (ILC2). KRT1 is atypical and could reflect contamination or doublets. Th2 cells share some markers; definitive distinction requires examining CD3/T-cell receptor expression, which this top-marker list does not establish."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0001117 is not in the pinned CL release (releases/2026-06-08). 'group 2 innate lymphoid cell' is the name of CL:0001069 (group 2 innate lymphoid cell)."], "seconds": 42.1}], "model": "gpt-astra", "task_id": "ct-a53a01a447"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "RAMP2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}], "rationale": "The combined enrichment of RAMP2, TM4SF1, AQP1, TIMP3 and ID1 supports kidney vascular endothelial cells. AQP1 also marks proximal tubular epithelium, but the overall marker combination favors endothelium. No listed gene clearly contradicts this annotation. These markers do not reliably establish an endothelial subtype; canonical endothelial markers such as PECAM1, CDH5 and VWF would provide additional confirmation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.1}], "model": "gpt-astra", "task_id": "ct-c22bc01239"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists KLRB1 as a marker of CL:0000940 (mucosal invariant T cell), cell types disjoint from CL:0000798.", "rule_id": "BEV025", "where": "evidence 4 (cluster=c06;gene=KLRB1)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "The strongest interpretation is gamma-delta T cells: TRDV2 provides lineage-specific evidence alongside widespread CD3E expression. IL7R, KLRB1 and CCR6 support a type-17-associated phenotype, but are not lineage-specific. BLK is compatible with some gamma-delta T-cell programs despite its association with B cells. Widespread LST1 is atypical and raises concern for mixed identity. Because TRDV2 is detected in only 35.3% of cells, the annotation is provisional; these markers do not establish a uniform Vδ2 or functional subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.9}], "model": "gpt-astra", "task_id": "ct-c84f57496a"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "", "cell_type_label": "", "decision": "uncertain", "markers": [{"gene": "MKI67", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}], "rationale": "These markers support actively cycling cells, with strong DNA replication and mitotic programs, but do not establish a cell lineage. VIM, STMN1, and tubulin genes are insufficiently specific to distinguish lung epithelial, immune, endothelial, or stromal cells. No supplied marker decisively contradicts a particular lineage; absence from this top-marker list is not evidence of absent expression. A specific Cell Ontology cell type cannot be assigned reliably."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 73.4}], "model": "gpt-astra", "task_id": "ct-c8e68f267e"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000768", "cell_type_label": "kidney connecting tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "CALB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}], "rationale": "The combined CALB1, HSD11B2 and KLK1 enrichment favors connecting tubule epithelium within the distal nephron. DEFB1, TMEM52B and RHCG provide supporting evidence, although they are not individually specific. No listed marker clearly contradicts this annotation; RHCG also occurs in intercalated cells. Mitochondrial genes and MALAT1 do not distinguish these cell types. Closely related distal tubule and collecting duct populations remain the main alternatives."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.3}], "model": "gpt-astra", "task_id": "ct-e7cab67ae5"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic ductal cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}], "rationale": "CFTR and SLC4A4 support the ion-transport and bicarbonate-secretion functions of pancreatic ductal cells. MMP7, SPP1, TACSTD2, ANXA4 and CD24 reinforce a ductal epithelial identity. No listed marker strongly contradicts this annotation. The supplied top markers support the broad cell type but do not establish a specific ductal subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 71.2}], "model": "gpt-astra", "task_id": "ct-ee90c8cca6"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000182", "cell_type_label": "hepatocyte", "decision": "annotate", "markers": [{"gene": "ALB", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "APOA2", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "FGA", "stance": "supports"}, {"gene": "FGB", "stance": "supports"}, {"gene": "FGG", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "TF", "stance": "supports"}, {"gene": "AMBP", "stance": "supports"}, {"gene": "SERPINA1", "stance": "supports"}, {"gene": "CYP2E1", "stance": "supports"}, {"gene": "APOH", "stance": "supports"}], "rationale": "Strong enrichment and near-universal expression of hepatocyte plasma-protein, apolipoprotein, and metabolic genes identify hepatocytes. CYP2E1 additionally supports hepatic metabolic identity. No listed markers clearly contradict this annotation; APOC1 is shared with macrophages but does not outweigh the coherent hepatocyte signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}], "model": "gpt-astra", "task_id": "ct-fa6e0d282d"} +{"attempts": [{"codes": ["BEV004", "BEV016", "BEV017"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "No row of the pinned table has cluster=c11, gene=STAB2. Closest gene values for cluster=c11: STAB1.", "rule_id": "BEV016", "where": "evidence 12 (cluster=c11;gene=STAB2)"}, {"message": "No row of the pinned table has cluster=c11, gene=LYVE1.", "rule_id": "BEV016", "where": "evidence 14 (cluster=c11;gene=LYVE1)"}, {"message": "The label 'liver sinusoidal endothelial cell' is not the name of CL:0002144 ('capillary endothelial cell'). 'liver sinusoidal endothelial cell' is the name of CL:1000398 (endothelial cell of hepatic sinusoid).", "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:0002144", "cell_type_label": "liver sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "CLDN5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CCL14", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "STAB2", "stance": "contradicts"}, {"gene": "CLEC4G", "stance": "contradicts"}, {"gene": "LYVE1", "stance": "contradicts"}], "rationale": "The cluster has a strong endothelial program (CLDN5, TM4SF1, GNG11, IGFBP7, TFPI, and HSPG2) together with liver sinusoidal endothelial-associated genes such as FCN2, FCN3, DNASE1L3, CCL14, and CRHBP. STAB2, CLEC4G, and LYVE1 are not present among the top markers, which weakens but does not exclude the sinusoidal subtype; no marker provides a strong contradictory lineage signal."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 57.9}, {"answer": {"cell_type_id": "CL:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "CLDN5", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "FCN2", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "CCL14", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}], "rationale": "The cluster has a clear endothelial program, including CLDN5, TM4SF1, GNG11, IGFBP7, TFPI, and HSPG2. FCN2, FCN3, DNASE1L3, CCL14, and CRHBP support specialization as hepatic sinusoidal endothelium. No listed marker provides strong contradictory evidence."}, "cli_tools": [], "error": null, "feedback": ["evidence 12 (cluster=c11;gene=STAB2): No row of the pinned table has cluster=c11, gene=STAB2. Closest gene values for cluster=c11: STAB1.", "evidence 14 (cluster=c11;gene=LYVE1): No row of the pinned table has cluster=c11, gene=LYVE1.", "object label: The label 'liver sinusoidal endothelial cell' is not the name of CL:0002144 ('capillary endothelial cell'). 'liver sinusoidal endothelial cell' is the name of CL:1000398 (endothelial cell of hepatic sinusoid)."], "seconds": 35.7}], "model": "gpt-luna", "task_id": "ct-04aaea9940"} +{"attempts": [{"codes": [], "evidence": 19, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "APOA4", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "APOA1", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "PRAP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "ANPEP", "stance": "supports"}, {"gene": "PHGR1", "stance": "supports"}, {"gene": "TMPRSS15", "stance": "supports"}, {"gene": "SLC26A3", "stance": "supports"}, {"gene": "FABP2", "stance": "supports"}, {"gene": "CDHR5", "stance": "supports"}, {"gene": "APOC3", "stance": "supports"}, {"gene": "SI", "stance": "supports"}, {"gene": "APOB", "stance": "supports"}, {"gene": "CES2", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "SLC5A1", "stance": "supports"}], "rationale": "The cluster is a mature absorptive intestinal enterocyte population. Strong support comes from enterocyte markers involved in nutrient and lipid absorption and brush-border function, including ALDOB, FABP1, FABP2, APOA1, APOA4, APOC3, APOB, RBP2, ANPEP, SI, SLC5A1, SLC26A3, CDHR5, and TMPRSS15. No listed marker argues meaningfully against the enterocyte annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.5}], "model": "gpt-luna", "task_id": "ct-085bedbfa5"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV025"], "evidence": 7, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'intestinal crypt stem cell' is not the name of CL:0002089 ('group 2 innate lymphoid cell, mouse'). 'intestinal crypt stem cell' is the name of CL:0002250 (intestinal crypt stem cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "The ASCT+B reference lists AGR2 as a marker of CL:0019003 (tracheobronchial goblet cell); CL:4033009 (goblet cell of epithelium of lobar bronchus); CL:4033022 (mucus secreting cell of bronchus submucosal gland), cell types disjoint from CL:0002089.", "rule_id": "BEV025", "where": "evidence 4 (cluster=c01;gene=AGR2)"}], "status": "rejected", "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:0002089", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "REG3A", "stance": "contradicts"}], "rationale": "The near-universal OLFM4 expression is characteristic of intestinal crypt stem/progenitor cells. REG1A, CCL25, AGR2, SPINK1, and DMBT1 support a regenerative, early intestinal epithelial program, particularly in the duodenum. REG3A suggests partial secretory or differentiated enterocyte-like maturation, so this may represent a stem/progenitor state with differentiation bias rather than a pure stem-cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.8}, {"answer": {"cell_type_id": "CL:0002250", "cell_type_label": "intestinal crypt stem cell", "decision": "annotate", "markers": [{"gene": "OLFM4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "REG3A", "stance": "contradicts"}], "rationale": "Near-universal OLFM4 expression strongly supports an intestinal crypt stem/progenitor population. REG1A, CCL25, AGR2, SPINK1, and DMBT1 support a regenerative crypt epithelial program. REG3A argues for some secretory or differentiated epithelial maturation, suggesting a stem/progenitor population with differentiation bias rather than a completely pure stem-cell state."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'intestinal crypt stem cell' is not the name of CL:0002089 ('group 2 innate lymphoid cell, mouse'). 'intestinal crypt stem cell' is the name of CL:0002250 (intestinal crypt stem cell)."], "seconds": 39.9}], "model": "gpt-luna", "task_id": "ct-0f769ebe10"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'melanocyte' is not the name of CL:0000586 ('germ cell'). 'melanocyte' is the name of CL:0000148 (melanocyte).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"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:0000586", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "GPNMB", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}, {"gene": "S100A2", "stance": "contradicts"}], "rationale": "The strong, highly specific combination of DCT, TYRP1, MLANA, PMEL, and MITF identifies pigment-producing melanocytes. GPNMB provides additional support. KRT14 and S100A2 are keratinocyte-associated markers and may indicate ambient RNA or minor doublet/contamination, but they do not outweigh the dominant melanocytic signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.0}, {"answer": {"cell_type_id": "CL:0000148", "cell_type_label": "melanocyte", "decision": "annotate", "markers": [{"gene": "DCT", "stance": "supports"}, {"gene": "TYRP1", "stance": "supports"}, {"gene": "MLANA", "stance": "supports"}, {"gene": "PMEL", "stance": "supports"}, {"gene": "MITF", "stance": "supports"}, {"gene": "GPNMB", "stance": "supports"}, {"gene": "KRT14", "stance": "contradicts"}, {"gene": "S100A2", "stance": "contradicts"}], "rationale": "The highly specific combination of DCT, TYRP1, MLANA, PMEL, and MITF is characteristic of pigment-producing melanocytes. GPNMB provides additional support. KRT14 and S100A2 are keratinocyte-associated markers and argue against a completely pure melanocyte profile, possibly reflecting contamination or a minor doublet, but they do not outweigh the dominant melanocytic signature."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'melanocyte' is not the name of CL:0000586 ('germ cell'). 'melanocyte' is the name of CL:0000148 (melanocyte)."], "seconds": 51.8}], "model": "gpt-luna", "task_id": "ct-1445edf08f"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "FABP1", "stance": "supports"}, {"gene": "RBP2", "stance": "supports"}, {"gene": "CPS1", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "REG1A", "stance": "supports"}, {"gene": "DMBT1", "stance": "supports"}, {"gene": "EPCAM", "stance": "supports"}, {"gene": "PIGR", "stance": "supports"}, {"gene": "CCL25", "stance": "supports"}], "rationale": "The cluster shows a strong absorptive intestinal epithelial program: FABP1, RBP2, CPS1 and GSTA1 are characteristic enterocyte markers, with REG1A, DMBT1, LGALS4 and PIGR supporting a mature/secretory-associated enterocyte state. No listed marker clearly argues against enterocytes; the absence of strong goblet, Paneth, enteroendocrine or immune markers further supports this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 67.1}], "model": "gpt-luna", "task_id": "ct-1fed4d68f2"} +{"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:0000359", "cell_type_label": "vascular smooth muscle cell", "decision": "annotate", "markers": [{"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "RGS5", "stance": "contradicts"}, {"gene": "CPE", "stance": "contradicts"}], "rationale": "The strong, widespread expression of TAGLN, MYL9, ACTA2, TPM2, CALD1, and MYH11 defines a contractile vascular smooth-muscle/mural-cell program. RGS5 and CPE are more characteristic of pericytes, suggesting possible pericyte admixture or a closely related mural-cell state, but the MYH11 and contractile-gene pattern favors vascular smooth muscle cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 55.8}], "model": "gpt-luna", "task_id": "ct-22fc152fbd"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'type 3 innate lymphoid cell (ILC3)' is not the name of CL:0001068 ('ILC1'). Closest names: CL:0001071 (group 3 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001069 (group 2 innate lymphoid cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"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:0001068", "cell_type_label": "type 3 innate lymphoid cell (ILC3)", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "ZBTB16", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "LINC00299", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LTA", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "The combination of IL7R, RORC and KIT strongly supports an ILC3 identity, with ZBTB16, TOX2, LINC00299, LTB and LTA providing additional innate-lymphoid support. Very high LST1 expression is atypical for a pure ILC3 population and may indicate myeloid contamination or a mixed/ transitional cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.4}, {"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LTA", "stance": "supports"}, {"gene": "ZBTB16", "stance": "supports"}, {"gene": "TOX2", "stance": "supports"}, {"gene": "LINC00299", "stance": "supports"}, {"gene": "HPN", "stance": "supports"}, {"gene": "SCN1B", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "IL7R, RORC, and KIT form a characteristic group 3 innate lymphoid cell program, supported by LTB, LTA, ZBTB16, TOX2, LINC00299, HPN, and SCN1B. High LST1 is atypical for a pure ILC3 and may reflect myeloid contamination or a mixed cluster, but the dominant marker combination supports group 3 innate lymphoid cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type 3 innate lymphoid cell (ILC3)' is not the name of CL:0001068 ('ILC1'). Closest names: CL:0001071 (group 3 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001069 (group 2 innate lymphoid cell)."], "seconds": 32.7}], "model": "gpt-luna", "task_id": "ct-307f739343"} +{"attempts": [{"codes": ["BEV023"], "evidence": 10, "findings": [{"message": "CL:0002276 (obsolete PP cell of pancreatic acinus) is obsolete in the pinned CL release. 'pancreatic alpha cell' is the name of CL:0000171 (pancreatic A cell).", "rule_id": "BEV023", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002276", "cell_type_label": "pancreatic alpha cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SLC30A8", "stance": "supports"}, {"gene": "ALDH1A1", "stance": "supports"}], "rationale": "The cluster is a pancreatic alpha-cell population. GCG is uniformly expressed and is the defining alpha-cell hormone; PCSK2 and the dense-core granule genes CHGA, CHGB, SCG2, SCG5, and SLC30A8 support an endocrine islet identity. TTR, GC, TM4SF4, and ALDH1A1 are compatible with human pancreatic alpha-cell expression. No listed marker strongly argues against this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 82.0}, {"answer": {"cell_type_id": "CL:0000171", "cell_type_label": "pancreatic A cell", "decision": "annotate", "markers": [{"gene": "GCG", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SLC30A8", "stance": "supports"}, {"gene": "TTR", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}], "rationale": "The cluster is a pancreatic A cell (alpha cell) population. Uniform GCG expression is the defining marker, while PCSK2, CHGA, CHGB, SCG2, SCG5, and SLC30A8 support pancreatic endocrine identity. TTR, GC, and TM4SF4 are compatible with human pancreatic alpha-cell profiles. No listed marker strongly argues against this annotation."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0002276 (obsolete PP cell of pancreatic acinus) is obsolete in the pinned CL release. 'pancreatic alpha cell' is the name of CL:0000171 (pancreatic A cell)."], "seconds": 45.4}], "model": "gpt-luna", "task_id": "ct-32e6a3a16d"} +{"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:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "PLVAP", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "RGCC", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "CD74", "stance": "contradicts"}, {"gene": "HLA-DRB1", "stance": "contradicts"}], "rationale": "The cluster has a strong vascular endothelial signature, especially PLVAP, RNASE1, CAVIN2, GNG11, RGCC, TM4SF1, and RAMP3. CD74 and HLA-DRB1 suggest interferon-stimulated or antigen-presenting activation and are atypical for resting endothelial cells, but the absence of canonical leukocyte markers and the strong endothelial program support endothelial identity overall."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}], "model": "gpt-luna", "task_id": "ct-32f05dbab5"} +{"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:0000451", "cell_type_label": "dendritic cell", "decision": "annotate", "markers": [{"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "FCER1A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "TYROBP", "stance": "contradicts"}, {"gene": "FCER1G", "stance": "contradicts"}], "rationale": "The strong, near-universal MHC-II program together with FCER1A, GPR183, LYZ and inflammatory CXCL8 supports an activated myeloid dendritic-cell identity, likely dermal/inflammatory DC. TYROBP and FCER1G indicate some macrophage/monocyte-like myeloid character and argue against a clean conventional DC subtype assignment. The absence of CD1A and CD207 argues against Langerhans cells, so the conservative Cell Ontology assignment is generic dendritic cell."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 63.8}], "model": "gpt-luna", "task_id": "ct-3385c5a4a1"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'pancreatic acinar cell' is not the name of CL:0002068 ('Purkinje myocyte'). 'pancreatic acinar cell' is the name of CL:0002064 (pancreatic acinar cell).", "rule_id": "BEV017", "where": "object label"}], "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:0002068", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PRSS1", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "OLFM4", "stance": "contradicts"}, {"gene": "DUOX2", "stance": "contradicts"}], "rationale": "The cluster is strongly pancreatic acinar: digestive enzyme genes (CTRB2, PRSS1, PNLIP, PLA2G1B, CPB1, CPA1/2, CEL) and acinar/regenerative genes (REG1A/B, REG3A, SPINK1) are broadly expressed within the cluster. OLFM4 and DUOX2 are more characteristic of ductal or intestinal-like epithelial programs and argue against a pure canonical acinar identity, suggesting an activated or atypical acinar state, but they do not outweigh the dominant acinar signature."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.8}, {"answer": {"cell_type_id": "CL:0002064", "cell_type_label": "pancreatic acinar cell", "decision": "annotate", "markers": [{"gene": "REG1A", "stance": "supports"}, {"gene": "REG3A", "stance": "supports"}, {"gene": "REG1B", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "CTRB2", "stance": "supports"}, {"gene": "PRSS1", "stance": "supports"}, {"gene": "PNLIP", "stance": "supports"}, {"gene": "PLA2G1B", "stance": "supports"}, {"gene": "CPB1", "stance": "supports"}, {"gene": "CPA1", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CEL", "stance": "supports"}, {"gene": "OLFM4", "stance": "contradicts"}, {"gene": "DUOX2", "stance": "contradicts"}], "rationale": "The cluster is a pancreatic acinar cell based on its coherent, high-frequency digestive enzyme program (CTRB2, PRSS1, PNLIP, PLA2G1B, CPB1, CPA1/2, CEL) together with acinar/regenerative genes REG1A, REG1B, REG3A, and SPINK1. OLFM4 and DUOX2 argue against a purely canonical acinar profile and may indicate an activated or atypical epithelial state, but they do not outweigh the dominant acinar signature."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic acinar cell' is not the name of CL:0002068 ('Purkinje myocyte'). 'pancreatic acinar cell' is the name of CL:0002064 (pancreatic acinar cell)."], "seconds": 48.8}], "model": "gpt-luna", "task_id": "ct-36d56001f7"} +{"attempts": [{"codes": ["BEV004", "BEV016", "BEV017"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "No row of the pinned table has cluster=c01, gene=SLC26A4. Closest gene values for cluster=c01: SLC26A7, SLC4A1.", "rule_id": "BEV016", "where": "evidence 10 (cluster=c01;gene=SLC26A4)"}, {"message": "The label 'kidney alpha-intercalated cell' is not the name of CL:0005013 ('single ciliated epithelial cell'). Closest names: CL:0005011 (renal alpha-intercalated cell); CL:0005010 (renal intercalated cell); CL:4030015 (kidney collecting duct alpha-intercalated 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:0005013", "cell_type_label": "kidney alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "CALB1", "stance": "supports"}, {"gene": "SLC26A4", "stance": "contradicts"}, {"gene": "ATP6V1B1", "stance": "contradicts"}], "rationale": "The combination of strong SLC4A1, ATP6V0D2, HSD11B2, RHCG, CA12 and SLC26A7 expression identifies a renal acid-secreting alpha-intercalated cell. DEFB1, TMEM213 and CALB1 are also compatible with collecting-duct intercalated cells. No canonical beta-intercalated marker such as SLC26A4 is present, and ATP6V1B1 is not among the listed markers; these are mild caveats rather than strong contradictions."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.9}, {"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}], "rationale": "The strong, specific combination of SLC4A1, HSD11B2, RHCG, CA12, ATP6V0D2, and SLC26A7 supports a renal alpha-intercalated cell. DEFB1 and TMEM213 are also compatible with collecting-duct intercalated-cell identity. No listed marker provides a clear contradiction."}, "cli_tools": [], "error": null, "feedback": ["evidence 10 (cluster=c01;gene=SLC26A4): No row of the pinned table has cluster=c01, gene=SLC26A4. Closest gene values for cluster=c01: SLC26A7, SLC4A1.", "object label: The label 'kidney alpha-intercalated cell' is not the name of CL:0005013 ('single ciliated epithelial cell'). Closest names: CL:0005011 (renal alpha-intercalated cell); CL:0005010 (renal intercalated cell); CL:4030015 (kidney collecting duct alpha-intercalated cell)."], "seconds": 23.8}], "model": "gpt-luna", "task_id": "ct-3cbc7c57fd"} +{"attempts": [{"codes": ["BEV004", "BEV016", "BEV017"], "evidence": 10, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "No row of the pinned table has cluster=c06, gene=CD4. Closest gene values for cluster=c06: CD2.", "rule_id": "BEV016", "where": "evidence 9 (cluster=c06;gene=CD4)"}, {"message": "No row of the pinned table has cluster=c06, gene=CD8A.", "rule_id": "BEV016", "where": "evidence 10 (cluster=c06;gene=CD8A)"}, {"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": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000814", "cell_type_label": "natural killer T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CD4", "stance": "contradicts"}, {"gene": "CD8A", "stance": "contradicts"}], "rationale": "The cluster shows a clear T-cell program (CD3D, TRAC, IL32, S100A4) together with NK/cytotoxic features (NKG7, CCL5, GZMA, HCST), supporting an NK-like T-cell or natural killer T-cell identity. CD4 and CD8A are not present among the provided top markers, arguing against assignment to a conventional CD4 or CD8 T-cell subtype, but this absence is not definitive."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.0}, {"answer": {"cell_type_id": "CL:0000814", "cell_type_label": "mature NK T cell", "decision": "annotate", "markers": [{"gene": "CD3D", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}], "rationale": "The cluster has a clear T-cell receptor program (CD3D, TRAC, CD2) combined with NK-like cytotoxic features (CCL5, NKG7, GZMA, HCST), supporting the Cell Ontology term mature NK T cell. No provided marker strongly argues against this assignment."}, "cli_tools": [], "error": null, "feedback": ["evidence 9 (cluster=c06;gene=CD4): No row of the pinned table has cluster=c06, gene=CD4. Closest gene values for cluster=c06: CD2.", "evidence 10 (cluster=c06;gene=CD8A): No row of the pinned table has cluster=c06, gene=CD8A.", "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": 29.2}], "model": "gpt-luna", "task_id": "ct-3f2898af5e"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "CFD", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL6A2", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "FBLN1", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "MMP2", "stance": "supports"}, {"gene": "CCDC80", "stance": "supports"}, {"gene": "SERPINF1", "stance": "supports"}], "rationale": "The cluster shows a strong extracellular-matrix and collagen-producing stromal program: DCN, LUM, COL1A1, COL1A2, COL3A1, COL6A2, FBLN1, SFRP2, MMP2, and CCDC80. CFD and CXCL14 further support a dermal fibroblast-like identity. No listed marker argues against fibroblast identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.8}], "model": "gpt-luna", "task_id": "ct-5e18af843a"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000169", "cell_type_label": "pancreatic beta cell", "decision": "annotate", "markers": [{"gene": "INS", "stance": "supports"}, {"gene": "IAPP", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "PDX1", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}, {"gene": "G6PC2", "stance": "supports"}, {"gene": "MAFA", "stance": "supports"}, {"gene": "ADCYAP1", "stance": "supports"}, {"gene": "HADH", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}], "rationale": "The strong INS and IAPP expression, together with beta-cell markers G6PC2, MAFA, PDX1, ABCC8, PCSK1, and ADCYAP1, identifies this cluster as pancreatic beta cells. No listed marker provides clear evidence against this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.3}], "model": "gpt-luna", "task_id": "ct-6ea69bcccb"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 13, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'enteroendocrine cell' is not the name of CL:0000165 ('neuroendocrine cell'). 'enteroendocrine cell' is the name of CL:0000164 (enteroendocrine cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "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:0000165", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "PCSK1N", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "TFF3", "stance": "contradicts"}], "rationale": "The cluster is clearly enteroendocrine based on widespread neuroendocrine markers (CHGA, CHGB, PCSK1N, NEUROD1, SCGN, SCG5, SCG2, INSM1, and CPE). SCT is compatible with a secretin-lineage subtype, while GC and MLN suggest additional enteroendocrine heterogeneity; therefore the broader enteroendocrine-cell annotation is more secure than a pure secretin-cell label. TFF3 is less specific and argues against an entirely pure endocrine subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.5}, {"answer": {"cell_type_id": "CL:0000164", "cell_type_label": "enteroendocrine cell", "decision": "annotate", "markers": [{"gene": "PCSK1N", "stance": "supports"}, {"gene": "CHGA", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "CPE", "stance": "supports"}, {"gene": "SCGN", "stance": "supports"}, {"gene": "SCG5", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "INSM1", "stance": "supports"}, {"gene": "SCT", "stance": "supports"}, {"gene": "GC", "stance": "supports"}, {"gene": "MLN", "stance": "supports"}, {"gene": "TFF3", "stance": "contradicts"}], "rationale": "The cluster is strongly enteroendocrine, with widespread neuroendocrine and secretory-vesicle markers including CHGA, CHGB, PCSK1N, NEUROD1, SCGN, SCG5, SCG2, INSM1, and CPE. SCT, GC, and MLN indicate enteroendocrine hormonal heterogeneity rather than a single pure subtype. TFF3 is less specific and argues against a completely pure endocrine profile, but does not outweigh the coherent endocrine-marker program."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'enteroendocrine cell' is not the name of CL:0000165 ('neuroendocrine cell'). 'enteroendocrine cell' is the name of CL:0000164 (enteroendocrine cell)."], "seconds": 45.9}], "model": "gpt-luna", "task_id": "ct-76f0318d60"} +{"attempts": [{"codes": ["BEV025"], "evidence": 13, "findings": [{"message": "The ASCT+B reference lists FCER1G as a marker of CL:0000767 (basophil); CL:0000775 (neutrophil); CL:0000784 (plasmacytoid dendritic cell) and 5 more, cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 6 (cluster=c09;gene=FCER1G)"}, {"message": "The ASCT+B reference lists CCL3 as a marker of CL:4033041 (CCL3-positive alveolar macrophage), cell types disjoint from CL:0000623.", "rule_id": "BEV025", "where": "evidence 10 (cluster=c09;gene=CCL3)"}], "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": "CMC1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}], "rationale": "The cluster is best annotated as natural killer cells, with strong NK receptor and cytotoxic/chemokine signatures: NKG7, KLRD1, KLRF1, CMC1, HCST, IL2RB, XCL2, CCL3 and CCL4. KLRB1 suggests a CD161-positive NK-like subset. No listed marker argues strongly against this annotation; the absence of clear T-cell markers such as CD3D, CD3E and TRBC argues against conventional T cells or NKT cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.8}], "model": "gpt-luna", "task_id": "ct-992627e517"} +{"attempts": [{"codes": ["BEV004", "BEV017", "BEV025"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'type 2 innate lymphoid cell (ILC2)' is not the name of CL:0001065 ('innate lymphoid cell'). Closest names: CL:0001069 (group 2 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001071 (group 3 innate lymphoid cell).", "rule_id": "BEV017", "where": "object label"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0001065.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=HPGDS)"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0001065.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=GATA3)"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV025"], "evidence": 6, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists HPGDS as a marker of CL:0002079 (pancreatic ductal cell), cell types disjoint from CL:0001069.", "rule_id": "BEV025", "where": "evidence 1 (cluster=c11;gene=HPGDS)"}, {"message": "The ASCT+B reference lists GATA3 as a marker of CL:1000454 (kidney collecting duct epithelial cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000716 (kidney outer medulla collecting duct principal cell) and 2 more, cell types disjoint from CL:0001069.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c11;gene=GATA3)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0001065", "cell_type_label": "type 2 innate lymphoid cell (ILC2)", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL10RA", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "HPGDS and PTGDR2 are highly specific for lung ILC2s, with strong GATA3 and KLRB1 expression supporting a type-2 innate lymphoid identity. IL32, TESPA1 and IL10RA are compatible with lymphoid cells. KRT1 is an epithelial/keratin marker and argues against a pure ILC2 profile, possibly reflecting ambient RNA or a doublet, but the coherent HPGDS–PTGDR2–GATA3 signature supports annotation as ILC2."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.3}, {"answer": {"cell_type_id": "CL:0001069", "cell_type_label": "group 2 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "HPGDS", "stance": "supports"}, {"gene": "PTGDR2", "stance": "supports"}, {"gene": "GATA3", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL10RA", "stance": "supports"}, {"gene": "KRT1", "stance": "contradicts"}], "rationale": "The coherent HPGDS–PTGDR2–GATA3 signature strongly supports a group 2 innate lymphoid cell identity, with KLRB1 and IL10RA compatible with this lymphoid population. KRT1 is an epithelial keratin marker and argues against a pure ILC2 profile, possibly reflecting ambient RNA or a doublet."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type 2 innate lymphoid cell (ILC2)' is not the name of CL:0001065 ('innate lymphoid cell'). Closest names: CL:0001069 (group 2 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001071 (group 3 innate lymphoid cell)."], "seconds": 41.0}], "model": "gpt-luna", "task_id": "ct-a53a01a447"} +{"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:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "TM4SF1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "NHERF2", "stance": "supports"}, {"gene": "IFITM3", "stance": "supports"}, {"gene": "S100A4", "stance": "contradicts"}, {"gene": "VIM", "stance": "contradicts"}], "rationale": "The combination of TM4SF1, RAMP2, IFI27, TIMP3, and AQP1 is most consistent with a renal microvascular endothelial population, likely peritubular/capillary endothelial cells. AQP1 can also mark proximal tubular or thin-limb epithelium, but the vascular-associated TM4SF1/RAMP2 pattern supports endothelial identity. S100A4 and VIM are nonspecific and provide weak contrary evidence; canonical endothelial markers such as PECAM1, EMCN, VWF, or KDR are not listed, so a more specific endothelial subtype cannot be assigned confidently."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.8}], "model": "gpt-luna", "task_id": "ct-c22bc01239"} +{"attempts": [{"codes": ["BEV004", "BEV025"], "evidence": 8, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The ASCT+B reference lists KLRB1 as a marker of CL:0000940 (mucosal invariant T cell), cell types disjoint from CL:0000798.", "rule_id": "BEV025", "where": "evidence 3 (cluster=c06;gene=KLRB1)"}], "status": "review_required", "to_expert": true}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "NCR3", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}, {"gene": "BLK", "stance": "contradicts"}], "rationale": "The combination of TRDV2 with CD3E identifies a gamma-delta T-cell population, with KLRB1, NCR3, CCR6, and IL7R supporting an activated/innate-like mucosal phenotype. LST1 and BLK are atypical for T cells and may reflect ambient RNA, contamination, or some doublet contribution, but the T-cell and TRDV2 signals are stronger."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.6}], "model": "gpt-luna", "task_id": "ct-c84f57496a"} +{"attempts": [], "calls": [{"answer": {"cell_type_id": "CL:0001064", "cell_type_label": "cycling cell", "decision": "uncertain", "markers": [{"gene": "STMN1", "stance": "supports"}, {"gene": "TOP2A", "stance": "supports"}, {"gene": "TYMS", "stance": "supports"}, {"gene": "MKI67", "stance": "supports"}, {"gene": "UBE2C", "stance": "supports"}, {"gene": "NUSAP1", "stance": "supports"}, {"gene": "CENPF", "stance": "supports"}, {"gene": "CDK1", "stance": "supports"}], "rationale": "The cluster is strongly proliferative/cycling, with canonical S-phase and G2/M markers including TYMS, MKI67, TOP2A, UBE2C, NUSAP1, CENPF, and CDK1. However, no lineage-specific markers are present, so these data do not establish whether the cycling cells are epithelial, immune, endothelial, stromal, or another lung lineage. No listed marker specifically argues against a cycling-cell state."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.8}], "model": "gpt-luna", "task_id": "ct-c8e68f267e"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 9, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'kidney distal convoluted tubule epithelial cell' is not the name of CL:0002309 ('corticotroph'). 'kidney distal convoluted tubule epithelial cell' is the name of CL:1000849 (kidney distal convoluted tubule epithelial 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:0002309", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "CALB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "MT-CO1", "stance": "contradicts"}, {"gene": "MALAT1", "stance": "contradicts"}], "rationale": "The combination of CALB1, HSD11B2, KLK1, RHCG, DEFB1 and ATP1B1 is characteristic of distal nephron tubular epithelium, most consistent with distal convoluted tubule/late distal tubule cells. The strong mitochondrial and MALAT1 signals are nonspecific and reduce marker specificity, but do not indicate a competing cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 54.6}, {"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "CALB1", "stance": "supports"}, {"gene": "HSD11B2", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}], "rationale": "CALB1, HSD11B2, KLK1, RHCG, DEFB1, ATP1B1 and TMEM52B together support a distal convoluted tubule epithelial identity. The mitochondrial genes and MALAT1 are abundant housekeeping/stress-associated signals and are not cell-type-specific, but they do not argue for a competing identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney distal convoluted tubule epithelial cell' is not the name of CL:0002309 ('corticotroph'). 'kidney distal convoluted tubule epithelial cell' is the name of CL:1000849 (kidney distal convoluted tubule epithelial cell)."], "seconds": 44.1}], "model": "gpt-luna", "task_id": "ct-e7cab67ae5"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 11, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'pancreatic ductal cell' is not the name of CL:0002072 ('nodal myocyte'). 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CFTR, SLC4A4, MMP7, ANXA4, and TACSTD2 are characteristic epithelial ductal markers, while SPP1, ANXA2, CD44, and TM4SF1 are consistent with an activated or SPP1-high ductal state. IFITM3 and HLA-B suggest interferon/stress activation rather than a distinct lineage and argue against a clean canonical ductal profile, but they do not outweigh the strong ductal marker combination. No convincing endocrine, acinar, immune, or endothelial marker program is present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.8}, {"answer": {"cell_type_id": "CL:0002079", "cell_type_label": "pancreatic ductal cell", "decision": "annotate", "markers": [{"gene": "CFTR", "stance": "supports"}, {"gene": "SLC4A4", "stance": "supports"}, {"gene": "MMP7", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}, {"gene": "CD44", "stance": "supports"}], "rationale": "The cluster is best identified as pancreatic ductal cells. CFTR, SLC4A4, MMP7, ANXA4, and TACSTD2 form a strong ductal epithelial program. SPP1, ANXA2, CD44, and TM4SF1 are consistent with an activated or SPP1-high ductal state. No listed marker provides convincing evidence for an opposing lineage; IFITM3 and HLA-B reflect interferon/stress-related state rather than contradiction."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic ductal cell' is not the name of CL:0002072 ('nodal myocyte'). 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"error_label_mismatch": { + "events": 11, + "n": 23, + "rate": 0.4783, + "wilson_95": [ + 0.2924, + 0.6704 + ] + }, + "error_marker_not_in_data": { + "events": 3, + "n": 23, + "rate": 0.1304, + "wilson_95": [ + 0.0454, + 0.3213 + ] + }, + "error_no_markers": { + "events": 0, + "n": 23, + "rate": 0.0, + "wilson_95": [ + 0.0, + 0.1431 + ] + }, + "error_not_a_cell_type": { + "events": 0, + "n": 23, + "rate": 0.0, + "wilson_95": [ + 0.0, + 0.1431 + ] + }, + "error_obsolete_id": { + "events": 1, + "n": 23, + "rate": 0.0435, + "wilson_95": [ + 0.0077, + 0.2099 + ] + }, + "error_unapproved_symbol": { + "events": 0, + "n": 23, + "rate": 0.0, + "wilson_95": [ + 0.0, + 0.1431 + ] + }, + "error_unknown_id": { + "events": 0, + "n": 23, + "rate": 0.0, + "wilson_95": [ + 0.0, + 0.1431 + ] + }, + "exact": { + "events": 3, + "n": 24, + "rate": 0.125, + "wilson_95": [ + 0.0434, + 0.31 + ] + }, + "finer": { + "events": 2, + "n": 24, + "rate": 0.0833, + "wilson_95": [ + 0.0232, + 0.2585 + ] + }, + "invalid": { + "events": 1, + "n": 24, + "rate": 0.0417, + "wilson_95": [ + 0.0074, + 0.2024 + ] + }, + "routed_to_a_person": { + "events": 0, + "n": 24, + "rate": 0.0, + "wilson_95": [ + 0.0, + 0.138 + ] + }, + "tasks": 24, + "to_an_expert_as_conflict": { + "events": 0, + "n": 24, + "rate": 0.0, + "wilson_95": [ + 0.0, + 0.138 + ] + }, + "with_identifier_or_marker_error": { + "events": 12, + "n": 23, + "rate": 0.5217, + "wilson_95": [ + 0.3296, + 0.7076 + ] + }, + "wrong": { + "events": 13, + "n": 24, + "rate": 0.5417, + "wilson_95": [ + 0.3507, + 0.7211 + ] + } + } + } + }, + "revised": 38, + "split": "pilot" +} diff --git a/evaluation/llm_benchmark/results/celltype-pilot/summary.md b/evaluation/llm_benchmark/results/celltype-pilot/summary.md new file mode 100644 index 0000000..51f13c7 --- /dev/null +++ b/evaluation/llm_benchmark/results/celltype-pilot/summary.md @@ -0,0 +1,31 @@ +# Single-cell cell-type annotation (pilot set) + +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) | 23/24 | 9/24 | 2/24 | 5/24 | 7/24 | 0/24 | 1/23 | 0/24 | +| Claude Opus 5.5 | Model + bioevidence gate (first answer) | 9/24 | 5/24 | 2/24 | 1/24 | 1/24 | 0/24 | 0/9 | 14/24 | +| Claude Opus 5.5 | Model + bioevidence feedback loop (last answer) | 9/24 | 5/24 | 2/24 | 1/24 | 1/24 | 0/24 | 0/9 | 14/24 | +| GPT-6-Astra | Model alone (first answer) | 23/24 | 9/24 | 3/24 | 2/24 | 8/24 | 1/24 | 2/23 | 0/24 | +| GPT-6-Astra | Model + bioevidence gate (first answer) | 16/24 | 8/24 | 3/24 | 0/24 | 5/24 | 0/24 | 0/16 | 7/24 | +| GPT-6-Astra | Model + bioevidence feedback loop (last answer) | 16/24 | 8/24 | 3/24 | 0/24 | 5/24 | 0/24 | 0/16 | 7/24 | +| Gemini 3.1 Pro | Model alone (first answer) | 23/24 | 8/24 | 5/24 | 3/24 | 7/24 | 0/24 | 4/23 | 0/24 | +| Gemini 3.1 Pro | Model + bioevidence gate (first answer) | 14/24 | 8/24 | 4/24 | 0/24 | 2/24 | 0/24 | 0/14 | 9/24 | +| Gemini 3.1 Pro | Model + bioevidence feedback loop (last answer) | 17/24 | 8/24 | 4/24 | 1/24 | 4/24 | 0/24 | 0/17 | 6/24 | +| Claude Haiku 4.5 | Model alone (first answer) | 23/24 | 6/24 | 3/24 | 2/24 | 12/24 | 0/24 | 12/23 | 0/24 | +| Claude Haiku 4.5 | Model + bioevidence gate (first answer) | 3/24 | 3/24 | 0/24 | 0/24 | 0/24 | 0/24 | 0/3 | 20/24 | +| Claude Haiku 4.5 | Model + bioevidence feedback loop (last answer) | 4/24 | 3/24 | 0/24 | 0/24 | 1/24 | 0/24 | 0/4 | 19/24 | +| GPT-5.6-Luna | Model alone (first answer) | 23/24 | 3/24 | 4/24 | 2/24 | 13/24 | 1/24 | 12/23 | 0/24 | +| GPT-5.6-Luna | Model + bioevidence gate (first answer) | 5/24 | 3/24 | 1/24 | 0/24 | 1/24 | 0/24 | 0/5 | 18/24 | +| GPT-5.6-Luna | Model + bioevidence feedback loop (last answer) | 10/24 | 5/24 | 1/24 | 2/24 | 2/24 | 0/24 | 0/10 | 13/24 | +| Gemini 3.8 Flash | Model alone (first answer) | 23/24 | 6/24 | 4/24 | 3/24 | 9/24 | 1/24 | 7/23 | 0/24 | +| Gemini 3.8 Flash | Model + bioevidence gate (first answer) | 9/24 | 5/24 | 3/24 | 0/24 | 1/24 | 0/24 | 0/9 | 14/24 | +| Gemini 3.8 Flash | Model + bioevidence feedback loop (last answer) | 11/24 | 6/24 | 3/24 | 0/24 | 2/24 | 0/24 | 0/11 | 12/24 | +| All models | Model alone (first answer) | 138/144 | 41/144 | 21/144 | 17/144 | 56/144 | 3/144 | 38/138 | 0/144 | +| All models | Model + bioevidence gate (first answer) | 56/144 | 32/144 | 13/144 | 1/144 | 10/144 | 0/144 | 0/56 | 82/144 | +| All models | Model + bioevidence feedback loop (last answer) | 67/144 | 35/144 | 13/144 | 4/144 | 15/144 | 0/144 | 0/67 | 71/144 | + +Errors in the models' first answers (all models): label mismatch 35/138, marker not in data 3/138, no markers 0/138, not a cell type 0/138, obsolete id 2/138, unapproved symbol 0/138, unknown id 1/138. + +144 episodes, 185 model calls (0 failed), 38 revised after feedback. Rule codes raised across all records: BEV004 87, BEV016 4, BEV017 39, BEV023 2, BEV025 29. diff --git a/evaluation/llm_benchmark/results/celltype-test/episodes.jsonl b/evaluation/llm_benchmark/results/celltype-test/episodes.jsonl new file mode 100644 index 0000000..97d8373 --- /dev/null +++ b/evaluation/llm_benchmark/results/celltype-test/episodes.jsonl @@ -0,0 +1,276 @@ +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}], "rationale": "This cluster is confidently identified as natural killer cells based on: (1) NK-specific receptors KLRD1 (CD94) and KLRC1 (NKG2A), which are hallmark markers not typically expressed on other lymphocytes; (2) cytotoxic effector molecules including perforin (PRF1), granzymes (GZMA/GZMB), and granulysin (GNLY) essential for NK cytotoxicity; (3) NK-associated signaling adaptor TYROBP (DAP12); (4) CD16 (FCGR3A), an activating Fc receptor on NK cells; and (5) chemokines and lymphotactins (CCL4, CCL5, XCL1, XCL2). The very high pct_in values (>76% for all markers, >90% for most) indicate a pure, homogeneous NK cell population with no evidence of admixed cell types or doublets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.5}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-0bcb90ea26"} +{"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": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "NFKBIA", "stance": "supports"}], "rationale": "Comprehensive HLA class II expression with high logFC across all class II molecules (HLA-DR, HLA-DP, HLA-DQ) indicates strong antigen-presenting function. Myeloid identity confirmed by AIF1 (IBA1) and TYROBP (DAP12), which are canonical macrophage markers. Inflammatory activation signature reflected in IL1B, CXCL8, CCL3, and RGS family members indicates activated macrophages. SRGN and PLAUR support immune cell identity. This is a clean, unambiguous macrophage population consistent with kidney-resident or infiltrating macrophages from human kidney tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-0c19dd5456"} +{"attempts": [{"codes": ["BEV017"], "evidence": 16, "findings": [{"message": "The label 'proximal tubule epithelial cell' is not the name of CL:0002304 ('non-pigmented ciliary epithelial cell'). Closest names: CL:1000494 (nephron tubule epithelial cell); CL:1000839 (kidney proximal straight tubule epithelial cell); CL:1000838 (kidney proximal convoluted tubule epithelial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002304", "cell_type_label": "proximal tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "RBP5", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}, {"gene": "PDZK1IP1", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1H", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}, {"gene": "MT1F", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "CYB5A", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}], "rationale": "The marker genes clearly identify proximal tubule epithelial cells. The signature includes hallmark metabolic enzymes (ALDOB for fructose metabolism, GATM for amino acid synthesis), reabsorption-associated proteins (FABP1 for lipid uptake, RBP5 for vitamin A reabsorption, MIOX for inositol metabolism), detoxification enzymes (GSTA1, UGT2B7, CYB5A), metal homeostasis genes (MT1 metallothioneins), and oxidative stress response genes (GPX3). This comprehensive metabolic and detoxification profile is diagnostic for proximal tubule cells, the primary site of tubular reabsorption and xenobiotic metabolism in the kidney."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.6}, {"answer": {"cell_type_id": "CL:1000838", "cell_type_label": "kidney proximal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "RBP5", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}, {"gene": "PDZK1IP1", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1H", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}, {"gene": "MT1F", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "CYB5A", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}], "rationale": "The marker genes clearly identify proximal tubule epithelial cells. The signature includes hallmark metabolic enzymes (ALDOB for fructose metabolism, GATM for amino acid synthesis), reabsorption-associated proteins (FABP1 for lipid uptake, RBP5 for vitamin A reabsorption, MIOX for inositol metabolism), detoxification enzymes (GSTA1, UGT2B7, CYB5A), metal homeostasis genes (MT1 metallothioneins), and oxidative stress response genes (GPX3). This comprehensive metabolic and detoxification profile is diagnostic for proximal convoluted tubule cells, the primary site of tubular reabsorption and xenobiotic metabolism in the kidney."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'proximal tubule epithelial cell' is not the name of CL:0002304 ('non-pigmented ciliary epithelial cell'). Closest names: CL:1000494 (nephron tubule epithelial cell); CL:1000839 (kidney proximal straight tubule epithelial cell); CL:1000838 (kidney proximal convoluted tubule epithelial cell)."], "seconds": 16.8}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-0f7cfea7f3"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"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": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000794", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "TRDV2 encodes a TCR delta chain component, the defining feature of gamma-delta T cells. Combined with high GZMK (cytotoxic granule marker) and KLRB1 (NK/NKT marker), this identifies an activated, effector gamma-delta T cell population. CD3E confirms T lymphocyte identity; IL7R, CD69, IL32, LTB, and CXCR4 are consistent with T cell activation and effector function."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.1}, {"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "TRDV2 encodes a TCR delta chain component, the defining feature of gamma-delta T cells. Combined with high GZMK (cytotoxic granule marker) and KLRB1 (NK/NKT marker), this identifies an activated, effector gamma-delta T cell population. CD3E confirms T lymphocyte identity; IL7R, CD69, IL32, LTB, and CXCR4 are consistent with T cell activation and effector function."}, "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": 9.8}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-1161617d72"} +{"attempts": [{"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'cytotoxic T lymphocyte' is not the name of CL:0000798 ('gamma-delta 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": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "cytotoxic T lymphocyte", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster shows a canonical T cell signature with CD3E, CD247 (CD3-zeta chain), and LCK (T cell-specific kinase) as top markers. The high expression of cytotoxic markers GZMA and NKG7 indicates effector/cytotoxic function. This combination is diagnostic for cytotoxic T lymphocytes (CTLs). CD7 and CD52 provide additional pan-T cell/leukocyte support. The duodenum location is consistent with intraepithelial lymphocytes (IELs), which are commonly cytotoxic T cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.9}, {"answer": {"cell_type_id": "CL:0000910", "cell_type_label": "cytotoxic T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster shows a canonical T cell signature with CD3E, CD247 (CD3-zeta chain), and LCK (T cell-specific kinase) as top markers. The high expression of cytotoxic markers GZMA and NKG7 indicates effector/cytotoxic function. This combination is diagnostic for cytotoxic T cells. CD7 and CD52 provide additional pan-T cell/leukocyte support. The duodenum location is consistent with intraepithelial lymphocytes (IELs), which are commonly cytotoxic T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cytotoxic T lymphocyte' is not the name of CL:0000798 ('gamma-delta T cell'). 'cytotoxic T lymphocyte' is the name of CL:0000910 (cytotoxic T cell)."], "seconds": 13.6}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-13d48ee1d6"} +{"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": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "CD79A and IGKC are diagnostic B cell markers. CD79A encodes the B cell antigen receptor component, while IGKC is the immunoglobulin kappa light chain produced by B cells. Supporting markers include HLA-DRA and CD74 (MHC-II molecules expressed on B cells), CD52 (lymphocyte marker), CXCR4 (chemokine receptor on B cells), and LTB (lymphotoxin associated with lymphoid responses). The marker profile is consistent with a B cell population without evidence of other cell types."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.0}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-18ce9fb955"} +{"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": "C1QC", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "This cluster shows a characteristic tissue macrophage signature. The strong and near-universal expression of MHC class II genes (HLA-DR, HLA-DQ, HLA-DP) and CD74 indicates antigen-presenting capability. The high expression of complement components (C1QA/B/C) is particularly diagnostic for macrophages. Additional supporting markers include AIF1 and LYZ (lysozyme), which are hallmarks of the monocyte-macrophage lineage, along with other myeloid-associated genes (MS4A6A, TYROBP, FCER1G). The homogeneous expression profile (pct_in typically >0.9) indicates a well-defined population of tissue macrophages from the duodenum lamina propria."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.1}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-1fcb853772"} +{"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:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CORO1A", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}], "rationale": "The cluster is identified as natural killer cells based on a strong and consistent signature of NK-specific markers. NKG7, GNLY, and GZMB are canonical NK cell markers indicating cytotoxic function. KLRD1 (CD94) is the NK cell co-receptor. CCL5 and CCL4 are chemokines characteristic of activated NK cells. CORO1A supports immune cell identity. IGKC (immunoglobulin kappa), a B cell marker, suggests minor contamination or doublets, but the overwhelming NK signature dominates the cluster identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.9}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-20d7fe4cf5"} +{"attempts": [{"codes": [], "evidence": 15, "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": "GZMB", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}], "rationale": "This cluster exhibits a classical NK cell signature dominated by cytotoxic effector molecules (granzymes A/B/H, perforin, granulysin, cathepsin W) and NK-specific markers (NKG7, FCGR3A/CD16, CX3CR1). The extremely high pct_in values (0.939–1.0) for most genes indicate consistent, robust expression across all cluster cells. NKG7 is particularly specific to NK cells among lymphoid populations. The co-expression of TYROBP and FCER1G reflects the importance of these adaptor proteins in NK cell signaling. CCL5 and CCL4 are consistent with NK cell chemokine secretion capacity. No markers contradict this classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.0}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-2e16bde736"} +{"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": "IGLC2", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}], "rationale": "The cluster is characterized by strong expression of immunoglobulin genes (IGKC, IGLC2), which are the hallmark of antibody-secreting cells. Combined with B cell lineage markers (CD79A, CD79B, MS4A1/CD20), this identifies plasma cells. The elevated MHC class II genes (HLA-DR, HLA-DP, HLA-DQ) and CD74 (invariant chain) indicate activated plasma cells capable of antigen presentation, consistent with plasma cells in the hepatic immune microenvironment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.1}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-33d5498243"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "SELE", "stance": "supports"}, {"gene": "ACKR1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "SPRY1", "stance": "supports"}], "rationale": "Cluster shows strong endothelial cell signature with canonical markers: SELE (selectin E on endothelium), ACKR1 (endothelial-specific chemokine receptor), AQP1 (abundant aquaporin in endothelial cells), CLDN5 (claudin 5 in endothelial tight junctions), and RAMP2 (endothelial marker). Interferon response genes (IFI27, IFITM3, TSC22D1) reflect activated/inflammatory endothelium consistent with skin tissue. No contradictory markers present. Likely skin dermal or microvascular endothelial cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.2}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-3875326824"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'T-helper 17 cell' is not the name of CL:0000912 ('helper T cell'). '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:0000912", "cell_type_label": "T-helper 17 cell", "decision": "annotate", "markers": [{"gene": "RORC", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "TNFAIP3", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "JAML", "stance": "supports"}], "rationale": "Strong Th17 signature defined by RORC (master regulator), CCR6 (Th17-homing chemokine receptor), and IL23R (IL-23 pathway required for Th17 maintenance). Supported by robust CD4+ T cell markers (IL7R, LTB, LST1) and immune activation signatures. Mesenchymal markers (VIM, S100A4/A6) consistent with activated effector phenotype. KIT expression is atypical but not diagnostic of alternative cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.5}, {"answer": {"cell_type_id": "CL:0000899", "cell_type_label": "T-helper 17 cell", "decision": "annotate", "markers": [{"gene": "RORC", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "TNFAIP3", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "JAML", "stance": "supports"}], "rationale": "Strong Th17 signature defined by RORC (master regulator), CCR6 (Th17-homing chemokine receptor), and IL23R (IL-23 pathway required for Th17 maintenance). Supported by robust CD4+ T cell markers (IL7R, LTB, LST1) and immune activation signatures. Mesenchymal markers (VIM, S100A4/A6) consistent with activated effector phenotype."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'T-helper 17 cell' is not the name of CL:0000912 ('helper T cell'). 'T-helper 17 cell' is the name of CL:0000899 (T-helper 17 cell)."], "seconds": 7.8}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-3ec5acbb2d"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'cholangiocyte' is not the name of CL:0000158 ('club cell'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte).", "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:0000158", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "FXYD2", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "Cluster exhibits canonical cholangiocyte gene signature: (1) High cytokeratin expression (KRT8, KRT18, KRT7) defining epithelial identity; (2) FXYD2 with extremely high specificity (logfc 2.479, pct_in 0.934, pct_out 0.006) is a hallmark cholangiocyte marker; (3) CD24 is established bile duct epithelium marker (pct_in 0.926, pct_out 0.036); (4) DEFB1, LGALS4, and TM4SF4 all expressed in bile duct cells; (5) ELF3 supports epithelial differentiation. No contradicting markers present. This is unambiguously a cholangiocyte population from liver tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.6}, {"answer": {"cell_type_id": "CL:1000488", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "FXYD2", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "Cluster exhibits canonical cholangiocyte gene signature: (1) High cytokeratin expression (KRT8, KRT18, KRT7) defining epithelial identity; (2) FXYD2 with extremely high specificity (logfc 2.479, pct_in 0.934, pct_out 0.006) is a hallmark cholangiocyte marker; (3) CD24 is established bile duct epithelium marker (pct_in 0.926, pct_out 0.036); (4) DEFB1, LGALS4, and TM4SF4 all expressed in bile duct cells; (5) ELF3 supports epithelial differentiation. No contradicting markers present. This is unambiguously a cholangiocyte population from liver tissue."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cholangiocyte' is not the name of CL:0000158 ('club cell'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte)."], "seconds": 12.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-4163a3b864"} +{"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": "IGKC", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "SSR3", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}], "rationale": "The cluster is dominated by immunoglobulin genes across multiple heavy chain types (IGHM, IGHG1-4, IGHA1) and light chains (IGKC, IGLC2-3), along with JCHAIN which encodes the joining chain found in multimeric IgM and IgA. MZB1 is a B cell lineage marker. The strong co-expression of endoplasmic reticulum proteins (HSP90B1, SEC11C, SSR3/4, FKBP11, DERL3) reflects the extensive secretory apparatus required for high-volume antibody synthesis. XBP1 is a key transcription factor driving plasma cell differentiation and antibody secretion. This combined signature is diagnostic of plasma cells—antibody-secreting effector B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.4}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-41fb1f6e39"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000632", "cell_type_label": "hepatic stellate cell", "decision": "annotate", "markers": [{"gene": "TIMP1", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "PRSS23", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}], "rationale": "This cluster shows a classic activated hepatic stellate cell (HSC) signature. TIMP1 and TIMP3 are hallmark HSC markers involved in extracellular matrix remodeling; IGFBP7 and HSPG2 indicate active matrix production. TAGLN (transgelin) is characteristic of myofibroblast-like activated HSCs. LIFR, RAMP3, ID1, and ID3 support HSC identity and activation state. The tissue context (liver caudate lobe) and the high expression and prevalence of these markers in the cluster strongly support hepatic stellate cell identity. Some endothelial-associated markers (PTPRB, ENG) and immune-related genes (C7, FCN3, IFI27, HLA-E) may reflect cellular interactions in the liver sinusoidal microenvironment or minor contamination but do not contradict the dominant stellate cell phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.6}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-4d4de5c13f"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT1", "stance": "supports"}, {"gene": "KRT10", "stance": "supports"}, {"gene": "DMKN", "stance": "supports"}, {"gene": "KRT14", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "KRTDAP", "stance": "supports"}, {"gene": "LY6D", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "DSP", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "SERPINB5", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "CLDN1", "stance": "supports"}], "rationale": "This cluster shows the characteristic marker profile of epidermal keratinocytes. Multiple keratin genes (KRT1, KRT10, KRT14) are among the top markers with very high expression in the cluster. Structural proteins essential for epithelial cell integrity (DSP, PERP, DMKN) are strongly expressed. Characteristic keratinocyte proteins (SFN, LGALS7B, LY6D, S100A14, AQP3) support this identity. The high pct_in values (>0.8 for nearly all genes) and moderate to low pct_out values indicate these genes are specifically enriched in this cluster. The predominance of KRT1 and KRT10 over KRT14 suggests a differentiated/superficial keratinocyte population from the upper epidermis rather than basal layer cells. No contradicting markers are evident."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.1}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-506f19166c"} +{"attempts": [{"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'pancreatic delta cell' is not the name of CL:0002335 ('brown preadipocyte'). 'pancreatic delta cell' is the name of CL:0000173 (pancreatic D 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:0002335", "cell_type_label": "pancreatic delta cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "CASR", "stance": "supports"}, {"gene": "BCHE", "stance": "supports"}, {"gene": "GABRG2", "stance": "supports"}], "rationale": "SST (somatostatin) is the canonical marker for pancreatic delta cells, with exceptionally high mean expression (logfc 5.665). Supporting markers include HHEX (delta cell transcription factor), CASR (glucose sensing in D-cells), PCSK1 (neuropeptide processing), RBP4 (retinoid metabolism in endocrine cells), BCHE (enzymatic marker), and GABRG2 (GABAergic properties). No markers contradict delta cell identity. The cluster represents somatostatin-secreting delta cells of the pancreatic islets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.8}, {"answer": {"cell_type_id": "CL:0000173", "cell_type_label": "pancreatic D cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "CASR", "stance": "supports"}, {"gene": "BCHE", "stance": "supports"}, {"gene": "GABRG2", "stance": "supports"}], "rationale": "SST (somatostatin) is the canonical marker for pancreatic delta cells, with exceptionally high mean expression (logfc 5.665) and expression in 100% of cells in this cluster but 99.9% outside. Supporting markers include HHEX (delta cell transcription factor), CASR (glucose sensing in D-cells), PCSK1 (neuropeptide processing), RBP4 (retinoid metabolism in endocrine cells), BCHE (enzymatic marker), and GABRG2 (GABAergic properties). No markers contradict delta cell identity. The cluster represents somatostatin-secreting delta cells of the pancreatic islets."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic delta cell' is not the name of CL:0002335 ('brown preadipocyte'). 'pancreatic delta cell' is the name of CL:0000173 (pancreatic D cell)."], "seconds": 10.5}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-50ec79996f"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'CD8-positive, alpha-beta T cell' is not the name of CL:0000546 ('T-helper 2 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": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000546", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "ZNF683", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "Overwhelming T cell identity from CD3E/CD3D (>96% of cells), CD8A expression marking CD8+ subset, and strong cytotoxic signature (GZMK, high logfc). ZNF683 and CXCR3 suggest tissue-resident memory phenotype consistent with lung immune compartment. TRDV2 signal is modest, indicating predominantly alpha-beta TCR."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.2}, {"answer": {"cell_type_id": "CL:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "ZNF683", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "Overwhelming T cell identity from CD3E/CD3D (>96% of cells), CD8A expression marking CD8+ subset, and strong cytotoxic signature (GZMK, high logfc). ZNF683 and CXCR3 suggest tissue-resident memory phenotype consistent with lung immune compartment. TRDV2 signal is modest, indicating predominantly alpha-beta TCR."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD8-positive, alpha-beta T cell' is not the name of CL:0000546 ('T-helper 2 cell'). 'CD8-positive, alpha-beta T cell' is the name of CL:0000625 (CD8-positive, alpha-beta T cell)."], "seconds": 9.7}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-52a80b5c6b"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'collecting duct principal cell' is not the name of CL:0000646 ('basal cell'). Closest names: CL:1001431 (kidney collecting duct principal cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000454 (kidney collecting duct epithelial 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:0000646", "cell_type_label": "collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "AQP2 (aquaporin-2) is the canonical marker for collecting duct principal cells, serving as a vasopressin-regulated water channel with high specificity (79.5% in cluster, 3.9% in others). FXYD4, a sodium/potassium ATPase regulatory protein, further confirms this identity with similar specificity. AQP3 and CDH16 are additional kidney epithelial markers consistent with collecting duct identity. The keratin genes (KRT19, KRT18), epithelial factors (TACSTD2, ELF3), and kidney-specific cadherin (CDH16) support the epithelial nature of these cells. Ubiquitous mitochondrial and long non-coding RNAs lack discriminatory power but do not contradict the assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.0}, {"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "AQP2 (aquaporin-2) is the canonical marker for collecting duct principal cells, serving as a vasopressin-regulated water channel with high specificity (79.5% in cluster, 3.9% outside). FXYD4, a sodium/potassium ATPase regulatory protein, further confirms this identity. AQP3, WFDC2, TACSTD2, and CDH16 are consistent with collecting duct epithelial identity. The keratin genes (KRT19, KRT18) and epithelial factors (ELF3) support the epithelial nature of these cells. Mitochondrial genes and MALAT1 are ubiquitous markers without discriminatory power."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'collecting duct principal cell' is not the name of CL:0000646 ('basal cell'). Closest names: CL:1001431 (kidney collecting duct principal cell); CL:1000714 (kidney cortex collecting duct principal cell); CL:1000454 (kidney collecting duct epithelial cell)."], "seconds": 11.4}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-54741cc370"} +{"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": "TNFRSF17", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGLL5", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "SPCS2", "stance": "supports"}, {"gene": "SPCS1", "stance": "supports"}, {"gene": "DNAJB9", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "UBE2J1", "stance": "supports"}], "rationale": "This is a differentiated plasma cell population, with classic B cell lineage markers (CD79A, IGLL5, MZB1, TNFRSF17) and the complete plasma cell signature: JCHAIN for antibody assembly, XBP1 driving the plasma cell transcriptional program, and extensive ER/secretory machinery (DERL3, HERPUD1, DNAJB9, SEC11C, SPCS1/2, FKBP11, UBE2J1) reflecting the massive protein synthesis burden of antibody production."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.9}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-560d5829d2"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'basal keratinocyte' is not the name of CL:0002238 ('male gonocyte'). Closest names: CL:4033013 (suprabasal keratinocyte); CL:0000312 (keratinocyte); CL:4052063 (nail bed keratinocyte).", "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:0002238", "cell_type_label": "basal keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}], "rationale": "Strong concordance of epidermis-specific basal layer markers. KRT5/KRT14 co-expression is pathognomonic for basal keratinocytes in the stratified squamous epithelium. Desmosomal proteins (DST, PERP) and basal-layer-specific genes (SFN, AQP3, MIR205HG) with high within-cluster specificity confirm identity. No contradictory markers detected."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.1}, {"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}], "rationale": "Strong concordance of epidermis-specific basal layer markers. KRT5/KRT14 co-expression is pathognomonic for basal keratinocytes in stratified squamous epithelium. Desmosomal proteins (DST, PERP), basal-layer-specific genes (SFN, AQP3, MIR205HG), and stem cell markers (KRT15) with high within-cluster specificity confirm keratinocyte identity with basal layer specification. No contradictory markers detected."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'basal keratinocyte' is not the name of CL:0002238 ('male gonocyte'). Closest names: CL:4033013 (suprabasal keratinocyte); CL:0000312 (keratinocyte); CL:4052063 (nail bed keratinocyte)."], "seconds": 44.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-5633d2ce11"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'proximal tubule cell' is not the name of CL:0000653 ('podocyte').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'proximal tubule epithelial cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:1000494 (nephron tubule epithelial cell); CL:1000839 (kidney proximal straight tubule epithelial cell); CL:1000838 (kidney proximal convoluted tubule epithelial 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:0000653", "cell_type_label": "proximal tubule cell", "decision": "annotate", "markers": [{"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}], "rationale": "This cluster represents proximal tubule cells based on highly consistent marker expression. WFDC2, CA12, and SLC26A4 are established proximal tubule markers involved in reabsorption and acid-base balance. The constellation of V-ATPase subunits (ATP6V genes) is particularly diagnostic—these are critical for H+ secretion in proximal tubule cells. Cytokeratin expression (KRT7, KRT8) confirms epithelial identity. Cell adhesion molecules (TSPAN8, HEPACAM2) and IGFBP5 further support the proximal tubule phenotype. High pct_in values and substantial logfc indicate genuine cluster-defining expression. No contradictory markers were identified."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.0}, {"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "proximal tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}], "rationale": "This cluster represents proximal tubule epithelial cells based on highly consistent marker expression. WFDC2, CA12, and SLC26A4 are established proximal tubule markers involved in reabsorption and acid-base balance. The constellation of V-ATPase subunits (ATP6V genes) is particularly diagnostic—these are critical for H+ secretion in proximal tubule cells. Cytokeratin expression (KRT7, KRT8) confirms epithelial identity. Cell adhesion molecules (TSPAN8, HEPACAM2) and IGFBP5 further support the proximal tubule phenotype. High pct_in values and substantial logfc indicate genuine cluster-defining expression. No contradictory markers were identified."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'proximal tubule cell' is not the name of CL:0000653 ('podocyte')."], "seconds": 15.7}, {"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "epithelial cell of proximal tubule", "decision": "annotate", "markers": [{"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}], "rationale": "This cluster represents epithelial cells of the proximal tubule based on highly consistent marker expression. WFDC2, CA12, and SLC26A4 are established proximal tubule markers involved in reabsorption and acid-base balance. The constellation of V-ATPase subunits (ATP6V genes) is particularly diagnostic—these are critical for H+ secretion in proximal tubule cells. Cytokeratin expression (KRT7, KRT8) confirms epithelial identity. Cell adhesion molecules (TSPAN8, HEPACAM2) and IGFBP5 further support the proximal tubule phenotype. High pct_in values and substantial logfc indicate genuine cluster-defining expression."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'proximal tubule epithelial cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:1000494 (nephron tubule epithelial cell); CL:1000839 (kidney proximal straight tubule epithelial cell); CL:1000838 (kidney proximal convoluted tubule epithelial cell)."], "seconds": 8.9}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-6807a1005a"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "The marker profile is highly characteristic of monocytes. The co-expression of S100A8 and S100A9 (calprotectin subunits) with TYROBP, LYZ, and AIF1 is diagnostic of classical monocytes. These genes are specifically enriched in circulating monocytes rather than resident macrophages. The high expression of HLA-DRA and CD74 reflects the role of monocytes as antigen-presenting cells. Other supporting markers include cathepsin S (CTSS) and complement component C1QA, both characteristic of myeloid lineage cells. The high pct_in values across most markers indicate a relatively homogeneous cell population consistent with a single cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.2}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-6846a2fbd5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000904 ('central memory CD4-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:0000904", "cell_type_label": "naive CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD8A", "stance": "supports"}, {"gene": "CD8B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "CD8A and CD8B expression (logfc 1.133–1.650) with pan-T marker CD3E define CD8+ T cells. High IL7R, SELL (CD62L), and CCR7 expression indicate naive or central memory differentiation state, with IL7R especially high in naive cells. TCF7 and LEF1 are T cell fate determinants. CD27 is a co-stimulatory marker. The marker profile is consistent with naive CD8+ T cells rather than activated or memory subsets."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.3}, {"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": "IL7R", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "CD8A and CD8B are the top markers (logfc 1.133–1.650) with pan-T marker CD3E (logfc 0.965), defining CD8-positive T cells. High IL7R (logfc 0.973), SELL/CD62L (logfc 1.107), and CCR7 (logfc 1.169) indicate lymph node-homing capacity typical of naive or central memory CD8+ T cells. TCF7 and LEF1 support T cell identity. CD27 co-stimulation marker is consistent with non-terminally differentiated CD8+ T cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive CD8-positive, alpha-beta T cell' is not the name of CL:0000904 ('central memory CD4-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": 13.1}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-6b9f55ce2e"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "AHSP", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "GYPA", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "ALAS2", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}], "rationale": "This cluster is clearly mature erythrocytes (red blood cells). The top markers are dominated by hemoglobin genes (HBB, HBA1, HBA2, HBD, HBM) with extremely high logfc values and 100% or near-100% expression within the cluster. Supporting markers include erythrocyte-specific genes: AHSP (hemoglobin assembly), CA1 (highly abundant RBC enzyme), SLC4A1/Band 3 (major RBC membrane protein), and glycophorins GYPA and GYPC (RBC membrane glycoproteins). Genes involved in heme synthesis (ALAS2, SLC25A37, BLVRB) are also expected in hemoglobin-producing cells. The expression pattern is highly specific to mature erythrocytes with no contradicting markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.1}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-73d8984fbc"} +{"attempts": [{"codes": ["BEV023"], "evidence": 16, "findings": [{"message": "CL:0002650 (obsolete epithelial cell of paranasal sinus part of viscerocranial mucosa) is obsolete in the pinned CL release. 'pancreatic stellate cell' is the name of CL:0002410 (pancreatic stellate cell).", "rule_id": "BEV023", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002650", "cell_type_label": "pancreatic stellate cell", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL5A1", "stance": "supports"}, {"gene": "COL5A2", "stance": "supports"}, {"gene": "COL6A1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "COL4A2", "stance": "supports"}, {"gene": "COL15A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}], "rationale": "The cluster is dominated by extracellular matrix genes, particularly multiple collagen isoforms (COL1A1, COL1A2, COL3A1, COL5, COL6, COL4, COL15), along with SPARC and FN1—all hallmarks of fibroblast identity and function in ECM production. Supporting markers include TIMP1 (fibroblast-secreted protease inhibitor), VIM (mesenchymal marker), CALD1 (smooth muscle/fibroblast marker), and IGFBP7/SFRP2 (secreted factors). This expression pattern is characteristic of pancreatic stellate cells, the primary fibroblast population in pancreatic tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.9}, {"answer": {"cell_type_id": "CL:0002410", "cell_type_label": "pancreatic stellate cell", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL5A1", "stance": "supports"}, {"gene": "COL5A2", "stance": "supports"}, {"gene": "COL6A1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "COL4A2", "stance": "supports"}, {"gene": "COL15A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}], "rationale": "The cluster is dominated by extracellular matrix genes, particularly multiple collagen isoforms (COL1A1, COL1A2, COL3A1, COL5, COL6, COL4, COL15), along with SPARC and FN1—all hallmarks of fibroblast identity and function in ECM production. Supporting markers include TIMP1 (fibroblast-secreted protease inhibitor), VIM (mesenchymal marker), CALD1 (smooth muscle/fibroblast marker), and IGFBP7/SFRP2 (secreted factors). This expression pattern is characteristic of pancreatic stellate cells, the primary fibroblast population in pancreatic tissue."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0002650 (obsolete epithelial cell of paranasal sinus part of viscerocranial mucosa) is obsolete in the pinned CL release. 'pancreatic stellate cell' is the name of CL:0002410 (pancreatic stellate cell)."], "seconds": 11.0}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-75516baf75"} +{"attempts": [{"codes": ["BEV017"], "evidence": 5, "findings": [{"message": "The label 'thick ascending limb cell' is not the name of CL:0002304 ('non-pigmented ciliary epithelial cell'). Closest names: CL:1001131 (vasa recta ascending limb cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 5, "findings": [{"message": "The label 'thick ascending limb cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:1001131 (vasa recta ascending limb cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002304", "cell_type_label": "thick ascending limb cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "This cluster is clearly a thick ascending limb (TAL) cell cluster based on definitive marker expression. SLC12A1 (NKCC2) is the canonical sodium-potassium-chloride cotransporter specific to TAL cells and essential for the countercurrent multiplication system. UMOD (uromodulin) is the most abundant urinary protein, produced exclusively by TAL epithelium. The high expression of Na+/K+-ATPase subunits (ATP1A1, ATP1B1) is consistent with the TAL's high metabolic demand for active salt transport. CA12 is another TAL-associated marker. The mitochondrial genes and other markers reflect the metabolically active nature of these cells rather than indicating other cell types."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.6}, {"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "thick ascending limb cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "UMOD (uromodulin) is the defining marker of TAL epithelium—it's the most abundant urinary protein produced exclusively by thick ascending limb cells. SLC12A1 encodes NKCC2 (Na-K-2Cl cotransporter), the apical membrane transporter essential for TAL salt reabsorption in the countercurrent multiplier system. ATP1A1 and ATP1B1 encode the Na+/K+-ATPase (α and β subunits), required for the high-capacity active transport characteristic of this nephron segment. CA12 (carbonic anhydrase XII) supports TAL function. The mitochondrial and other housekeeping genes reflect the metabolic intensity of these cells rather than contradicting the TAL identification."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'thick ascending limb cell' is not the name of CL:0002304 ('non-pigmented ciliary epithelial cell'). Closest names: CL:1001131 (vasa recta ascending limb cell)."], "seconds": 38.4}, {"answer": {"cell_type_id": "unknown", "cell_type_label": "thick ascending limb cell", "decision": "uncertain", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "UMOD (uromodulin) and SLC12A1 (NKCC2) are exclusive markers of thick ascending limb epithelium. UMOD is virtually specific to TAL as the most abundant Tamm-Horsfall protein in urine. SLC12A1 encodes the essential apical sodium-potassium-chloride cotransporter defining TAL salt reabsorption. ATP1A1/ATP1B1 (Na+/K+-ATPase) and CA12 support the high metabolic activity of TAL. However, I cannot reliably provide the correct CL identifier without verification against the pinned Cell Ontology release.\""}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'thick ascending limb cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:1001131 (vasa recta ascending limb cell)."], "seconds": 33.4}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-7954bd765f"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}], "rationale": "This cluster is unambiguously red blood cells (mature erythrocytes). The dominant markers are hemoglobin subunits (HBB, HBA1, HBA2, HBD, HBM) with the highest log fold changes (7.17, 6.24, 5.49, 2.20, 0.59) and very high expression percentages within the cluster, which is pathognomonic for erythrocytes. GYPC (glycophorin C) is a major red cell surface glycoprotein. SLC25A37 and SLC25A39 encode mitochondrial carriers involved in iron transport for heme synthesis, consistent with erythrocyte biology. The weaker signals (SNCA, FBXO7, FKBP8, UBBP4) do not contradict the erythrocyte identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-838e09fefd"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000359", "cell_type_label": "vascular smooth muscle cell", "decision": "annotate", "markers": [{"gene": "ACTA2", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "BGN", "stance": "supports"}, {"gene": "SOD3", "stance": "supports"}], "rationale": "The marker gene profile is dominated by smooth muscle structural and contractile proteins. ACTA2 (alpha-smooth muscle actin), MYH11 (myosin heavy chain 11), TPM2 (tropomyosin), CALD1 (caldesmon), MYL9 (myosin light chain), and TAGLN (transgelin) are canonical smooth muscle markers with high logfc and strong cluster specificity. RGS5 marks smooth muscle and is particularly abundant here. MGP, BGN, SPARCL1, and SOD3 are vascular-associated markers. This signature is characteristic of vascular smooth muscle cells found in kidney vessels, not pericytes (which would show different markers like PDGFRB) or myofibroblasts."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-884f62d6f1"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'kidney collecting duct intercalated cell' is not the name of CL:0000737 ('striated muscle cell'). 'kidney collecting duct intercalated cell' is the name of CL:1001432 (kidney collecting duct intercalated 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:0000737", "cell_type_label": "kidney collecting duct intercalated cell", "decision": "annotate", "markers": [{"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of vacuolar H+-ATPase subunits (ATP6V genes), which are the hallmark of proton-secreting intercalated cells. Supporting markers include SLC4A1 (anion exchanger 1/Band 3), SLC26A7 (chloride-bicarbonate exchanger), RHCG (ammonia transporter), and CA12 (carbonic anhydrase XII)—all critical for acid-base balance and characteristic of kidney collecting duct intercalated cells. The V-ATPase signature particularly suggests alpha-intercalated cells (proton-secreting subtype). No contradictory markers are evident."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.6}, {"answer": {"cell_type_id": "CL:1001432", "cell_type_label": "kidney collecting duct intercalated cell", "decision": "annotate", "markers": [{"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of vacuolar H+-ATPase subunits (ATP6V genes), which are the hallmark of proton-secreting intercalated cells. Supporting markers include SLC4A1 (anion exchanger 1/Band 3), SLC26A7 (chloride-bicarbonate exchanger), RHCG (ammonia transporter), and CA12 (carbonic anhydrase XII)—all critical for acid-base balance and characteristic of kidney collecting duct intercalated cells. The V-ATPase signature particularly suggests alpha-intercalated cells (proton-secreting subtype). No contradictory markers are evident."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct intercalated cell' is not the name of CL:0000737 ('striated muscle cell'). 'kidney collecting duct intercalated cell' is the name of CL:1001432 (kidney collecting duct intercalated cell)."], "seconds": 10.8}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-90023ca6ff"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'goblet cell' is not the name of CL:0000150 ('glandular secretory epithelial cell'). 'goblet cell' is the name of CL:0000160 (goblet 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:0000150", "cell_type_label": "goblet cell", "decision": "annotate", "markers": [{"gene": "MUC2", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}], "rationale": "This cluster exhibits the canonical mucus-secretory cell signature of intestinal goblet cells. MUC2 (the major mucin component) shows high logfc and exceptional specificity (94% in-cluster, 6.7% out). TFF3, CLCA1, and ITLN1 are established goblet cell markers with similar specificity patterns. AGR2 and SPINK4 are involved in mucin synthesis and secretion machinery. REG4 and ZG16 support goblet cell identity in the duodenal context. No markers contradict this classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.9}, {"answer": {"cell_type_id": "CL:0000160", "cell_type_label": "goblet cell", "decision": "annotate", "markers": [{"gene": "MUC2", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}], "rationale": "This cluster exhibits the canonical mucus-secretory cell signature of intestinal goblet cells. MUC2 (the major mucin component) shows high logfc and exceptional specificity (94% in-cluster, 6.7% out). TFF3, CLCA1, and ITLN1 are established goblet cell markers with similar specificity patterns. AGR2 and SPINK4 are involved in mucin synthesis and secretion machinery. REG4 and ZG16 support goblet cell identity in the duodenal context. No markers contradict this classification."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'goblet cell' is not the name of CL:0000150 ('glandular secretory epithelial cell'). 'goblet cell' is the name of CL:0000160 (goblet cell)."], "seconds": 8.5}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-9ce2902282"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'pancreatic polypeptide secreting cell' is not the name of CL:0000179 ('progesterone secreting cell'). 'pancreatic polypeptide secreting cell' is the name of CL:0002275 (pancreatic PP 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:0000179", "cell_type_label": "pancreatic polypeptide secreting cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PAM", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "ETV1", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "MEIS2", "stance": "supports"}], "rationale": "PPY is the top marker (logfc 6.381) with 100% expression in the cluster, diagnostic for pancreatic polypeptide cells. The high expression of neuroendocrine markers (CHGB, PAM, PCSK2, SCG2) and endocrine transcription factors (NEUROD1, ETV1, MEIS2, ID2) confirms endocrine cell identity. No contradicting markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.3}, {"answer": {"cell_type_id": "CL:0002275", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PAM", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "ETV1", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "MEIS2", "stance": "supports"}], "rationale": "PPY is the top marker (logfc 6.381) with 100% expression in the cluster, diagnostic for pancreatic polypeptide (PP) cells. The high expression of neuroendocrine markers (CHGB, PAM, PCSK2, SCG2) and endocrine transcription factors (NEUROD1, ETV1, MEIS2, ID2) confirms endocrine cell identity. No contradicting markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic polypeptide secreting cell' is not the name of CL:0000179 ('progesterone secreting cell'). 'pancreatic polypeptide secreting cell' is the name of CL:0002275 (pancreatic PP cell)."], "seconds": 9.2}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-a26635e6cd"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}], "rationale": "The cluster is characterized by strong myeloid markers (TYROBP, FCER1G, AIF1) and monocyte-specific genes including lysozyme (LYZ), cathepsin S (CTSS), and pro-inflammatory cytokines (IL1B, CXCL8) with robust expression across most cluster cells. These markers are the canonical signature of circulating monocytes or monocyte-like cells. The consistent upregulation of immune receptor genes and inflammatory mediators, combined with high expression of monocyte proteases and enzymes, confidently identifies this as a monocyte cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.7}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-b2d44d2eda"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'natural killer cell' is not the name of CL:0000951 ('IgE short lived plasma cell'). 'natural killer cell' is the name of CL:0000623 (natural killer 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:0000951", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}], "rationale": "Cluster exhibits canonical NK cell signature: NKG7 with KLRB1/KLRC1 killer receptors; TYROBP as critical signaling adaptor; cytotoxic granule proteins (GZMK, GZMA, CST7); chemokine repertoire (CCL3/4/5, XCL1/2) consistent with activated effector lymphocytes; IL2RB supporting cytokine responsiveness. High and consistent intra-cluster expression (pct_in 0.8–0.99) across all diagnostic markers. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.8}, {"answer": {"cell_type_id": "CL:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}], "rationale": "Cluster exhibits canonical NK cell signature: NKG7 with KLRB1/KLRC1 killer cell lectin-like receptors; TYROBP as critical DAP12 signaling adaptor; cytotoxic granule proteins (GZMK, GZMA, CST7); chemokine repertoire (CCL3/4/5, XCL1/2) consistent with activated effector lymphocytes; IL2RB supporting cytokine responsiveness. High and consistent intra-cluster expression (pct_in 0.8–0.99) across all diagnostic markers. No contradictory markers present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'natural killer cell' is not the name of CL:0000951 ('IgE short lived plasma cell'). 'natural killer cell' is the name of CL:0000623 (natural killer cell)."], "seconds": 12.8}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-bb928b569a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 15, "findings": [{"message": "The label 'Kupffer cell' is not the name of CL:0000864 ('tissue-resident macrophage'). 'Kupffer cell' is the name of CL:0000091 (Kupffer 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:0000864", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}], "rationale": "This cluster is Kupffer cells, the resident macrophages of the liver. The marker profile is unambiguously macrophage: C1QA/B/C are canonical complement-based macrophage markers, CD163 is a tissue macrophage scavenger receptor, MARCO is a macrophage-specific receptor, and the constellation of MHC class II molecules (HLA-DRA, CD74), lysosomal enzymes (CTSB, CTSS), and immune receptors (MS4A6A/7, FCER1G, TYROBP) are all hallmarks of professional antigen-presenting phagocytes. AIF1/Iba1 and HMOX1 further support macrophage identity. The iron metabolism genes (FTL, SLC40A1) reflect the phagocytic burden of hepatic macrophages. Given the liver tissue context, this is specifically Kupffer cell rather than a generic tissue macrophage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.8}, {"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}], "rationale": "This cluster is Kupffer cells, the resident macrophages of the liver. The marker profile is unambiguously macrophage: C1QA/B/C are canonical complement-based macrophage markers, CD163 is a tissue macrophage scavenger receptor, MARCO is a macrophage-specific receptor, and the constellation of MHC class II molecules (HLA-DRA, CD74), lysosomal enzymes (CTSB, CTSS), and immune receptors (MS4A6A/7, FCER1G, TYROBP) are all hallmarks of professional antigen-presenting phagocytes. AIF1/Iba1 and HMOX1 further support macrophage identity. The iron metabolism genes (FTL, SLC40A1) reflect the phagocytic burden of hepatic macrophages. Given the liver tissue context, this is specifically Kupffer cell rather than a generic tissue macrophage."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'Kupffer cell' is not the name of CL:0000864 ('tissue-resident macrophage'). 'Kupffer cell' is the name of CL:0000091 (Kupffer cell)."], "seconds": 11.0}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-c12bd3b011"} +{"attempts": [{"codes": ["BEV017"], "evidence": 5, "findings": [{"message": "The label 'distal convoluted tubule cell' is not the name of CL:0002307 ('brush border cell of the proximal tubule'). Closest names: CL:1000849 (kidney distal convoluted tubule epithelial 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:0002307", "cell_type_label": "distal convoluted tubule cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "SLC12A3 (NCCT) is the defining marker of distal convoluted tubule segment 1 (DCT1). Combined with WNK1 (regulator of NCC-mediated salt reabsorption) and the epithelial ion-transport machinery (ATP1A1/ATP1B1), this cluster clearly represents DCT1 principal cells. CA12 supports kidney tubule identity. Mitochondrial genes reflect high metabolic demand in active transport-engaged epithelium."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.4}, {"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "SLC12A3 (NCCT/NCC sodium-chloride cotransporter) is the cardinal marker of distal convoluted tubule principal cells, expressed in 97.5% of cluster cells and only 3.6% of cells outside. WNK1 is the key kinase regulator of NCC-mediated salt reabsorption. ATP1A1/ATP1B1 form the Na+/K+-ATPase essential for active transcellular transport. CA12 (carbonic anhydrase XII) participates in ion transport and acid-base balance. Together these constitute the functional signature of DCT epithelium. Mitochondrial genes reflect high metabolic demand of active ion-transporting cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'distal convoluted tubule cell' is not the name of CL:0002307 ('brush border cell of the proximal tubule'). Closest names: CL:1000849 (kidney distal convoluted tubule epithelial cell)."], "seconds": 16.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-c7858eb46a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'lymphatic endothelial cell' is not the name of CL:0000528 ('nitrergic neuron'). 'lymphatic endothelial cell' is the name of CL:0002138 (endothelial cell of lymphatic vessel).", "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:0000528", "cell_type_label": "lymphatic endothelial cell", "decision": "annotate", "markers": [{"gene": "LYVE1", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "CCL21", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}], "rationale": "Lymphatic endothelial cells are identified by the distinctive combination of LYVE1 and PROX1, the latter being the master transcription factor for lymphatic identity. CCL21 is highly specific to lymphatic endothelium. The additional markers represent canonical endothelial cell features (tight junction proteins, adhesion molecules, matrix components, and caveolae-associated proteins). No markers contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.5}, {"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "endothelial cell of lymphatic vessel", "decision": "annotate", "markers": [{"gene": "LYVE1", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "CCL21", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}], "rationale": "Lymphatic endothelial cells are identified by the distinctive combination of LYVE1 and PROX1, the latter being the master transcription factor for lymphatic identity. CCL21 is highly specific to lymphatic endothelium. The additional markers represent canonical endothelial cell features (tight junction proteins, adhesion molecules, matrix components, and caveolae-associated proteins). No markers contradict this identity."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'lymphatic endothelial cell' is not the name of CL:0000528 ('nitrergic neuron'). 'lymphatic endothelial cell' is the name of CL:0002138 (endothelial cell of lymphatic vessel)."], "seconds": 9.7}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-cc1cfcedd3"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}], "rationale": "This cluster shows a clear pericyte signature in kidney tissue. RGS5 is a canonical pericyte marker consistently highly expressed across the cluster (pct_in 0.927). IGFBP5 and IGFBP7 are characteristic markers of perivascular cells and fibroblasts that associate with blood vessels. TM4SF1 marks endothelial-adjacent cells and pericytes. TIMP3, an ECM-modifying protease inhibitor, is typical of pericyte function in maintaining vessel stability. The remaining top markers (IFI27, HSPA1A, CDKN1A, IRF1, CCL2, SOCS3) appear to reflect an activated or stressed state of pericytes rather than contradicting their identity, possibly indicating response to tissue injury or inflammatory conditions."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.0}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-d9bc81cfff"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'best4+ enterocyte' is not the name of CL:0000584 ('enterocyte'). 'best4+ enterocyte' is the name of CL:4030026 (BEST4+ enterocyte).", "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:0000584", "cell_type_label": "best4+ enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "GSN", "stance": "supports"}], "rationale": "BEST4 (logfc 2.161, highly specific pct_out 0.013) is the defining marker of a specialized enterocyte subtype in the intestinal epithelium. This is strongly supported by CFTR, GUCA2A/2B, KRT20, CPA2, and other intestinal epithelial markers. All top markers are consistent with absorptive intestinal epithelial cell identity with no contradictory signals."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.6}, {"answer": {"cell_type_id": "CL:4030026", "cell_type_label": "BEST4+ enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "GSN", "stance": "supports"}], "rationale": "BEST4 (logfc 2.161, highly specific pct_out 0.013) is the defining marker of BEST4+ enterocytes, a specialized absorptive enterocyte subtype in the duodenal epithelium. This is strongly supported by CFTR, GUCA2A/2B, KRT20, CPA2, and other intestinal epithelial markers. All top markers are consistent with BEST4+ enterocyte identity with no contradictory signals."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'best4+ enterocyte' is not the name of CL:0000584 ('enterocyte'). 'best4+ enterocyte' is the name of CL:4030026 (BEST4+ enterocyte)."], "seconds": 9.6}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-daa29fa7c3"} +{"attempts": [{"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": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}], "rationale": "The cluster is characterized by strong expression of NK cell-specific markers (GNLY, NKG7), cytotoxic granule proteins (GZMB, GZMA), and NK cell receptors (KLRD1/CD94). High logfc values and low pct_out for these markers indicate they are highly specific to this cluster. The chemokines CCL5 and CCL4 are characteristic products of activated NK cells. No TCR genes are present, ruling out T cell identity. The constellation of markers is diagnostic for natural killer cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.7}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-def3067099"} +{"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": "CD2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of IL7R, CD2, and CD52, which are definitive T cell markers. IL7R shows exceptional specificity (57.4% in vs 1.7% out), CD2 is a pan-T cell surface antigen (58.8% in vs 1.1% out), and CD52 is expressed on all T cells (65.3% in vs 4.9% out). PTPRC (CD45) and CXCR4 support immune cell identity and T cell trafficking capacity. No contradictory markers suggesting other cell types are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.4}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-e0c7aa5d8b"} +{"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:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "EMCN", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "contradicts"}, {"gene": "CD74", "stance": "contradicts"}], "rationale": "EMCN and IGFBP5 are expressed in nearly 100% of cells in this cluster with high specificity, and PLAT is a classically endothelial-restricted gene. These three markers alone are highly predictive of endothelial identity. Additional endothelial markers (RAMP2, GNG11, CRHBP, RNASE1) strengthen this assignment. The expression of MHC class II molecules (HLA-DRB1, CD74) is atypical for endothelium and more consistent with antigen-presenting cells, but kidney endothelium frequently upregulates MHC expression, particularly in response to inflammatory stimuli, so these do not definitively contradict the endothelial assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.3}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-e6fd6bbd15"} +{"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": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CREM", "stance": "supports"}, {"gene": "PTPRCAP", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}], "rationale": "CD3D is diagnostic for T cells (TCR-CD3 complex component). All top markers are consistent with T lymphocytes: CD69 (activation), IL32 (T cell cytokine), CXCR4 (T cell chemokine receptor), PTPRC (CD45, pan-leukocyte), and others support T cell identity. No markers contradict this identification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.7}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-e76b10ee43"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"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"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000819", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "Regulatory T cells are characterized by high FOXP3 expression (master transcription factor) and CTLA4 (immunosuppressive marker). Both show dramatic enrichment in this cluster (FOXP3: 59% in vs 0.5% out; CTLA4: 61% in vs 1% out). The cluster also expresses canonical T cell markers (CD3E, TRAC, CD2, CD27, CD52, SELL) consistent with the T lymphocyte lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.7}, {"answer": {"cell_type_id": "CL:0000815", "cell_type_label": "regulatory T cell", "decision": "annotate", "markers": [{"gene": "FOXP3", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}], "rationale": "Regulatory T cells are characterized by high FOXP3 expression (master transcription factor) and CTLA4 (immunosuppressive marker). Both show dramatic enrichment in this cluster (FOXP3: 59% in vs 0.5% out; CTLA4: 61% in vs 1% out). The cluster also expresses canonical T cell markers (CD3E, TRAC, CD2, CD27, CD52, SELL) consistent with the T lymphocyte lineage."}, "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)."], "seconds": 8.5}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-f3161764a6"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 15, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'naive T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-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": ["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:0000900", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CORO1B", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "RGS10", "stance": "supports"}, {"gene": "VIM", "stance": "contradicts"}, {"gene": "AIF1", "stance": "contradicts"}], "rationale": "Strong and consistent T cell signature across 13 markers including the definitive T cell marker CD3E. The co-expression of SELL and CCR7 at high levels is characteristic of naive T cells specifically. VIM and AIF1 suggest minor contamination from mesenchymal or myeloid cells but do not diminish the clear naive T cell identity of the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.5}, {"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CORO1B", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "RGS10", "stance": "supports"}, {"gene": "VIM", "stance": "contradicts"}, {"gene": "AIF1", "stance": "contradicts"}], "rationale": "Strong and consistent T cell signature across 13 markers including the definitive T cell marker CD3E. The co-expression of SELL and CCR7 at high levels is characteristic of naive T cells specifically. VIM and AIF1 suggest minor contamination from mesenchymal or myeloid cells but do not diminish the clear naive T cell identity of the cluster."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). 'naive T cell' is the name of CL:0000898 (naive T cell)."], "seconds": 11.7}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-f5c625b34c"} +{"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:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "CXCL14", "stance": "supports"}, {"gene": "ADAMDEC1", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "DCN", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "TCF21", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "RARRES2", "stance": "supports"}, {"gene": "MFAP4", "stance": "supports"}, {"gene": "C1S", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "IFITM3", "stance": "contradicts"}, {"gene": "CTSC", "stance": "contradicts"}], "rationale": "Cluster is clearly a fibroblast population based on the strong enrichment of extracellular matrix genes (COL1A2, COL3A1, LUM, DCN, MFAP4), fibroblast-specific markers (CXCL14, ADAMDEC1, TCF21), and mesenchymal markers (VIM, CALD1, IGFBP7). The supporting markers show high logfc and high pct_in with very low pct_out, indicating specificity to this cluster. IFITM3 and CTSC show elevated pct_out (0.248 and 0.323 respectively), suggesting either immune cell contamination/doublets or interferon-stimulated activation of the fibroblasts in this inflamed duodenal tissue, but do not negate the clear fibroblast identity driven by the dominant marker signal."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.8}], "model": "claude-haiku", "protocol": 2, "task_id": "ct-f7c13b08bb"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}], "rationale": "Strong cytotoxic genes (GNLY, NKG7, PRF1, GZMB, GZMA, CST7, CTSW) plus NK receptors KLRD1 and KLRC1, the adaptors TYROBP and FCER1G, CD16 (FCGR3A), and XCL1/XCL2. No CD3 or TRAC genes appear among the top markers, which suggests NK cells rather than cytotoxic T cells. This is a typical lung NK cell cluster, mixing CD16-high and XCL1/NKG2A-high NK cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-0bcb90ea26"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "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": "SRGN", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "RGS1", "stance": "supports"}], "rationale": "These are myeloid immune cells: TYROBP and AIF1 are highly specific to the cluster. High MHC class II genes (HLA-DR/DP/DQ, CD74) mean they present antigen. IL1B, CXCL8, CXCL2, CCL3, PLAUR and NFKBIA show an activated, inflammatory state, consistent with monocyte-derived macrophages or monocytes that have moved into the kidney. The top genes lack clear markers to separate monocytes, macrophages and dendritic cells, so the broader term mononuclear phagocyte is used. No markers suggest a different cell type mixed into the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-0c19dd5456"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "epithelial cell of proximal tubule", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "PDZK1IP1", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}, {"gene": "RBP5", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1H", "stance": "supports"}, {"gene": "MT1F", "stance": "supports"}, {"gene": "CYB5A", "stance": "supports"}, {"gene": "SUCLG1", "stance": "supports"}], "rationale": "The cluster has a typical proximal tubule profile. It expresses gluconeogenic and metabolic genes (ALDOB, MIOX, HPD, ASS1, SUCLG1), the creatine synthesis gene GATM, PDZK1IP1 (MAP17), and the detoxification and transport genes GSTA1, UGT2B7 and FABP1. It also expresses GPX3, which proximal tubule cells secrete in large amounts. Metallothionein genes (MT1G/H/F/X) are strongly expressed in proximal tubule cells. None of the top markers point to another nephron segment, so the cluster does not look mixed. I used the broad proximal tubule term because these genes do not cleanly separate the S1/S2 segments from S3."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-0f7cfea7f3"} +{"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:0000940", "cell_type_label": "mucosal invariant T cell", "decision": "annotate", "markers": [{"gene": "SLC4A10", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "TRDV2", "stance": "contradicts"}], "rationale": "These cells are T cells (CD3E, IL7R, LTB, IL32). They also have an innate-like, type-17 profile: high KLRB1 (CD161), IL23R and GZMK. SLC4A10 is found in about 50% of cells in the cluster and about 5% outside it. It is a highly specific MAIT-cell marker, so this fits mucosal-associated invariant T (MAIT) cells best, and MAIT cells are common in lung. CD69 and the immediate-early genes (DUSP1, FOSB, NFKBIA, TNFAIP3) point to tissue residency or activation. TRDV2 is found in about 44% of cells, which means Vδ2 γδ T cells are probably mixed in. Those cells share the KLRB1+ IL23R+ GZMK+ innate-like program. So this is likely a mixed MAIT and Vδ2 γδ innate-like T-cell cluster, with MAIT as the main label."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.0}], "model": "claude-opus", "protocol": 2, "task_id": "ct-1161617d72"} +{"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": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CORO1A", "stance": "supports"}, {"gene": "PTPRCAP", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "ACAP1", "stance": "supports"}], "rationale": "Cells express CD3E, CD247 and LCK specifically, which marks a TCR-expressing T-cell population. CD7, KLRB1, GZMA and NKG7 point to cytotoxic or effector-memory T cells, which in duodenum are often intraepithelial or lamina propria T cells. CD8A/B and TRDC are not among the top markers, so the subset cannot be resolved further and the broad T cell term is used."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-13d48ee1d6"} +{"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": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "CD79A is highly specific (59% in the cluster vs 0.3% outside) and IGKC is in the same fraction of cells, showing B-lineage identity. High CD74 and HLA-DRA reflect MHC class II antigen presentation. CD52, CXCR4 and LTB are lymphocyte markers that fit circulating B cells. Retained MHC-II and only moderate IGKC argue against plasma cells. Ribosomal protein genes and MALAT1 fit small, resting lymphocytes. No marker clearly points to another cell type, though some T or NK cells could be mixed in."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.0}], "model": "claude-opus", "protocol": 2, "task_id": "ct-18ce9fb955"} +{"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": "MS4A6A", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "High expression of the complement genes C1QA/B/C together with SELENOP, MS4A6A, AIF1, TYROBP and FCER1G, plus strong MHC class II expression (HLA-DR/DP/DQ, CD74), points to tissue-resident macrophages of the intestinal lamina propria. Expression of C1Q and SELENOP argues against dendritic cells and monocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-1fcb853772"} +{"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:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CORO1A", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}], "rationale": "The cluster has strong, specific expression of cytotoxic and NK genes: GNLY, NKG7, GZMB, FGFBP2, KLRD1, CCL5 and CCL4. FGFBP2 and GZMB with KLRD1 point to circulating CD56dim-type NK cells. Effector CD8 T cells share these genes, but with no CD3 or CD8 genes among the top markers, NK is favoured. TUBA1B, HMGB2, HMGN2 and H4C3 suggest a proliferating fraction. IGKC suggests some B/plasma-cell contamination or ambient RNA."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.9}], "model": "claude-opus", "protocol": 2, "task_id": "ct-20d7fe4cf5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 20, "findings": [{"message": "The label 'CD16-positive, CD56-dimly positive natural killer cell, human' is not the name of CL:0000939 ('CD16-positive, CD56-dim natural killer cell, human'). Closest names: CL:0000939 (CD16-positive, CD56-dim natural killer cell, human); CL:0002338 (CD56-positive, CD161-positive immature natural killer cell, human); CL:0002426 (CD11b-positive, CD27-positive natural killer cell, mouse).", "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:0000939", "cell_type_label": "CD16-positive, CD56-dimly positive natural killer cell, human", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "MYOM2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "This cluster expresses a strong cytotoxic program (GZMB, PRF1, GNLY, NKG7, GZMA, GZMH, CST7, CTSW). Several NK-associated adaptor and receptor genes are also high: FCER1G and TYROBP in nearly all cells, plus SPON2, CLIC3 and MYOM2. FCGR3A (CD16) is present in 94% of cells, and FGFBP2, CX3CR1 and ADGRG1 are also expressed, which together fit the mature CD16+ CD56dim NK subset. No T-cell receptor or CD3 genes are among the top markers, and FCER1G/TYROBP/MYOM2 are high, which argues against effector-memory CD8 T cells (TEMRA). This is an inference from absence, because the list shows only the top 20 genes. The cells are most likely lung-resident or circulating CD56dim NK cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.8}, {"answer": {"cell_type_id": "CL:0000939", "cell_type_label": "CD16-positive, CD56-dim natural killer cell, human", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "MYOM2", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "This cluster expresses a strong cytotoxic program (GZMB, PRF1, GNLY, NKG7, GZMA, GZMH, CST7, CTSW). NK-associated adaptor and receptor genes are also high: FCER1G and TYROBP in nearly all cells, plus SPON2, CLIC3 and MYOM2. FCGR3A (CD16) is expressed in 94% of cells, together with FGFBP2, CX3CR1 and ADGRG1, which fits the mature CD16+ CD56dim NK subset. No TCR or CD3 genes are among the top markers, and FCER1G, TYROBP and MYOM2 are high, which argues against effector-memory CD8 T cells (TEMRA). That is partly an inference from absence, because only the top 20 genes are shown."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'CD16-positive, CD56-dimly positive natural killer cell, human' is not the name of CL:0000939 ('CD16-positive, CD56-dim natural killer cell, human'). Closest names: CL:0000939 (CD16-positive, CD56-dim natural killer cell, human); CL:0002338 (CD56-positive, CD161-positive immature natural killer cell, human); CL:0002426 (CD11b-positive, CD27-positive natural killer cell, mouse)."], "seconds": 15.4}], "model": "claude-opus", "protocol": 2, "task_id": "ct-2e16bde736"} +{"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": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}], "rationale": "CD79A, CD79B and MS4A1 are highly specific to this cluster (pct_out ≤0.07), which defines B cells. Strong MHC class II and CD74 expression fits antigen-presenting B cells, and CD37, CD52, LTB and CXCR4 are lymphocyte genes. IGKC and IGLC2 levels are moderate, suggesting mature or naive B cells rather than plasma cells. No marker points to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.5}], "model": "claude-opus", "protocol": 2, "task_id": "ct-33d5498243"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002543", "cell_type_label": "vein endothelial cell", "decision": "annotate", "markers": [{"gene": "ACKR1", "stance": "supports"}, {"gene": "SELE", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "PCAT19", "stance": "supports"}, {"gene": "MCTP1", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-E", "stance": "supports"}, {"gene": "RCAN1", "stance": "supports"}], "rationale": "Pan-endothelial markers (CLDN5, RAMP2, AQP1, TM4SF1, GNG11, SPARCL1) together with ACKR1 (DARC) and SELE, the hallmark markers of postcapillary venule/venous endothelium in skin, plus inflammatory/activation genes (RCAN1, SOCS3, CD74, HLA-E). These point to venous (postcapillary venule) blood vascular endothelial cells. None of the markers point to a different lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-3875326824"} +{"attempts": [{"codes": [], "evidence": 11, "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": "RORC", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "TMIGD2", "stance": "supports"}, {"gene": "JAML", "stance": "supports"}], "rationale": "The cluster expresses RORC, IL23R, CCR6, KIT (CD117) and IL7R, with high LTB, IL4I1 and LST1 and no T-cell receptor or CD3 genes among the top markers. This is the canonical ILC3 profile; KIT and LST1 together favour ILC3 (including LTi-like cells) over Th17 cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-3ec5acbb2d"} +{"attempts": [{"codes": [], "evidence": 18, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000488", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "KRT7", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}, {"gene": "CLU", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}, {"gene": "GSTP1", "stance": "supports"}], "rationale": "KRT7 (83% in vs 0.3% out), SPP1, FXYD2, DEFB1, ANXA4, CD24, SLPI, TM4SF4, LGALS4, ELF3 and CLU are canonical human liver cholangiocyte markers. KRT8 and KRT18 indicate simple epithelium, and ATP1A1/ATP1B1 fit ductal ion transport. GC is a hepatocyte gene but is broadly expressed (about 50% out) with a modest fold change, so it is likely ambient RNA. The cluster is biliary epithelial cells (cholangiocytes); intrahepatic cholangiocyte (CL:0002538) is also consistent."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.2}], "model": "claude-opus", "protocol": 2, "task_id": "ct-4163a3b864"} +{"attempts": [{"codes": [], "evidence": 13, "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": "IGKC", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}], "rationale": "Strong, specific expression of JCHAIN and MZB1, plus DERL3, and high levels of many immunoglobulin genes covering several antibody classes (IgM, IgG, IgA; kappa and lambda chains). Protein-secretion genes are also up (XBP1, FKBP11, SSR3/4, SEC11C, HSP90B1). Together this marks antibody-secreting plasma cells. No markers from other cell types appear."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-41fb1f6e39"} +{"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:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "PRSS23", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TAGLN", "stance": "contradicts"}, {"gene": "C7", "stance": "contradicts"}], "rationale": "DNASE1L3, FCN3, RAMP3, INMT, LIFR and PRSS23 are hallmark genes of human liver sinusoidal endothelial cells. PTPRB, ENG, HSPG2, ID1/ID3, IFI27 and RNASE1 support an endothelial identity. TAGLN and C7 are more typical of hepatic stellate cells, mesenchymal cells or smooth muscle. They may point to some stellate-cell admixture or doublets, but the overall profile is clearly LSEC."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.0}], "model": "claude-opus", "protocol": 2, "task_id": "ct-4d4de5c13f"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT1", "stance": "supports"}, {"gene": "KRT10", "stance": "supports"}, {"gene": "KRTDAP", "stance": "supports"}, {"gene": "DMKN", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "LY6D", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "DSP", "stance": "supports"}, {"gene": "KRT14", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "SERPINB5", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "CLDN1", "stance": "supports"}], "rationale": "KRT1/KRT10, KRTDAP, DMKN, SFN and LGALS7B show differentiating epidermal keratinocytes. Junction genes (DSP, PERP, CLDN1), KRT14, MIR205HG and the keratinocyte chemokine CCL27 support epidermal keratinocyte identity. Because KRT14 and MIR205HG add a basal signal, the broader term keratinocyte is used. No markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.3}], "model": "claude-opus", "protocol": 2, "task_id": "ct-506f19166c"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000173", "cell_type_label": "pancreatic D cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "PRG4", "stance": "supports"}, {"gene": "BCHE", "stance": "supports"}, {"gene": "LEPR", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "CASR", "stance": "supports"}, {"gene": "GABRG2", "stance": "supports"}, {"gene": "UNC5B", "stance": "supports"}, {"gene": "ISL1", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "UCHL1", "stance": "supports"}], "rationale": "SST is the top marker by a wide margin (logFC 5.7). HHEX is a transcription factor that specifies delta cells. BCHE, LEPR, PRG4, RBP4, CASR, GABRG2 and UNC5B are known delta-cell-enriched genes in human islet single-cell datasets. ISL1, SEC11C, UCHL1 and PCSK1 are general endocrine markers. The near-universal SST in other cells (pct_out 0.999) is probably ambient RNA contamination, which is common in CEL-seq2 data."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.4}], "model": "claude-opus", "protocol": 2, "task_id": "ct-50ec79996f"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "SIRPG", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TRDV2", "stance": "supports"}, {"gene": "ZNF683", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The pan-T-cell genes CD3E and CD3D are expressed in about 97–98% of the cluster's cells, along with IL32. The cluster combines two T-cell programmes. One is GZMK+ CD8 memory-like: GZMK, CD8A, CD27, CXCR3, TCF7, SIRPG and ITM2C. The other is gamma-delta: TRDV2 is in 35% of cells versus 4% elsewhere, and ZNF683 is also present. This looks like a mixed cluster of CD8 memory and Vδ2 gamma-delta T cells that are not well separated, so I've given the broader term \"T cell\" rather than a single subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.8}], "model": "claude-opus", "protocol": 2, "task_id": "ct-52a80b5c6b"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}], "rationale": "AQP2 (pct_in 0.80 vs 0.04), AQP3 and FXYD4 are canonical collecting duct principal cell markers; CDH16, WFDC2, KRT19/KRT18, ELF3 and TACSTD2 support collecting duct epithelium. No markers indicate a contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-54741cc370"} +{"attempts": [{"codes": [], "evidence": 13, "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": "IGLL5", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "TNFRSF17", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "DNAJB9", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}], "rationale": "The strongest markers in this cluster are JCHAIN, IGLL5, MZB1, DERL3, TNFRSF17 (BCMA) and CD79A. Together these identify antibody-secreting plasma cells. Genes for the secretory machinery and the unfolded protein response (XBP1, SSR4, SEC11C, SPCS1/2, HERPUD1, DNAJB9, FKBP11, UBE2J1) are also high, which fits plasma cells. In the duodenum these are most likely IgA-secreting cells that make J chain. JCHAIN is detected in almost every cell outside the cluster (pct_out 0.99), probably because of ambient RNA. Even so, its very large fold change supports this call. No markers point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.1}], "model": "claude-opus", "protocol": 2, "task_id": "ct-560d5829d2"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002187", "cell_type_label": "basal cell of epidermis", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "SERPINB5", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "FGFBP1", "stance": "supports"}], "rationale": "Nearly every cell expresses KRT5 and KRT14, which marks keratinocytes. Basal-layer markers (KRT15, DST, MIR205HG, AQP3, TACSTD2) and other epidermal genes (SFN, PERP, LGALS7B, CCL27) are also present. Suprabasal differentiation markers (KRT1, KRT10) are missing from the top list. Together this points to basal keratinocytes of the epidermis."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.2}], "model": "claude-opus", "protocol": 2, "task_id": "ct-5633d2ce11"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'renal beta-intercalated cell' is not the name of CL:0005012 ('multiciliated epithelial cell'). 'renal beta-intercalated cell' is the name of CL:0002201 (renal beta-intercalated 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:0005012", "cell_type_label": "renal beta-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}], "rationale": "Several V-ATPase subunits (ATP6V1B1, ATP6V0D2, ATP6V1G3) together with TMEM213, HEPACAM2 and CA12 point to collecting-duct intercalated cells. SLC26A4 (pendrin) is highly specific here: 77% of cells in the cluster express it versus 0.8% outside. That, plus no SLC4A1 or AQP2 among the top markers, makes this the type B (beta) intercalated cell rather than the type A cell or the principal cell. Pendrin is also expressed by non-A non-B intercalated cells, so they cannot be fully ruled out. WFDC2, KRT7 and KRT8 are consistent with distal nephron and collecting-duct epithelium. No markers clearly point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.2}, {"answer": {"cell_type_id": "CL:0002201", "cell_type_label": "renal beta-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}], "rationale": "Several V-ATPase subunits (ATP6V1B1, ATP6V0D2, ATP6V1G3) together with TMEM213, HEPACAM2 and CA12 point to collecting-duct intercalated cells. SLC26A4 (pendrin) is highly specific here: 77% of cells in the cluster express it versus 0.8% outside. That, plus no SLC4A1 or AQP2 among the top markers, makes this the type B (beta) intercalated cell rather than the type A cell or the principal cell. Pendrin is also expressed by non-A non-B intercalated cells, so they cannot be fully ruled out. WFDC2, KRT7 and KRT8 are consistent with distal nephron and collecting-duct epithelium. No markers clearly point to a different cell type. The CL identifier is corrected to CL:0002201, the term for renal beta-intercalated cell."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'renal beta-intercalated cell' is not the name of CL:0005012 ('multiciliated epithelial cell'). 'renal beta-intercalated cell' is the name of CL:0002201 (renal beta-intercalated cell)."], "seconds": 10.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-6807a1005a"} +{"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:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "S100A9", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "S100A11", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "C1QA", "stance": "contradicts"}], "rationale": "Strong S100A8/S100A9, LYZ, LST1, AIF1, FCER1G and TYROBP, together with MHC-II genes (HLA-DRA, CD74), point to classical monocytes, which in liver are often called inflammatory monocyte/macrophages. C1QA is expressed in 63% of cells, which suggests some resident macrophages (Kupffer cells) are mixed in. Kupffer-specific genes (CD5L, MARCO) are not among the top markers, so the cluster is mainly monocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.3}], "model": "claude-opus", "protocol": 2, "task_id": "ct-6846a2fbd5"} +{"attempts": [{"codes": [], "evidence": 15, "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": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "LINC02446", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}, {"gene": "S100B", "stance": "supports"}, {"gene": "RGS10", "stance": "supports"}], "rationale": "CD8A/CD8B plus CD3E mark these as CD8 alpha-beta T cells. They also express a strong naive/quiescent program: CCR7, SELL, LEF1, TCF7, IL7R, CD27 and LTB. LRRN3 and LINC02446 are known markers of naive CD8 T cells, and so is S100B. No effector or cytotoxic genes (GZMs, NKG7, CCL5) appear, which argues against memory or effector CD8 cells. AIF1 is a little unusual but has been reported in naive CD8 T cells, so it doesn't clearly point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.2}], "model": "claude-opus", "protocol": 2, "task_id": "ct-6b9f55ce2e"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "AHSP", "stance": "supports"}, {"gene": "ALAS2", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "GYPA", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SNCA", "stance": "supports"}, {"gene": "BNIP3L", "stance": "supports"}, {"gene": "HMBS", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}], "rationale": "Nearly every cell in the cluster expresses the hemoglobin genes (HBB, HBA1/2, HBD, HBM). Several other erythroid-specific genes are present, mostly in over 80% of the cluster and almost absent elsewhere: AHSP, ALAS2, CA1, SLC4A1 (Band 3), GYPA, SNCA, SLC25A37 and HMBS. BNIP3L is also present, which points to mitophagy during erythroid maturation. Erythropoiesis doesn't normally happen in the adult liver, so these are probably circulating red blood cells. The heme-synthesis transcripts (ALAS2, HMBS) suggest some are reticulocytes. No markers clearly point to another lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-73d8984fbc"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002410", "cell_type_label": "pancreatic stellate cell", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "COL5A1", "stance": "supports"}, {"gene": "COL15A1", "stance": "supports"}, {"gene": "CYGB", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "PXDN", "stance": "supports"}, {"gene": "SERPINE1", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}], "rationale": "The top markers are almost all collagen and matrix genes (COL1A1/1A2/3A1/5A1/5A2/6A1/6A3/4A2/15A1, SPARC, FN1, PXDN), plus VIM and CALD1, so these are matrix-producing mesenchymal cells. CYGB (cytoglobin) is a typical stellate-cell marker and SFRP2 is strongly cluster-specific, which point to pancreatic stellate cells, the usual mesenchymal population in CEL-seq2 pancreas data. SERPINE1, TIMP1 and MICAL2 suggest the cells are activated. No markers point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.9}], "model": "claude-opus", "protocol": 2, "task_id": "ct-75516baf75"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1001106", "cell_type_label": "kidney loop of Henle thick ascending limb epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A1", "stance": "supports"}, {"gene": "UMOD", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}], "rationale": "SLC12A1 (NKCC2) is found in 96% of cells in this cluster and only 5% of other cells. Together with UMOD (Tamm-Horsfall protein), this is the defining marker pair for thick ascending limb (TAL) epithelium. KNG1, DEFB1, CA12 and CD24 are also typical of TAL/distal tubule cells. High Na+/K+-ATPase expression (ATP1A1, ATP1B1) fits the high transport activity of the TAL. The strong mitochondrial transcript signal fits this mitochondria-rich segment. No markers point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-7954bd765f"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "FBXO7", "stance": "supports"}, {"gene": "SNCA", "stance": "supports"}], "rationale": "The cluster's top markers are hemoglobin genes: HBB, HBA1, HBA2, HBD and HBM. HBD and HBM are almost never detected outside the cluster (pct_out 0.004 and 0.001). Several other erythroid genes are also enriched: SLC25A37 (mitoferrin-1, which brings iron into mitochondria for heme synthesis), SLC25A39, GYPC (glycophorin C), FBXO7 and SNCA (both highly expressed late in red-cell development). There are no markers from other lineages, so this doesn't look like a mixed or doublet cluster. In a skin sample, these are most likely red blood cells from the blood in the tissue."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.4}], "model": "claude-opus", "protocol": 2, "task_id": "ct-838e09fefd"} +{"attempts": [{"codes": [], "evidence": 13, "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": "MYL9", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "FLNA", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "BGN", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "SOD3", "stance": "supports"}], "rationale": "Strong contractile smooth muscle program (TAGLN, MYL9, ACTA2, TPM2, CALD1, FLNA) with the specific mature SMC marker MYH11 (72% in vs 2% out), plus RGS5 and vascular matrix genes (MGP, BGN, SPARCL1, SOD3, C11orf96) indicating vascular mural cells in kidney. Some pericyte/mesangial admixture is possible given high RGS5, but MYH11 favors vascular smooth muscle."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-884f62d6f1"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "ADGRF5", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}], "rationale": "SLC4A1 (AE1) and SLC26A7 are specific to type A intercalated cells. The V-ATPase subunits ATP6V1B1, ATP6V1G3 and ATP6V0D2 mark acid-secreting intercalated cells. TMEM213, ADGRF5 and SPINK1 are known type A intercalated cell markers, and RHCG and CA12 also fit. The type B marker SLC26A4 is absent."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.4}], "model": "claude-opus", "protocol": 2, "task_id": "ct-90023ca6ff"} +{"attempts": [{"codes": ["BEV016"], "evidence": 15, "findings": [{"message": "No row of the pinned table has cluster=c10, gene=FCGBP. Closest gene values for cluster=c10: FABP2.", "rule_id": "BEV016", "where": "evidence 9 (cluster=c10;gene=FCGBP)"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000495", "cell_type_label": "small intestine goblet cell", "decision": "annotate", "markers": [{"gene": "MUC2", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "FCGBP", "stance": "supports"}, {"gene": "ST6GALNAC1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "LRRC26", "stance": "supports"}, {"gene": "STARD10", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}], "rationale": "The cluster shows the standard goblet cell secretory program. MUC2 is expressed in 94% of cluster cells versus 7% of other cells. Other goblet-cell genes are also high: TFF3, CLCA1, SPINK4, ZG16, REG4, ITLN1, AGR2, ST6GALNAC1, KLK1 and LRRC26. LGALS4 and KRT18 mark intestinal epithelium. The tissue is duodenum, so this is a small intestine goblet cell. No markers clearly point to another cell type: no enterocyte, Paneth cell (DEFA5/6), enteroendocrine or immune genes are enriched. REG4 is also found in some Paneth and deep crypt secretory cells, but it fits goblet cells here."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}, {"answer": {"cell_type_id": "CL:1000495", "cell_type_label": "small intestine goblet cell", "decision": "annotate", "markers": [{"gene": "MUC2", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "ST6GALNAC1", "stance": "supports"}, {"gene": "KLK1", "stance": "supports"}, {"gene": "LRRC26", "stance": "supports"}, {"gene": "STARD10", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}], "rationale": "The cluster shows the standard goblet cell secretory program. MUC2 is expressed in 94% of cluster cells versus 7% of other cells. Other goblet-cell genes are also high: TFF3, CLCA1, SPINK4, ZG16, REG4, ITLN1, AGR2, ST6GALNAC1, KLK1 and LRRC26. LGALS4 and KRT18 mark intestinal epithelium. The tissue is duodenum, so this is a small intestine goblet cell. No markers clearly point to another cell type: no enterocyte, Paneth cell (DEFA5/6), enteroendocrine or immune genes are enriched among the top markers."}, "cli_tools": [], "error": null, "feedback": ["evidence 9 (cluster=c10;gene=FCGBP): No row of the pinned table has cluster=c10, gene=FCGBP. Closest gene values for cluster=c10: FABP2."], "seconds": 10.5}], "model": "claude-opus", "protocol": 2, "task_id": "ct-9ce2902282"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002275", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "ETV1", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "THSD7A", "stance": "supports"}, {"gene": "SERTM1", "stance": "supports"}, {"gene": "ID2", "stance": "supports"}, {"gene": "MEIS2", "stance": "supports"}, {"gene": "SLC6A4", "stance": "supports"}, {"gene": "PAX6", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "PEG10", "stance": "supports"}, {"gene": "GAD2", "stance": "supports"}, {"gene": "ABCC8", "stance": "supports"}], "rationale": "PPY (pancreatic polypeptide) is overwhelmingly the top marker (logFC 6.4, 100% of cells). The cluster also expresses genes known to be specific to human PP cells (ETV1, AQP3, THSD7A, SERTM1, ID2, MEIS2, SLC6A4) and general islet endocrine genes (PAX6, NEUROD1, SCG2, CHGB, PCSK2, PAM, PEG10, GAD2, ABCC8). INS, GCG and SST are absent, so this is a PP (gamma) cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.1}], "model": "claude-opus", "protocol": 2, "task_id": "ct-a26635e6cd"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "BCL2A1", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}], "rationale": "These are myeloid cells: TYROBP, FCER1G, LST1, AIF1, CTSS and SRGN are expressed in nearly all cells of the cluster. LYZ and S100A9 point to monocytes rather than tissue macrophages. IL1B, CXCL8, CXCL2, CCL3, PLAUR, BCL2A1 and G0S2 show an inflammatory activation state. Typical neutrophil markers (FCGR3B, CSF3R, CXCR2) are not among the top genes, and strong LST1, AIF1 and LYZ favour monocytes. Classical monocyte (CL:0000860) is plausible, but CD14 is not in the list, so the broader monocyte term is used."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.9}], "model": "claude-opus", "protocol": 2, "task_id": "ct-b2d44d2eda"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000938", "cell_type_label": "CD16-negative, CD56-bright natural killer cell, human", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "TRDC", "stance": "supports"}], "rationale": "The top markers are NK-cell genes: TYROBP, NKG7, IL2RB, GZMA, CST7, CCL3, CCL4 and CCL5. The cluster also has high GZMK, XCL1, XCL2 and KLRC1 (NKG2A). Several cytotoxic genes linked to the CD56dim subset (FCGR3A, GNLY, FGFBP2, GZMB) are missing from the top-20 list. This pattern matches CD56bright/CD16-negative NK cells, which are common among lung-resident NK cells. NK cells can express TRDC transcripts, so TRDC fits. A GZMK+ gamma-delta T-cell population is a less likely alternative."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.9}], "model": "claude-opus", "protocol": 2, "task_id": "ct-bb928b569a"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}], "rationale": "Complement C1Q genes, CD163, MS4A7, AIF1 and TYROBP/FCER1G mark macrophages. MARCO together with iron-recycling genes (SLC40A1, HMOX1, FTL) points to liver-resident non-inflammatory Kupffer cells in human liver tissue. No markers contradict this."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.0}], "model": "claude-opus", "protocol": 2, "task_id": "ct-c12bd3b011"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}], "rationale": "SLC12A3 (the thiazide-sensitive NCC cotransporter) is found in 97.5% of cells in this cluster and only 3.6% of other cells. That makes it the defining marker of distal convoluted tubule (DCT) cells. Several other genes fit the same call. TMEM52B, KNG1, WNK1 (which regulates NCC) and CA12 are all enriched in the DCT and connecting tubule. DEFB1 is a distal nephron marker. ATP1A1 and ATP1B1 (Na/K-ATPase) are highly expressed in the DCT. SPP1 is found in the distal tubule and loop of Henle. The mitochondrial genes and MALAT1 are not specific to any cell type. None of the markers point clearly to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-c7858eb46a"} +{"attempts": [{"codes": [], "evidence": 15, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "endothelial cell of lymphatic vessel", "decision": "annotate", "markers": [{"gene": "CCL21", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "ECSCR", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "PPFIBP1", "stance": "supports"}, {"gene": "SNCG", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "FABP4", "stance": "supports"}], "rationale": "Strong lymphatic endothelial signature: PROX1, LYVE1, CCL21, TFF3, MMRN1 are specific to lymphatic endothelium. Pan-endothelial genes (CLDN5, ECSCR, RAMP2, GNG11, CAVIN2, TFPI) are also expressed. No marker clearly points to another cell type, so this looks like dermal lymphatic endothelial cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}], "model": "claude-opus", "protocol": 2, "task_id": "ct-cc1cfcedd3"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "APOLD1", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}], "rationale": "RGS5 is highly specific (93% in vs 7.5% out) and is the classic pericyte/mural cell marker. C11orf96, IGFBP5, IGFBP7 and TIMP3 fit a mural/stromal profile. TM4SF1, IFI27 and APOLD1 reflect the small-vessel wall context. CCL2, SOCS3, JUNB, CEBPD, heat-shock genes and MT1A probably reflect a stress/inflammatory state from dissociation, not the cell's identity. Vascular smooth muscle and mesangial cells are close alternatives that these markers cannot separate."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.2}], "model": "claude-opus", "protocol": 2, "task_id": "ct-d9bc81cfff"} +{"attempts": [{"codes": ["BEV017"], "evidence": 16, "findings": [{"message": "The label 'BEST4+ intestinal epithelial cell, human' is not the name of CL:4030026 ('BEST4+ enterocyte'). Closest names: CL:0002563 (intestinal epithelial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:4030026", "cell_type_label": "BEST4+ intestinal epithelial cell, human", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1E", "stance": "supports"}, {"gene": "MT1H", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}, {"gene": "MT2A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}, {"gene": "CTSE", "stance": "supports"}, {"gene": "FXYD3", "stance": "supports"}], "rationale": "Highly specific BEST4, SPIB, CA7 and CPA2 expression, together with GUCA2A/GUCA2B, CFTR and strong metallothionein expression, is the classic profile of human BEST4+ intestinal epithelial cells. LYZ is commonly expressed by BEST4+ cells in the human small intestine, and no other Paneth cell genes (DEFA5, DEFA6) suggest a mixed cluster. The CL identifier was recalled from memory and not checked."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.1}, {"answer": {"cell_type_id": "CL:4030026", "cell_type_label": "BEST4+ enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}, {"gene": "MT1E", "stance": "supports"}, {"gene": "MT1H", "stance": "supports"}, {"gene": "MT1X", "stance": "supports"}, {"gene": "MT2A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}, {"gene": "CTSE", "stance": "supports"}, {"gene": "FXYD3", "stance": "supports"}], "rationale": "BEST4, SPIB, CA7 and CPA2 are expressed in this cluster and rarely elsewhere. Together with GUCA2A/GUCA2B, CFTR and strong metallothionein expression, this is the typical profile of human BEST4+ enterocytes. Human small-intestinal BEST4+ cells commonly express LYZ. No other Paneth cell genes (such as DEFA5 or DEFA6) are among the top markers, so nothing points to a mixed cluster. The label has been corrected to the ontology name of CL:4030026, 'BEST4+ enterocyte'."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'BEST4+ intestinal epithelial cell, human' is not the name of CL:4030026 ('BEST4+ enterocyte'). Closest names: CL:0002563 (intestinal epithelial cell)."], "seconds": 10.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-daa29fa7c3"} +{"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": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "The cluster has a strong cytotoxic lymphocyte program. GNLY, NKG7, GZMB, GZMA and CST7 are each expressed in about 80–96% of the cluster's cells and almost none outside it. KLRD1 (CD94) and HCST (DAP10) are also specific to the cluster. FGFBP2 is expressed in 62% of the cluster versus 0.3% elsewhere; together with high GZMB and GNLY, it fits CD56dim cytotoxic NK cells. No T-cell genes (CD3D/E, CD8A, TRAC) appear among the top markers, which favours NK cells over cytotoxic CD8 T cells. However, effector CD8 T cells can show a similar profile, so the call is NK cell with that caveat."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.6}], "model": "claude-opus", "protocol": 2, "task_id": "ct-def3067099"} +{"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": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "BTG1", "stance": "supports"}, {"gene": "TMSB4X", "stance": "supports"}], "rationale": "The cluster expresses immune genes that are nearly absent from the rest of the kidney dataset. PTPRC (CD45) and CD52 mark it as leukocytes. CD2 and IL7R point specifically to lymphocytes, and most likely T cells: CD2 is found in 59% of cells here versus 1% elsewhere, and IL7R in 57% versus 2%. CXCR4, BTG1 and SRGN fit quiescent, circulating T cells. The high ribosomal protein genes and MALAT1 are typical of resting lymphocytes. The list doesn't include CD3 genes or CD4/CD8, so I'm annotating at the general T cell level rather than naming a subset. IL7R suggests naive or memory T cells, though IL7R can also be expressed by ILCs (innate lymphoid cells). No markers point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.2}], "model": "claude-opus", "protocol": 2, "task_id": "ct-e0c7aa5d8b"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1001005", "cell_type_label": "glomerular capillary endothelial cell", "decision": "annotate", "markers": [{"gene": "EMCN", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "SOST", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "PLPP3", "stance": "supports"}, {"gene": "TGFBR2", "stance": "supports"}, {"gene": "IFI27", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "NHERF2", "stance": "supports"}, {"gene": "PLPP1", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}], "rationale": "EMCN, RAMP2, GNG11, PLPP3, PLPP1, TGFBR2, IFI27 and MGP form a general capillary endothelial signature. PLAT, CRHBP, SOST (86% in vs 3% out) and IGFBP5 are known markers of glomerular endothelium in human kidney atlases. CD74 and the HLA class I/II genes fit renal endothelium, which expresses MHC class II. No markers point to a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.7}], "model": "claude-opus", "protocol": 2, "task_id": "ct-e6fd6bbd15"} +{"attempts": [{"codes": [], "evidence": 14, "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": "IL32", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "PTPRCAP", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "ARHGDIB", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "DUSP2", "stance": "supports"}, {"gene": "STK17B", "stance": "supports"}, {"gene": "SAMSN1", "stance": "supports"}], "rationale": "CD3D (specific, pct_out 0.048) together with IL32, LTB, CD52, PTPRC/PTPRCAP and HCST define T lymphocytes. CD69, CXCR4, DUSP2 and CREM indicate activated or tissue-resident T cells in skin. Without CD4/CD8/FOXP3/TRDC markers, the general T cell term is used."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.2}], "model": "claude-opus", "protocol": 2, "task_id": "ct-e76b10ee43"} +{"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": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD5", "stance": "supports"}, {"gene": "SIRPG", "stance": "supports"}, {"gene": "PIM2", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "DGKA", "stance": "supports"}], "rationale": "These are T cells: CD3E, TRAC, CD2 and CD5 are expressed. FOXP3 (59% of cells in the cluster vs 0.5% outside) and CTLA4 (61% vs 1%) are highly specific to this cluster. TNFRSF1B (TNFR2), PIM2, IL32 and LTB fit the regulatory T cell (Treg) profile. SELL, LEF1, CD27 and ID3 suggest that many of these Tregs are in a resting or central state. No markers clearly point to another cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 9.4}], "model": "claude-opus", "protocol": 2, "task_id": "ct-f3161764a6"} +{"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": "TCF7", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}], "rationale": "Strong naive/resting T cell signature (CCR7, SELL, LEF1, TCF7, LRRN3, CAMK4, IL7R, CD27, LTB) on CD3E+ cells; CD40LG specificity indicates the CD4 lineage. No markers clearly indicate contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.8}], "model": "claude-opus", "protocol": 2, "task_id": "ct-f5c625b34c"} +{"attempts": [{"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "TCF21", "stance": "supports"}, {"gene": "ADAMDEC1", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "CFD", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "RARRES2", "stance": "supports"}, {"gene": "MFAP4", "stance": "supports"}, {"gene": "C1S", "stance": "supports"}, {"gene": "ADH1B", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "APOE", "stance": "supports"}], "rationale": "This cluster expresses the core fibroblast markers DCN, LUM, COL1A2, COL3A1, TCF21 and MFAP4, plus VIM and CALD1. Mesenchymal genes such as CFD, C1S, GPX3, RARRES2 and ADH1B are also present. ADAMDEC1, CXCL14 and CXCL6 are typical of intestinal lamina propria fibroblasts (the ADAMDEC1+ crypt/villus stromal fibroblasts). No markers for epithelial, immune, endothelial, smooth muscle or pericyte cells are among the top genes, so this looks like a single, clean fibroblast population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.5}], "model": "claude-opus", "protocol": 2, "task_id": "ct-f7c13b08bb"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}], "rationale": "The top differentially expressed marker genes include classic natural killer (NK) cell receptors and signaling molecules (KLRD1, KLRC1, FCGR3A/CD16, TYROBP, FCER1G), cytotoxic effector molecules (GNLY, PRF1, GZMA, GZMB, NKG7, CST7, CTSW), and characteristic chemokines (XCL1, XCL2, CCL3, CCL4, CCL5). The absence of CD3 complex genes together with high expression of GNLY, KLRD1, and FCGR3A strongly supports the annotation of this cluster as natural killer cells (CL:0000623)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.3}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-0bcb90ea26"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CXCL2", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}], "rationale": "The expression profile of this cluster is characteristic of macrophages. It features classic myeloid and macrophage lineage markers such as TYROBP and AIF1 (IBA1), strong expression of MHC class II antigen presentation molecules (HLA-DRA, HLA-DRB1, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, and CD74), as well as macrophage-associated inflammatory cytokines and chemokines (IL1B, CXCL8, CCL3, CXCL2) and activation markers (PLAUR, SRGN). None of the marker genes contradict a macrophage identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.5}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-0c19dd5456"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "epithelial cell of proximal tubule", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "PDZK1IP1", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}, {"gene": "RBP5", "stance": "supports"}, {"gene": "MT1G", "stance": "supports"}], "rationale": "This cluster strongly expresses canonical marker genes of kidney proximal tubule epithelial cells, including ALDOB, GPX3, PDZK1IP1 (MAP17), GATM, GSTA1, MIOX, FABP1, HPD, ASS1, and UGT2B7, as well as multiple metallothionein family members (MT1G, MT1H, MT1X, MT1F). There is no expression of conflicting markers from other kidney cell lineages (such as loop of Henle, distal tubule, collecting duct, podocytes, or immune cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.4}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-0f7cfea7f3"} +{"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": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "SLC4A10", "stance": "contradicts"}], "rationale": "The cluster strongly expresses CD3E, establishing it as a T cell population, along with cytotoxic and innate-like T cell markers such as GZMK, KLRB1 (CD161), IL23R, and CD69. Most definitively, TRDV2 (T-cell receptor delta variable 2) is highly and specifically enriched in this cluster (logfc 1.140, pct_in 0.439 vs pct_out 0.040), identifying these as gamma-delta T cells (specifically Vgamma9Vdelta2 T cells, CL:0000798). SLC4A10 is a canonical marker for MAIT cells (mucosal-associated invariant T cells) and likely reflects a minor co-clustering or mixed representation of MAIT cells due to shared innate-like T cell transcriptional profiles."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.3}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-1161617d72"} +{"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": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "PTPRCAP", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster shows robust, highly specific expression of canonical T cell receptor complex components and signaling machinery, including CD3E, CD247 (CD3 zeta chain), and LCK, along with pan-T/lymphocyte surface markers CD7 and CD52. The co-expression of cytotoxic and activation-associated markers such as KLRB1 (CD161), GZMA, NKG7, and HCST further indicates effector/tissue-resident T cells commonly found in the mucosal lamina propria and epithelium of the human duodenum. There are no contradictory markers of other lineages such as B cells, myeloid cells, or epithelial cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.4}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-13d48ee1d6"} +{"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": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "The cluster displays specific expression of canonical B cell markers, notably CD79A (a defining component of the B cell antigen receptor complex) and IGKC (immunoglobulin kappa constant), along with high expression of MHC class II molecules (CD74, HLA-DRA) and lymphocyte markers such as CD52, CXCR4, and LTB. These markers collectively support the annotation of this cluster as B cells (CL:0000236)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-18ce9fb955"} +{"attempts": [{"codes": [], "evidence": 19, "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": "MS4A6A", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}], "rationale": "The marker gene profile is characteristic of tissue-resident macrophages in the human intestine. In particular, the complement component genes C1QA, C1QB, and C1QC are canonical markers distinguishing macrophages from other myeloid lineages (such as monocytes or dendritic cells). This is complemented by strong expression of core macrophage/myeloid lineage markers including AIF1 (Iba1), MS4A6A, TYROBP, FCER1G, and LYZ, as well as high levels of MHC Class II antigen presentation molecules (CD74, HLA-DRA, HLA-DPB1, HLA-DPA1, HLA-DQA1, HLA-DRB1, HLA-DQB1, and HLA-DMA). There are no contradictory lineage markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.0}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-1fcb853772"} +{"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:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}], "rationale": "This cluster expresses classic cytotoxicity and natural killer (NK) cell marker genes, including GNLY (granulysin), NKG7, GZMB (granzyme B), FGFBP2, and KLRD1 (CD94), as well as chemokines CCL5 and CCL4, which collectively strongly identify this population as natural killer cells (CL:0000623). The presence of IGKC (immunoglobulin kappa constant), a B cell/plasma cell marker, contradicts this phenotype and likely represents ambient transcript contamination or doublet contribution."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.6}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-20d7fe4cf5"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "MYOM2", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical natural killer (NK) cell markers, including cytolytic effector molecules (GNLY, PRF1, GZMB, GZMH, GZMA), NK cell-associated surface receptors and signaling adapters (FCGR3A/CD16, TYROBP/DAP12, FCER1G), transcription factors (TBX21/T-bet), and characteristic NK transcripts (NKG7, SPON2, FGFBP2, CLIC3, CST7, CX3CR1, MYOM2) in the absence of lineage-defining T-cell receptor components (CD3D, CD3E, CD3G). Together, these features decisively identify this cluster as natural killer cells (CL:0000623)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-2e16bde736"} +{"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": "CD37", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster exhibits classic markers of B cells (CL:0000236), including the lineage markers CD79A, CD79B, and MS4A1 (CD20), the tetraspanin CD37, immunoglobulin light chains (IGKC, IGLC2), as well as prominent expression of MHC class II molecules and invariant chain (CD74, HLA-DRA, HLA-DPB1, HLA-DQB1, HLA-DPA1, HLA-DRB1). There are no contradictory marker genes present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.5}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-33d5498243"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000071", "cell_type_label": "blood vessel endothelial cell", "decision": "annotate", "markers": [{"gene": "CLDN5", "stance": "supports"}, {"gene": "ACKR1", "stance": "supports"}, {"gene": "SELE", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical blood vessel endothelial cell markers including CLDN5 (tight junction protein in vascular endothelium), RAMP2, GNG11, AQP1, and TM4SF1. Furthermore, specific markers such as ACKR1 (DARC) and SELE (E-selectin) distinguish blood vascular endothelial cells (specifically venular endothelial cells) from lymphatic endothelial cells. No markers contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.7}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-3875326824"} +{"attempts": [{"codes": [], "evidence": 7, "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": "RORC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}], "rationale": "The marker profile is characteristic of group 3 innate lymphoid cells (ILC3s). Key canonical markers include RORC (the lineage-defining transcription factor for ILC3s), IL7R (CD127, characteristic of helper-like ILCs), KIT (CD117, key surface marker distinguishing ILC3s), CCR6, IL23R, LTB (lymphotoxin beta), and IL4I1."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 15.2}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-3ec5acbb2d"} +{"attempts": [{"codes": ["BEV017"], "evidence": 15, "findings": [{"message": "The label 'cholangiocyte' is not the name of CL:0000107 ('autonomic neuron'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte).", "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:0000107", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "ANXA4", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "CLU", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}], "rationale": "This cluster originates from the human liver and expresses hallmark markers of cholangiocytes (intrahepatic bile duct epithelial cells). Specifically, KRT7 (cytokeratin 7) is the classic diagnostic marker distinguishing cholangiocytes from hepatocytes in human liver. The cluster also strongly expresses key biliary epithelial markers including FXYD2, SPP1 (osteopontin), CD24, ANXA4, DEFB1, TM4SF4, S100A6, and the biliary transcription factor ELF3, alongside the simple epithelial keratins KRT8 and KRT18."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.1}, {"answer": {"cell_type_id": "CL:1000488", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "ANXA4", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "CLU", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "ANXA2", "stance": "supports"}], "rationale": "This cluster from human liver caudate lobe displays a canonical biliary epithelial / cholangiocyte expression profile. It strongly expresses KRT7, the definitive diagnostic marker separating cholangiocytes from hepatocytes in human liver, together with key cholangiocyte markers such as FXYD2, SPP1, CD24, ANXA4, DEFB1, TM4SF4, S100A6, and the biliary transcription factor ELF3, along with epithelial keratins KRT8 and KRT18. The appropriate Cell Ontology identifier for cholangiocyte is CL:1000488."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cholangiocyte' is not the name of CL:0000107 ('autonomic neuron'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte)."], "seconds": 11.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-4163a3b864"} +{"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": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "ISG20", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "CYBA", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "SSR3", "stance": "supports"}], "rationale": "The top upregulated genes are quintessential markers of plasma cells, characterized by extremely high expression of immunoglobulin chains (IGKC, IGLC2, IGLC3, IGHM, IGHG1, IGHG2, IGHG3, IGHG4, IGHA1, and JCHAIN) along with key plasma cell-associated regulators and endoplasmic reticulum/unfolded protein response components essential for high-rate antibody synthesis and secretion (MZB1, FKBP11, XBP1, DERL3, SEC11C, HSP90B1, SSR4, SSR3)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.4}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-41fb1f6e39"} +{"attempts": [{"codes": ["BEV004", "BEV017"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0002198 ('oncocyte').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV004", "BEV017"], "evidence": 14, "findings": [{"message": "Contradicting evidence remains unresolved.", "rule_id": "BEV004", "where": "statement.evidence lines[1]"}, {"message": "The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0002139 ('endothelial cell of vascular tree').", "rule_id": "BEV017", "where": "object label"}], "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:0002198", "cell_type_label": "hepatic sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "PRSS23", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "TAGLN", "stance": "contradicts"}], "rationale": "The cluster displays strong, specific expression of classic liver sinusoidal endothelial cell (LSEC) markers, particularly DNASE1L3, FCN3, RAMP3, INMT, and LIFR, alongside general endothelial cell markers such as ENG (CD105), PTPRB, IGFBP7, and RNASE1. TAGLN is typically a marker for vascular smooth muscle cells/hepatic stellate cells, which contradicts the endothelial identity and may reflect slight ambient RNA or doublet contribution."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.0}, {"answer": {"cell_type_id": "CL:0002139", "cell_type_label": "hepatic sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "PRSS23", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "TAGLN", "stance": "contradicts"}], "rationale": "The cluster displays strong and specific expression of classic liver sinusoidal endothelial cell (LSEC) marker genes, including DNASE1L3, FCN3, RAMP3, INMT, and LIFR, alongside general endothelial cell markers such as ENG (CD105), PTPRB, IGFBP7, and RNASE1. TAGLN is typically expressed in vascular smooth muscle cells and hepatic stellate cells, contradicting pure sinusoidal endothelial identity and likely indicating minor doublet or ambient RNA contamination. The correct Cell Ontology accession for hepatic sinusoidal endothelial cell is CL:0002139."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0002198 ('oncocyte')."], "seconds": 24.1}, {"answer": {"cell_type_id": "CL:0002139", "cell_type_label": "endothelial cell of vascular tree", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "PRSS23", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "TAGLN", "stance": "contradicts"}], "rationale": "The cluster shows specific expression of classic liver endothelial / liver sinusoidal endothelial cell (LSEC) marker genes including DNASE1L3, FCN3, RAMP3, INMT, and LIFR, along with general endothelial markers such as ENG, PTPRB, RNASE1, and IGFBP7. TAGLN is characteristic of vascular smooth muscle cells and hepatic stellate cells, contradicting pure endothelial identity and likely reflecting minor doublet or ambient RNA contamination. In the Cell Ontology, CL:0002139 has the official term label 'endothelial cell of vascular tree'."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'hepatic sinusoidal endothelial cell' is not the name of CL:0002139 ('endothelial cell of vascular tree')."], "seconds": 35.8}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-4d4de5c13f"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT1", "stance": "supports"}, {"gene": "DMKN", "stance": "supports"}, {"gene": "KRT10", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "KRTDAP", "stance": "supports"}, {"gene": "LY6D", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "LYPD3", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "DSP", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "SERPINB5", "stance": "supports"}, {"gene": "KRT14", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "RNF144B", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "CLDN1", "stance": "supports"}, {"gene": "FXYD3", "stance": "supports"}], "rationale": "The top marker genes are canonical markers of epidermal keratinocytes (specifically differentiating/suprabasal keratinocytes of the skin), including KRT1, KRT10, DMKN (dermokine), KRTDAP (keratinocyte differentiation-associated protein), SFN (stratifin), LGALS7B (galectin-7), PERP, DSP, and AQP3, alongside CCL27 (a skin-keratinocyte-specific chemokine). In the Cell Ontology, these cells map to 'keratinocyte' (CL:0000312)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.2}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-506f19166c"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000173", "cell_type_label": "pancreatic D cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "LEPR", "stance": "supports"}, {"gene": "BCHE", "stance": "supports"}, {"gene": "PRG4", "stance": "supports"}, {"gene": "CASR", "stance": "supports"}, {"gene": "ISL1", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}], "rationale": "The cluster shows high and specific expression of SST (somatostatin), the canonical hormone produced by pancreatic delta cells (pancreatic D cells). Furthermore, HHEX is the defining transcription factor for mature pancreatic delta cells, and RBP4, LEPR, BCHE, CASR, and PRG4 are well-established specific markers for human pancreatic delta cells in single-cell transcriptomic datasets. General islet endocrine markers PCSK1 and ISL1 are also present. No conflicting markers of other pancreatic endocrine or exocrine lineages (such as INS, GCG, or PPY) are present among the top markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 13.1}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-50ec79996f"} +{"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": "IL32", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "TRDV2", "stance": "contradicts"}, {"gene": "AIF1", "stance": "contradicts"}, {"gene": "CNN2", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "ZNF683", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "COTL1", "stance": "supports"}, {"gene": "SIRPG", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical T cell markers (CD3E, CD3D) and the CD8 lineage marker CD8A, together with effector/memory and activation-associated markers such as GZMK, CD27, CXCR3, ZNF683 (Hobit), TCF7, and IL32, identifying it as a CD8-positive, alpha-beta T cell population (CL:0000625). TRDV2 (a gamma-delta TCR chain variable region) and AIF1 (a myeloid/macrophage marker) contradict this primary cell type identity and likely indicate minor contamination, doublets, or mixed sub-populations within the cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 54.8}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-52a80b5c6b"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'kidney collecting duct principal cell' is not the name of CL:0002201 ('renal beta-intercalated cell'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal 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:0002201", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}], "rationale": "The cluster specifically and strongly expresses classic canonical markers of renal collecting duct principal cells, including AQP2 (water channel aquaporin-2, highly specific to collecting duct principal cells), AQP3 (aquaporin-3 basolateral water channel), and FXYD4 (corticosteroid hormone-induced factor, CHIF), alongside distal tubule/collecting duct epithelial markers such as CDH16, TACSTD2, and WFDC2."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.3}, {"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}], "rationale": "The cluster specifically and strongly expresses classic canonical markers of renal collecting duct principal cells, including AQP2 (water channel aquaporin-2, highly specific to collecting duct principal cells), AQP3 (aquaporin-3 basolateral water channel), and FXYD4 (corticosteroid hormone-induced factor), alongside distal tubule/collecting duct epithelial markers such as CDH16, TACSTD2, and WFDC2."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct principal cell' is not the name of CL:0002201 ('renal beta-intercalated cell'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal cell)."], "seconds": 9.4}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-54741cc370"} +{"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": "IGLL5", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "HERPUD1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "TNFRSF17", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "SPCS2", "stance": "supports"}, {"gene": "DNAJB9", "stance": "supports"}, {"gene": "ITM2C", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical plasma cell markers including JCHAIN, MZB1, IGLL5, TNFRSF17 (BCMA), XBP1, and CD79A, along with extensive endoplasmic reticulum and protein secretion machinery genes (DERL3, FKBP11, SSR4, SEC11C, HERPUD1, DNAJB9) characteristic of antibody-secreting plasma cells in the human intestinal lamina propria."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.8}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-560d5829d2"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002187", "cell_type_label": "basal cell of epidermis", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}], "rationale": "The cluster exhibits strong, specific expression of canonical basal epidermal keratinocyte markers, including keratin 14 (KRT14), keratin 5 (KRT5), and keratin 15 (KRT15). Additionally, it expresses dystonin (DST, a key hemidesmosomal component anchoring basal cells to the basement membrane), MIR205HG (host gene for miR-205, enriched in basal progenitor keratinocytes), aquaporin 3 (AQP3), S100A2, SFN (stratifin), and CCL27. Together, this marker profile uniquely matches the basal cell of epidermis (CL:0002187)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 14.6}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-5633d2ce11"} +{"attempts": [{"codes": ["BEV017"], "evidence": 14, "findings": [{"message": "The label 'kidney collecting duct type B intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). Closest names: CL:1001432 (kidney collecting duct intercalated cell); CL:4030005 (kidney collecting duct beta-intercalated cell); CL:4030015 (kidney collecting duct alpha-intercalated cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0005010", "cell_type_label": "kidney collecting duct type B intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "LGALS3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}], "rationale": "The cluster displays hallmark markers of intercalated cells of the kidney collecting duct, specifically type B intercalated cells (IC-B). Multiple subunits of the vacuolar H+-ATPase (ATP6V1B1, ATP6V0D2, ATP6V1G3, ATP6V0B, ATP6AP2) identify these as intercalated cells. Crucially, SLC26A4 (Pendrin), the apical Cl-/HCO3- exchanger, is the canonical defining marker for type B intercalated cells (nearly absent outside this cluster with pct_out = 0.008). In addition, CA12, TMEM213, TSPAN8, HEPACAM2, and WFDC2 are well-established human kidney markers that specifically characterize the type B intercalated cell lineage over type A intercalated cells or principal cells. General collecting duct markers like KRT7, KRT8, and LGALS3 are also robustly expressed. No conflicting cell type markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.7}, {"answer": {"cell_type_id": "CL:4030005", "cell_type_label": "kidney collecting duct beta-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "TSPAN8", "stance": "supports"}, {"gene": "HEPACAM2", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "LGALS3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}], "rationale": "The cluster exhibits hallmark expression profiles of type B (beta) intercalated cells of the kidney collecting duct. Multiple subunits of the vacuolar H+-ATPase (ATP6V1B1, ATP6V0D2, ATP6V1G3, ATP6V0B, ATP6AP2) identify intercalated cells. Crucially, SLC26A4 (pendrin), the apical Cl-/HCO3- exchanger, is the definitive canonical marker distinguishing beta-intercalated cells from alpha-intercalated cells (nearly exclusively expressed in this cluster with pct_out = 0.008). Additionally, CA12, TMEM213, TSPAN8, HEPACAM2, and WFDC2 are well-established human markers characterizing kidney collecting duct beta-intercalated cells. Collecting duct markers KRT7, KRT8, and LGALS3 are also strongly expressed. No conflicting cell type markers are observed."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct type B intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). Closest names: CL:1001432 (kidney collecting duct intercalated cell); CL:4030005 (kidney collecting duct beta-intercalated cell); CL:4030015 (kidney collecting duct alpha-intercalated cell)."], "seconds": 10.7}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-6807a1005a"} +{"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": "S100A9", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}], "rationale": "This cluster corresponds to the inflammatory intrahepatic macrophage population from the human liver dataset (MacParland et al., 2018). It expresses key pan-macrophage and myeloid markers (AIF1, TYROBP, LYZ, CTSS, FCER1G, C1QA, CST3), antigen presentation molecules (HLA-DRA, CD74), and high levels of S100-family alarmins/pro-inflammatory genes characteristic of monocyte-derived/inflammatory macrophages in the liver (S100A8, S100A9, S100A4, S100A6)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.3}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-6846a2fbd5"} +{"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": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster displays high and specific expression of canonical T cell receptor and lineage coreceptors CD3E, CD8A, and CD8B, establishing it as a CD8+ alpha-beta T cell population. Furthermore, it strongly expresses key hallmarks of naive T cells, including lymph-node homing receptors (CCR7, SELL/CD62L), naive-associated transcription factors (LEF1, TCF7), and naive-state markers (LRRN3, NOSIP, IL7R, CD27). Together, these markers unambiguously identify the cluster as naive thymus-derived CD8-positive, alpha-beta T cells (CL:0000900)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 16.7}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-6b9f55ce2e"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "AHSP", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "ALAS2", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "BLVRB", "stance": "supports"}, {"gene": "SNCA", "stance": "supports"}, {"gene": "GYPA", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}, {"gene": "BNIP3L", "stance": "supports"}, {"gene": "BSG", "stance": "supports"}, {"gene": "YBX3", "stance": "supports"}, {"gene": "GLRX5", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "HMBS", "stance": "supports"}], "rationale": "The cluster demonstrates robust and specific expression of canonical hemoglobin genes (HBB, HBA1, HBA2, HBD, HBM), erythrocyte membrane proteins (GYPA, GYPC, SLC4A1/Band 3, BSG), and key erythroid-specific enzymes/regulators involved in heme biosynthesis and stabilization (AHSP, ALAS2, CA1, SLC25A37, BLVRB, HMBS, BNIP3L). These markers unambiguously identify the cluster as erythrocytes (CL:0000232)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-73d8984fbc"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002410", "cell_type_label": "pancreatic stellate cell", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "COL6A1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "COL4A2", "stance": "supports"}, {"gene": "COL5A1", "stance": "supports"}, {"gene": "COL15A1", "stance": "supports"}, {"gene": "COL5A2", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "MICAL2", "stance": "supports"}, {"gene": "PXDN", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "SERPINE1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CYGB", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}], "rationale": "This cluster expresses classic extracellular matrix and mesenchymal markers characteristic of pancreatic stromal/stellate cells, including numerous collagen genes (COL1A1, COL1A2, COL3A1, COL6A1, COL6A3, COL4A2, COL5A1, COL5A2, COL15A1), fibronectin (FN1), SPARC, and vimentin (VIM). Notably, it expresses cytoglobin (CYGB), a specific marker distinguishing pancreatic stellate cells from other cell types, along with myofibroblastic/remodeling markers such as CALD1, TIMP1, SERPINE1, PXDN, and SFRP2."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.5}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-75516baf75"} +{"attempts": [{"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'kidney loop of Henle thick ascending limb epithelial cell' is not the name of CL:0002343 ('decidual natural killer cell, human'). 'kidney loop of Henle thick ascending limb epithelial cell' is the name of CL:1001106 (kidney loop of Henle thick ascending limb epithelial 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:0002343", "cell_type_label": "kidney loop of Henle thick ascending limb epithelial cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster is characterized by high, specific expression of canonical thick ascending limb (TAL) markers, most notably SLC12A1 (NKCC2, the apical Na-K-2Cl cotransporter) and UMOD (uromodulin / Tamm-Horsfall protein). Additionally, high expression of Na+/K+ ATPase subunits (ATP1A1, ATP1B1) alongside high levels of mitochondrial transcripts reflects the high metabolic demand and active ion transport characteristic of TAL epithelial cells. Secondary markers like DEFB1, KNG1, and CA12 further support distal nephron / loop of Henle epithelial identity, with no markers indicating a contaminating or alternate cell lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.6}, {"answer": {"cell_type_id": "CL:1001106", "cell_type_label": "kidney loop of Henle thick ascending limb epithelial cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster shows robust and specific expression of canonical thick ascending limb (TAL) markers, notably SLC12A1 (encoding NKCC2) and UMOD (uromodulin). Supporting markers including Na+/K+ ATPase subunits (ATP1A1, ATP1B1) alongside KNG1, DEFB1, and CA12 confirm the identity of kidney loop of Henle thick ascending limb epithelial cell (CL:1001106)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney loop of Henle thick ascending limb epithelial cell' is not the name of CL:0002343 ('decidual natural killer cell, human'). 'kidney loop of Henle thick ascending limb epithelial cell' is the name of CL:1001106 (kidney loop of Henle thick ascending limb epithelial cell)."], "seconds": 10.4}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-7954bd765f"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "SNCA", "stance": "supports"}], "rationale": "The cluster exhibits high and specific expression of adult hemoglobin subunits (HBB, HBA2, HBA1, HBD) and other hemoglobin genes (HBM), the erythrocyte membrane structural glycoprotein GYPC (glycophorin C), and mitochondrial transporters essential for heme biosynthesis in erythroid cells (SLC25A37 / mitoferrin-1 and SLC25A39). These markers definitively identify the cluster as erythrocytes (CL:0000232)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-838e09fefd"} +{"attempts": [{"codes": [], "evidence": 13, "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": "MYL9", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "ADIRF", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "BGN", "stance": "supports"}, {"gene": "SOD3", "stance": "supports"}, {"gene": "FLNA", "stance": "supports"}], "rationale": "The marker expression profile is characteristic of vascular smooth muscle cells (vascular associated smooth muscle cells). The cluster shows high and specific expression of canonical smooth muscle contractile apparatus genes, including ACTA2 (alpha-smooth muscle actin), TAGLN (transgelin/SM22-alpha), MYH11 (myosin heavy chain 11, a highly specific marker distinguishing mature smooth muscle cells from other mural cells such as pericytes), MYL9, TPM2, and CALD1, along with the mural cell regulator RGS5 and extracellular matrix/structural components like MGP, SPARCL1, and BGN."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 17.2}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-884f62d6f1"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'kidney collecting duct alpha-intercalated cell' is not the name of CL:0005011 ('renal alpha-intercalated cell'). 'kidney collecting duct alpha-intercalated cell' is the name of CL:4030015 (kidney collecting duct alpha-intercalated 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:0005011", "cell_type_label": "kidney collecting duct alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "TMEM213", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster exhibits characteristic and specific marker expression for kidney collecting duct alpha-intercalated cells (type A intercalated cells). Most notably, it strongly expresses SLC4A1 (anion exchanger 1 / AE1) and SLC26A7, which are canonical basolateral chloride/bicarbonate exchangers specific to alpha-intercalated cells. Additionally, TMEM213 and SPINK1 are well-established specific markers for this cell type in human kidney. The cluster also expresses multiple subunits of the vacuolar H+-ATPase (ATP6V0D2, ATP6V1G3, ATP6V1B1, ATP6V0B, ATP6AP2) responsible for apical proton secretion, RHCG (ammonia transporter), and carbonic anhydrase XII (CA12), alongside high mitochondrial gene expression (MT-CO1, MT-ND1, MT-CO3) characteristic of mitochondrion-rich intercalated cells. There is no significant expression of type B intercalated cell markers (e.g., SLC26A4/pendrin) or principal cell markers (e.g., AQP2), confirming an unambiguous annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.5}, {"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "TMEM213", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "SPINK1", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster exhibits canonical marker gene expression defining renal alpha-intercalated cells (type A intercalated cells). Key diagnostic markers include SLC4A1 (AE1) and SLC26A7, which are basolateral anion exchangers specific to alpha-intercalated cells in the kidney collecting system. TMEM213 and SPINK1 are also highly enriched, specific markers for this cell population in human kidney. In addition, the cluster strongly expresses proton-secreting vacuolar H+-ATPase subunits (ATP6V0D2, ATP6V1G3, ATP6V1B1, ATP6V0B, ATP6AP2), the ammonia transporter RHCG, and carbonic anhydrase XII (CA12). High expression of mitochondrial genes (MT-CO1, MT-ND1, MT-CO3) is also consistent with the mitochondrion-rich nature of intercalated cells. Lack of beta-intercalated markers (e.g., SLC26A4) or principal cell markers (e.g., AQP2) confirms the identity as renal alpha-intercalated cell (CL:0005011)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct alpha-intercalated cell' is not the name of CL:0005011 ('renal alpha-intercalated cell'). 'kidney collecting duct alpha-intercalated cell' is the name of CL:4030015 (kidney collecting duct alpha-intercalated cell)."], "seconds": 19.4}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-90023ca6ff"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000160", "cell_type_label": "goblet cell", "decision": "annotate", "markers": [{"gene": "TFF3", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}, {"gene": "MUC2", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}], "rationale": "The cluster is characterized by high, specific expression of canonical intestinal goblet cell markers, including mucin 2 (MUC2), trefoil factor 3 (TFF3), SPINK4, CLCA1, ZG16, ITLN1, and REG4. These genes are specialized for mucus synthesis, packaging, and secretion in the intestinal epithelium."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 10.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-9ce2902282"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002275", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "PAX6", "stance": "supports"}, {"gene": "ETV1", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}], "rationale": "The cluster is definitively identified as pancreatic PP cells (also known as gamma or F cells). PPY (pancreatic polypeptide) is the defining hormone marker of this lineage and is by far the top marker by log fold change (logfc 6.381) with 100% expression in the cluster. Other top markers including SCG2, CHGB, PCSK2, NEUROD1, and PAX6 reflect the neuroendocrine and islet endocrine identity, and ETV1 is a known transcription factor associated with PP cells. No contradictory markers from other islet lineages (such as INS, GCG, or SST) are present in the top marker list."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.6}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-a26635e6cd"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "G0S2", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "BCL2A1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "PLAUR", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "CXCL2", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}], "rationale": "The marker profile is characteristic of monocytes (CL:0000576). High expression and cluster-specific enrichment of classic myeloid/monocyte markers including LYZ, S100A9, LST1, TYROBP, FCER1G, CTSS, and AIF1, together with inflammatory cytokines and activation markers typically induced in circulating monocytes during tissue dissociation (IL1B, CXCL8, CXCL2, CCL3, G0S2, PLAUR, and BCL2A1), identify this cluster as monocytes captured from the kidney vasculature. All top marker genes are consistent with a monocyte identity, with no contradicting lineage markers present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.3}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-b2d44d2eda"} +{"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:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "NKG7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "TRDC", "stance": "contradicts"}], "rationale": "The cluster demonstrates high expression of natural killer (NK) cell identity and activation markers including TYROBP (DAP12), NKG7, IL2RB (CD122), KLRC1 (NKG2A), and KLRB1 (CD161), along with cytotoxic molecules (GZMA, GZMK, CST7, SRGN) and hallmark NK cell chemokines/cytokines (XCL1, XCL2, CCL3, CCL4, CCL5). The lack of CD3 subunits (CD3D, CD3E, CD3G) rules out classical T cells. The presence of TRDC (T cell receptor delta constant) points to gamma-delta T cells, likely reflecting either sterile TCR transcripts or a minor subset/doublet contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.1}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-bb928b569a"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "SAT1", "stance": "supports"}, {"gene": "GPX1", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "This cluster from human liver strongly expresses hallmark markers of Kupffer cells (liver-resident tissue macrophages). Key distinguishing markers include MARCO and CD163, which identify sinusoidal Kupffer cells, as well as genes central to erythrophagocytosis and iron recycling in the liver, such as SLC40A1 (ferroportin), HMOX1 (heme oxygenase-1), and FTL. In addition, the cluster exhibits high expression of complement components (C1QA, C1QB, C1QC), antigen-presentation machinery (HLA-DRA, CD74), and myeloid/macrophage-lineage markers (AIF1, MS4A6A, MS4A7, TYROBP, FCER1G, CTSB, CTSS)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.0}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-c12bd3b011"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'kidney distal convoluted tubule epithelial cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). 'kidney distal convoluted tubule epithelial cell' is the name of CL:1000849 (kidney distal convoluted tubule epithelial 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:0002306", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}], "rationale": "The cluster expresses SLC12A3 (NCC), which is the canonical and specific marker for kidney distal convoluted tubule (DCT) epithelial cells, responsible for thiazide-sensitive sodium and chloride reabsorption. Other top marker genes strongly supporting DCT identity include WNK1 (a kinase specifically regulating SLC12A3 trafficking/activity in DCT), KNG1, TMEM52B, DEFB1, CA12, as well as high levels of Na+/K+-ATPase subunits (ATP1A1, ATP1B1) and mitochondrial genes characteristic of metabolically active distal tubular transport epithelium. There are no contradicting marker genes pointing to other renal lineages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.9}, {"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}], "rationale": "The cluster specifically expresses SLC12A3 (NCC), the canonical marker for distal convoluted tubule (DCT) epithelial cells. Co-expression of WNK1 (which regulates SLC12A3), KNG1, TMEM52B, CA12, and DEFB1 along with high levels of Na+/K+-ATPase subunits (ATP1A1, ATP1B1) and mitochondrial respiration genes further confirms its identity as kidney distal convoluted tubule epithelial cells (CL:1000849)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney distal convoluted tubule epithelial cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). 'kidney distal convoluted tubule epithelial cell' is the name of CL:1000849 (kidney distal convoluted tubule epithelial cell)."], "seconds": 13.3}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-c7858eb46a"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "lymphatic endothelial cell", "decision": "annotate", "markers": [{"gene": "CCL21", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "ECSCR", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}], "rationale": "This cluster specifically and strongly expresses classic canonical markers of lymphatic endothelial cells, including the master transcription factor PROX1, lymphatic-specific surface and structural markers LYVE1, MMRN1, CCL21, and TFF3, alongside pan-endothelial markers such as CLDN5, ECSCR, and TFPI. There are no contradicting markers detected."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-cc1cfcedd3"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "CCL2", "stance": "supports"}], "rationale": "This cluster strongly expresses canonical markers of kidney pericytes / perivascular mural cells, most notably RGS5, which is highly specific (pct_in 0.927 vs pct_out 0.075) and widely recognized as a definitive pericyte marker. Supporting mural and extracellular matrix/secreted factors such as IGFBP5, TIMP3, IGFBP7, and C11orf96 further confirm the pericyte identity without significant expression of contradictory epithelial or immune lineage markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.7}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-d9bc81cfff"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'best4-positive, otop2-positive enterocyte' is not the name of CL:0009020 ('tuft cell of appendix').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'best4-positive, otop2-positive enterocyte' is not the name of CL:0009019 ('nephrogenic zone cell').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'enterocyte of epithelium of small intestine' is not the name of CL:0002071 ('enterocyte of epithelium of large intestine'). 'enterocyte of epithelium of small intestine' is the name of CL:1000334 (enterocyte of epithelium of small intestine).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0009020", "cell_type_label": "best4-positive, otop2-positive enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CTSE", "stance": "supports"}], "rationale": "This cluster exhibits high and specific expression of canonical marker genes defining BEST4+ enterocytes (best4-positive, otop2-positive enterocytes) in the human intestinal epithelium, including BEST4, CA7, SPIB, CFTR, CPA2, CTSE, GUCA2A, and GUCA2B."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.6}, {"answer": {"cell_type_id": "CL:0009019", "cell_type_label": "best4-positive, otop2-positive enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CTSE", "stance": "supports"}], "rationale": "This cluster exhibits high and specific expression of canonical marker genes defining BEST4+ enterocytes (best4-positive, otop2-positive enterocytes, CL:0009019) in the human intestinal epithelium, including BEST4, CA7, SPIB, CFTR, CPA2, CTSE, GUCA2A, and GUCA2B."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'best4-positive, otop2-positive enterocyte' is not the name of CL:0009020 ('tuft cell of appendix')."], "seconds": 28.2}, {"answer": {"cell_type_id": "CL:0002071", "cell_type_label": "enterocyte of epithelium of small intestine", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "CTSE", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}], "rationale": "This cluster originates from human duodenum (small intestine) and demonstrates high expression of enterocyte markers (GUCA2B, GUCA2A, KRT20) alongside signature markers defining the specialized BEST4+ enterocyte subpopulation (BEST4, CA7, SPIB, CFTR, CPA2, CTSE). In the Cell Ontology, enterocytes of the small intestinal epithelium are classified under term CL:0002071 ('enterocyte of epithelium of small intestine')."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'best4-positive, otop2-positive enterocyte' is not the name of CL:0009019 ('nephrogenic zone cell')."], "seconds": 122.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-daa29fa7c3"} +{"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": "GZMB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "The cluster strongly expresses canonical cytotoxicity and NK cell markers including GNLY, NKG7, GZMB, GZMA, CST7, FGFBP2, HCST, and KLRD1 (CD94), alongside chemokines CCL4 and CCL5, with high cluster specificity (pct_in >> pct_out). The lack of T cell receptor/CD3 markers distinguishes this cluster as natural killer cells (CL:0000623)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.6}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-def3067099"} +{"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": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "The cluster is characterized by high, specific expression of pan-immune/leukocyte marker PTPRC (CD45) and T cell lineage markers CD2 and IL7R (CD127), along with lymphocyte-associated markers CD52, CXCR4, and SRGN. There are no contradicting marker genes from other cell lineages present in the top markers."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 11.0}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-e0c7aa5d8b"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'glomerular capillary endothelial cell' is not the name of CL:0002251 ('epithelial cell of alimentary canal'). 'glomerular capillary endothelial cell' is the name of CL:1001005 (glomerular capillary endothelial 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:0002251", "cell_type_label": "glomerular capillary endothelial cell", "decision": "annotate", "markers": [{"gene": "SOST", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "EMCN", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}], "rationale": "The marker profile is characteristic of glomerular capillary endothelial cells (CL:0002251) in the human kidney. General endothelial markers such as EMCN, RAMP2, GNG11, and RNASE1 confirm endothelial lineage, while SOST, PLAT, CRHBP, and IGFBP5 are canonical and specific marker genes distinguishing glomerular capillary endothelium from other renal endothelial subpopulations (such as peritubular capillaries and vasa recta)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.0}, {"answer": {"cell_type_id": "CL:1001005", "cell_type_label": "glomerular capillary endothelial cell", "decision": "annotate", "markers": [{"gene": "SOST", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "CRHBP", "stance": "supports"}, {"gene": "EMCN", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}], "rationale": "The marker gene profile demonstrates endothelial lineage markers (EMCN, RAMP2, GNG11, RNASE1) along with specific markers for glomerular capillary endothelial cells (SOST, PLAT, CRHBP, IGFBP5). In the Cell Ontology, 'glomerular capillary endothelial cell' corresponds to identifier CL:1001005."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'glomerular capillary endothelial cell' is not the name of CL:0002251 ('epithelial cell of alimentary canal'). 'glomerular capillary endothelial cell' is the name of CL:1001005 (glomerular capillary endothelial cell)."], "seconds": 9.7}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-e6fd6bbd15"} +{"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": "CD69", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRCAP", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "The cluster shows robust and specific expression of canonical T cell markers, particularly CD3D (part of the CD3/T-cell receptor complex) and PTPRCAP, along with pan-leukocyte/lymphocyte marker PTPRC (CD45). Additional highly expressed genes such as IL32, CD52, LTB, CXCR4, and the tissue-residence/activation marker CD69 strongly support the identification of this cluster as skin-resident T cells (CL:0000084)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.0}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-e76b10ee43"} +{"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": "FOXP3", "stance": "supports"}, {"gene": "CTLA4", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD5", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "The cluster strongly expresses CD3E, TRAC, CD2, and CD5, identifying it as T cells. The high and specific expression of FOXP3 (pct_in 0.593 vs pct_out 0.005) and CTLA4 (pct_in 0.613 vs pct_out 0.010), together with TNFRSF1B (TNFR2) and CD27, uniquely defines regulatory T cells (Tregs)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.1}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-f3161764a6"} +{"attempts": [{"codes": [], "evidence": 14, "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": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "NOSIP", "stance": "supports"}, {"gene": "RGS10", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CAMK4", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster expresses canonical T cell lineage markers (CD3E, CD52) alongside classic naive T cell markers (TCF7, LEF1, SELL/CD62L, CCR7, NOSIP, RGS10, CAMK4). The specific expression of LRRN3 and CD40LG, along with high IL7R and CD27 and the absence of CD8 lineage markers (CD8A, CD8B), identifies this cluster as naive CD4+ alpha-beta T cells (CL:0000895: naive thymus-derived CD4-positive, alpha-beta T cell)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 50.9}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-f5c625b34c"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "DCN", "stance": "supports"}, {"gene": "LUM", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "TCF21", "stance": "supports"}, {"gene": "MFAP4", "stance": "supports"}, {"gene": "CFD", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "ADH1B", "stance": "supports"}, {"gene": "ADAMDEC1", "stance": "supports"}], "rationale": "The top marker profile is characterized by canonical extracellular matrix components and stromal/fibroblast identity markers, including DCN, LUM, COL1A2, COL3A1, and MFAP4, along with the fibroblast lineage transcription factor TCF21, structural marker VIM, and stromal secretory factors such as CFD, CXCL14, and ADH1B, all characteristic of intestinal fibroblasts."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 12.8}], "model": "gemini-flash", "protocol": 2, "task_id": "ct-f7c13b08bb"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HOPX", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "CMC1", "stance": "supports"}, {"gene": "PLEK", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of genes characteristic of natural killer (NK) cells. This includes cytotoxic effector molecules (GNLY, PRF1, GZMA, GZMB), NK cell receptors (KLRD1, KLRC1, FCGR3A/CD16), and other genes highly enriched in the NK cell lineage (NKG7, TYROBP). The absence of defining T-cell markers (like CD3 components) among the top differentially expressed genes further confirms the identity of these cells as natural killer cells rather than cytotoxic T lymphocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.5}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-0bcb90ea26"} +{"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": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}], "rationale": "The prominent expression of numerous MHC class II molecules (HLA-DRA, HLA-DPA1, HLA-DPB1, HLA-DRB1) and CD74 strongly indicates a professional antigen-presenting cell type. The co-expression of robust myeloid/macrophage-specific markers such as TYROBP and AIF1 (IBA1), alongside inflammatory cytokines and chemokines typically secreted by activated macrophages (IL1B, CCL3, CXCL8, CXCL2), identifies this cluster as macrophages."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.5}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-0c19dd5456"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'proximal tubule epithelial cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:1000494 (nephron tubule epithelial cell); CL:1000839 (kidney proximal straight tubule epithelial cell); CL:1000838 (kidney proximal convoluted tubule epithelial 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:0002306", "cell_type_label": "proximal tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}], "rationale": "The provided top marker genes, including ALDOB, GATM, MIOX, FABP1, GSTA1, ASS1, HPD, and UGT2B7, are well-established genes highly and specifically expressed in the epithelial cells of the proximal tubule of the kidney. The cluster shows strong expression of metabolic enzymes characteristic of proximal tubule functions."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.5}, {"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "epithelial cell of proximal tubule", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}], "rationale": "The provided top marker genes, including ALDOB, GATM, MIOX, FABP1, GSTA1, ASS1, HPD, and UGT2B7, are well-established genes highly and specifically expressed in the epithelial cells of the proximal tubule of the kidney. The cluster shows strong expression of metabolic enzymes characteristic of proximal tubule functions."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'proximal tubule epithelial cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:1000494 (nephron tubule epithelial cell); CL:1000839 (kidney proximal straight tubule epithelial cell); CL:1000838 (kidney proximal convoluted tubule epithelial cell)."], "seconds": 15.2}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-0f7cfea7f3"} +{"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:0000940", "cell_type_label": "mucosal invariant T cell", "decision": "annotate", "markers": [{"gene": "LTB", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "TRDV2", "stance": "contradicts"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "TNFAIP3", "stance": "supports"}, {"gene": "DUSP2", "stance": "supports"}, {"gene": "SPOCK2", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "NFKBIA", "stance": "supports"}, {"gene": "TC2N", "stance": "supports"}, {"gene": "S100A6", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "FOSB", "stance": "supports"}, {"gene": "DUSP1", "stance": "supports"}, {"gene": "SLC4A10", "stance": "supports"}], "rationale": "The cluster expresses pan-T cell markers like CD3E, alongside genes highly associated with innate-like T cells, such as KLRB1 (CD161), IL23R, IL7R, and the cytotoxic molecule GZMK. The highly specific marker SLC4A10 identifies a large fraction of the cells as mucosal invariant T (MAIT) cells. However, the presence of TRDV2 (a definitive marker for Vdelta2 gamma-delta T cells) indicates that this is a mixed cluster consisting of both MAIT cells and gamma-delta T cells, which often cluster together in human lung datasets due to their shared innate-like transcriptional profiles. The cluster is annotated as MAIT cells, with TRDV2 noted as a contradicting marker reflecting the gamma-delta T cell subpopulation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-1161617d72"} +{"attempts": [{"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}], "rationale": "The cluster robustly expresses definitive T-cell lineage markers, primarily components of the T-cell receptor/CD3 complex (CD3E, CD247/CD3z) and critical T-cell signaling kinase LCK. CD7 is also highly expressed and is a typical marker for T cells and NK cells. Additional markers like KLRB1, GZMA, and NKG7 suggest these may be cytotoxic T cells, natural killer T (NKT) cells, or intraepithelial lymphocytes common in the intestinal mucosa, but their core lineage remains T cell (due to the presence of CD3E and CD247, which distinguishes them from classical NK cells)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.9}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-13d48ee1d6"} +{"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": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster exhibits high expression of well-established B cell markers. CD79A is a classic B cell-specific surface antigen (part of the B cell receptor complex). IGKC (immunoglobulin kappa constant) indicates the presence of mature B cells expressing immunoglobulin light chains. CD74 and HLA-DRA are MHC class II molecules strongly expressed by antigen-presenting cells such as B cells. CD52, CXCR4, and LTB are also highly consistent with mature lymphocytes, specifically B cells in this context. The high expression of ribosomal proteins is a common transcriptomic feature and does not contradict the B cell assignment."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-18ce9fb955"} +{"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": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "TMSB4X", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "HLA-DMA", "stance": "supports"}], "rationale": "The cluster exhibits high expression of multiple MHC class II genes (HLA-DPB1, HLA-DPA1, HLA-DRA, HLA-DQA1, HLA-DRB1, HLA-DQB1, HLA-DMA) and the invariant chain CD74, indicating it is an antigen-presenting cell. Crucially, the prominent expression of complement components (C1QA, C1QB, C1QC), together with AIF1 (IBA1), TYROBP (DAP12), MS4A6A, FCER1G, and LYZ, establishes this as a macrophage cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.9}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-1fcb853772"} +{"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:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}], "rationale": "The cluster expresses classic cytotoxic and natural killer (NK) cell markers such as GNLY, NKG7, GZMB, CCL5, FGFBP2, KLRD1, and CCL4. The robust expression of these markers without defining T-cell receptor components strongly points to a natural killer cell identity, and in particular the CD56dim cytotoxic NK subset (evidenced by high FGFBP2 and GNLY). The high expression of IGKC, an immunoglobulin gene, contradicts the NK cell identity and likely represents ambient RNA contamination or doublets with B or plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.9}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-20d7fe4cf5"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "SPON2", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CLIC3", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "ADGRG1", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}, {"gene": "CTSW", "stance": "supports"}, {"gene": "MYOM2", "stance": "supports"}], "rationale": "The cluster is characterized by high expression of genes encoding cytotoxic granule proteins (GNLY, GZMB, GZMH, GZMA, PRF1), which are highly characteristic of cytotoxic lymphocytes. The presence of FCGR3A (CD16), TYROBP (DAP12), and FCER1G, along with SPON2 and FGFBP2, strongly points towards a mature natural killer (NK) cell identity, specifically the CD56dim CD16+ subset. T cell markers (like CD3 complex genes) are notably absent from the top markers, further supporting an NK cell over a cytotoxic T cell designation. All listed marker genes are consistent with a natural killer cell phenotype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-2e16bde736"} +{"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": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of classic B cell markers, most notably the B cell receptor complex components CD79A and CD79B, the B cell specific antigen CD20 (MS4A1), and the leukocyte antigen CD37. Additionally, it expresses immunoglobulin light chains (IGKC, IGLC2). The presence of MHC class II genes (CD74, HLA-DRA, HLA-DPB1, HLA-DQB1, HLA-DPA1, HLA-DRB1) further supports this professional antigen-presenting cell identity. These features unambiguously identify the cluster as B cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-33d5498243"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "CLDN5", "stance": "supports"}, {"gene": "SELE", "stance": "supports"}, {"gene": "ACKR1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical endothelial cell markers, such as the tight junction protein CLDN5, the adhesion molecule SELE (E-selectin), and the venular endothelial marker ACKR1. The high expression of AQP1, RAMP2, GNG11, and TM4SF1 provides further support for the endothelial lineage, confidently identifying this cluster as endothelial cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.8}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-3875326824"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'type 3 innate lymphoid cell' is not the name of CL:0001071 ('group 3 innate lymphoid cell'). Closest names: CL:0001071 (group 3 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001069 (group 2 innate lymphoid 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:0001071", "cell_type_label": "type 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster exhibits high expression of IL7R, which is characteristic of innate lymphoid cells (ILCs) and T cells. The high expression of the transcription factor RORC alongside the receptors IL23R, CCR6, and KIT is strongly indicative of type 3 innate lymphoid cells (ILC3s). Furthermore, LTB is highly expressed by ILC3 subpopulations such as lymphoid tissue inducer (LTi) cells. The absence of canonical T cell co-receptors in the top marker list supports the ILC3 designation over Th17 cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.7}, {"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster exhibits high expression of IL7R, which is characteristic of innate lymphoid cells (ILCs) and T cells. The high expression of the transcription factor RORC alongside the receptors IL23R, CCR6, and KIT is strongly indicative of group 3 innate lymphoid cells (ILC3s). Furthermore, LTB is highly expressed by ILC3 subpopulations such as lymphoid tissue inducer (LTi) cells. The absence of canonical T cell co-receptors in the top marker list supports the ILC3 designation over Th17 cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type 3 innate lymphoid cell' is not the name of CL:0001071 ('group 3 innate lymphoid cell'). Closest names: CL:0001071 (group 3 innate lymphoid cell); CL:0001065 (innate lymphoid cell); CL:0001069 (group 2 innate lymphoid cell)."], "seconds": 15.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-3ec5acbb2d"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'cholangiocyte' is not the name of CL:0000646 ('basal cell'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte).", "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:0000646", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "ANXA4", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "CLU", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical cholangiocyte (biliary epithelial cell) markers, including KRT7, KRT8, KRT18, CD24, and SPP1. Other highly expressed and specific genes such as ANXA4, DEFB1, FXYD2, TM4SF4, and ELF3 are also characteristic of the biliary epithelium in the liver."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.4}, {"answer": {"cell_type_id": "CL:1000488", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "ANXA4", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "CLU", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical cholangiocyte (biliary epithelial cell) markers, including KRT7, KRT8, KRT18, CD24, and SPP1. Other highly expressed and specific genes such as ANXA4, DEFB1, FXYD2, TM4SF4, and ELF3 are also characteristic of the biliary epithelium in the liver."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cholangiocyte' is not the name of CL:0000646 ('basal cell'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte)."], "seconds": 16.6}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-4163a3b864"} +{"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": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGLC3", "stance": "supports"}, {"gene": "IGHG3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "SSR4", "stance": "supports"}, {"gene": "IGHG4", "stance": "supports"}, {"gene": "HSP90B1", "stance": "supports"}, {"gene": "ISG20", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "CYBA", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "IGHG2", "stance": "supports"}, {"gene": "SSR3", "stance": "supports"}], "rationale": "The cluster expresses very high levels of various immunoglobulin genes (IGKC, IGHM, IGHG1, IGLC2, IGHA1, IGLC3, IGHG3, IGHG4, IGHG2) and joining chain (JCHAIN), which are the defining characteristics of antibody-secreting cells. Furthermore, it highly expresses genes associated with endoplasmic reticulum stress, protein folding, and the secretory pathway (MZB1, FKBP11, SSR4, SSR3, HSP90B1, SEC11C, DERL3), along with the master transcription factor for plasma cell differentiation, XBP1. Collectively, these markers confidently identify the cluster as plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 20.5}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-41fb1f6e39"} +{"attempts": [{"codes": [], "evidence": 14, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "PRSS23", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "ID1", "stance": "supports"}, {"gene": "LIFR", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "ID3", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "PLAC8", "stance": "supports"}], "rationale": "The cluster highly expresses general endothelial markers such as ENG (CD105), PTPRB, RAMP3, IGFBP7, and PRSS23. Additionally, it strongly expresses FCN3, DNASE1L3, and INMT, which are well-established specific markers for liver sinusoidal endothelial cells (LSECs). This marker profile clearly identifies the cluster as endothelial cells of the hepatic sinusoid."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-4d4de5c13f"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT1", "stance": "supports"}, {"gene": "KRT10", "stance": "supports"}, {"gene": "DMKN", "stance": "supports"}, {"gene": "KRT14", "stance": "supports"}, {"gene": "KRTDAP", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "DSP", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "LY6D", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "CLDN1", "stance": "supports"}], "rationale": "The given marker genes strongly identify this cluster as keratinocytes. KRT1 and KRT10 are canonical markers of suprabasal differentiating keratinocytes in the epidermis, while KRT14 is typically expressed in basal keratinocytes (but can be detected here as well). DMKN (Dermokine) and KRTDAP (Keratinocyte differentiation-associated protein) are specifically associated with keratinocyte differentiation. SFN (Stratifin), LGALS7B, LY6D, and TACSTD2 are also classic markers of stratified squamous epithelia and epidermal keratinocytes. Desmosomal proteins such as PERP and DSP, as well as AQP3 and CLDN1, further support the identification of this cluster as keratinocytes making up the epidermal layer."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.5}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-506f19166c"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000173", "cell_type_label": "pancreatic D cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "ISL1", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "UCHL1", "stance": "supports"}], "rationale": "The strong expression of SST (somatostatin) is a classic and definitive marker for pancreatic D cells (delta cells). The cluster also expresses other well-established pancreatic endocrine markers such as ISL1, PCSK1, and UCHL1. Furthermore, genes like HHEX and RBP4 are known to be highly enriched in pancreatic D cells. The absence of canonical markers for other main endocrine cell types (e.g., INS for beta cells, GCG for alpha cells) further confirms its identity as a pure pancreatic D cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-50ec79996f"} +{"attempts": [{"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:0000625", "cell_type_label": "CD8-positive, alpha-beta T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "TRDV2", "stance": "contradicts"}], "rationale": "The cluster is predominantly characterized by core T cell markers (CD3E, CD3D) and the cytotoxic T cell marker CD8A, identifying it as a CD8-positive T cell population. The expression of GZMK and CXCR3 further suggests an effector or memory state. The marker TRDV2 is highly specific for gamma-delta T cells; its presence in a subset (35%) of this cluster likely represents a subpopulation of gamma-delta T cells, which contradicts the alpha-beta T cell designation for those specific cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.2}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-52a80b5c6b"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'kidney collecting duct principal cell' is not the name of CL:1000714 ('kidney cortex collecting duct principal cell'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal 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:1000714", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}], "rationale": "The cluster is characterized by the robust expression of AQP2 and AQP3, which are classic and definitive markers for collecting duct principal cells in the kidney. FXYD4 is also highly expressed and known to localize to the collecting duct. Additionally, the cluster expresses various epithelial markers such as keratins (KRT18, KRT19) and the kidney-specific cadherin CDH16, which further support its identity as a distal tubule or collecting duct epithelial cell type. There are no clear markers indicating a different cell type among the top genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 22.6}, {"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}], "rationale": "The cluster is characterized by the robust expression of AQP2 and AQP3, which are classic and definitive markers for collecting duct principal cells in the kidney. FXYD4 is also highly expressed and known to localize to the collecting duct. Additionally, the cluster expresses various epithelial markers such as keratins (KRT18, KRT19) and the kidney-specific cadherin CDH16, which further support its identity as a distal tubule or collecting duct epithelial cell type. There are no clear markers indicating a different cell type among the top genes."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct principal cell' is not the name of CL:1000714 ('kidney cortex collecting duct principal cell'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal cell)."], "seconds": 16.0}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-54741cc370"} +{"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": "JCHAIN", "stance": "supports"}, {"gene": "IGLL5", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "TNFRSF17", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}], "rationale": "The cluster is characterized by classic markers of B lineage and antibody-secreting cells, including JCHAIN, IGLL5, MZB1, CD79A, and TNFRSF17 (BCMA). Furthermore, the high expression of genes associated with the endoplasmic reticulum and the unfolded protein response (such as XBP1, FKBP11, DERL3, HERPUD1, and SSR4) reflects the massive protein synthesis machinery required for antibody secretion, strongly identifying this cluster as plasma cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 18.6}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-560d5829d2"} +{"attempts": [{"codes": ["BEV017"], "evidence": 6, "findings": [{"message": "The label 'basal cell of epidermis' is not the name of CL:0000064 ('ciliated cell'). 'basal cell of epidermis' is the name of CL:0002187 (basal cell of epidermis).", "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:0000064", "cell_type_label": "basal cell of epidermis", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}], "rationale": "The cluster strongly expresses classic marker genes for basal cells of the epidermis (basal keratinocytes), notably KRT14 and KRT5, which form the primary intermediate filament network in the basal layer of stratified squamous epithelia. Additional markers such as KRT15, DST (a component of hemidesmosomes that anchors basal cells to the basement membrane), and AQP3 further confirm this identity. The presence of these genes uniquely identifies this population as basal epidermal cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.4}, {"answer": {"cell_type_id": "CL:0002187", "cell_type_label": "basal cell of epidermis", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}], "rationale": "The cluster strongly expresses classic marker genes for basal cells of the epidermis (basal keratinocytes), notably KRT14 and KRT5, which form the primary intermediate filament network in the basal layer of stratified squamous epithelia. Additional markers such as KRT15, DST (a component of hemidesmosomes that anchors basal cells to the basement membrane), and AQP3 further confirm this identity. The presence of these genes uniquely identifies this population as basal epidermal cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'basal cell of epidermis' is not the name of CL:0000064 ('ciliated cell'). 'basal cell of epidermis' is the name of CL:0002187 (basal cell of epidermis)."], "seconds": 15.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-5633d2ce11"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'kidney collecting duct beta intercalated cell' is not the name of CL:1001111 ('kidney loop of Henle thin descending limb epithelial cell'). 'kidney collecting duct beta intercalated cell' is the name of CL:4030005 (kidney collecting duct beta-intercalated 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:1001111", "cell_type_label": "kidney collecting duct beta intercalated cell", "decision": "annotate", "markers": [{"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}], "rationale": "The cluster expresses markers characteristic of kidney collecting duct cells, particularly the keratins KRT7 and KRT8, and WFDC2. Crucially, it highly expresses multiple subunits of the vacuolar-type H+-ATPase (V-ATPase) complex (ATP6V1G3, ATP6V0B, ATP6V0D2, ATP6V1B1, ATP6AP2) as well as CA12 (carbonic anhydrase 12), which are classic markers for intercalated cells in the collecting duct. The prominent and specific expression of SLC26A4 (pendrin) decisively identifies this population as type B (beta) intercalated cells, as pendrin is the apical chloride/bicarbonate exchanger characteristic of beta intercalated cells and is absent in type A (alpha) intercalated cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.7}, {"answer": {"cell_type_id": "CL:4030005", "cell_type_label": "kidney collecting duct beta-intercalated cell", "decision": "annotate", "markers": [{"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}], "rationale": "The cluster expresses markers characteristic of kidney collecting duct cells, particularly the keratins KRT7 and KRT8, and WFDC2. Crucially, it highly expresses multiple subunits of the vacuolar-type H+-ATPase (V-ATPase) complex (ATP6V1G3, ATP6V0B, ATP6V0D2, ATP6V1B1, ATP6AP2) as well as CA12 (carbonic anhydrase 12), which are classic markers for intercalated cells in the collecting duct. The prominent and specific expression of SLC26A4 (pendrin) decisively identifies this population as type B (beta) intercalated cells, as pendrin is the apical chloride/bicarbonate exchanger characteristic of beta intercalated cells and is absent in type A (alpha) intercalated cells."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct beta intercalated cell' is not the name of CL:1001111 ('kidney loop of Henle thin descending limb epithelial cell'). 'kidney collecting duct beta intercalated cell' is the name of CL:4030005 (kidney collecting duct beta-intercalated cell)."], "seconds": 15.8}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-6807a1005a"} +{"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": "S100A9", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}], "rationale": "The cluster expresses high levels of myeloid lineage markers (TYROBP, AIF1, LYZ) and MHC class II molecules (HLA-DRA, CD74), which are characteristic of antigen-presenting cells such as macrophages and monocytes. The high expression of S100A8, S100A9, and LYZ suggests an inflammatory macrophage or monocyte population. The presence of C1QA and CTSS further supports a macrophage identity, likely corresponding to monocyte-derived macrophages or circulating monocytes in the liver."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-6846a2fbd5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "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": 10, "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": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}], "rationale": "The cluster expresses the pan-T cell marker CD3E along with the co-receptors CD8A and CD8B, identifying the cells as CD8-positive T cells. It also highly expresses canonical markers of the naive state, including lymphoid homing receptors CCR7 and SELL (CD62L), critical transcription factors for the naive state LEF1 and TCF7, and IL7R. LRRN3 and CD27 are also strongly associated with naive T cells. Together, these uniquely specify a naive CD8-positive, alpha-beta T cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.0}, {"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": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}], "rationale": "The cluster expresses the pan-T cell marker CD3E along with the co-receptors CD8A and CD8B, identifying the cells as CD8-positive T cells. It also highly expresses canonical markers of the naive state, including lymphoid homing receptors CCR7 and SELL (CD62L), critical transcription factors for the naive state LEF1 and TCF7, and IL7R. LRRN3 and CD27 are also strongly associated with naive T cells. Together, these uniquely specify a naive CD8-positive, alpha-beta T cell population, with the term CL:0000900 specifically designated as '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": 17.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-6b9f55ce2e"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "AHSP", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "ALAS2", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "GYPA", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}], "rationale": "The top marker genes for this cluster include canonical hemoglobin genes (HBB, HBA1, HBA2, HBD, HBM) that define red blood cells. It also highly expresses proteins essential for hemoglobin stabilization (AHSP) and heme biosynthesis (ALAS2, SLC25A37), as well as characteristic erythrocyte membrane and structural proteins (SLC4A1/Band 3, GYPA, GYPC). This expression profile unambiguously identifies these cells as erythrocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 27.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-73d8984fbc"} +{"attempts": [{"codes": [], "evidence": 20, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "COL6A1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "COL4A2", "stance": "supports"}, {"gene": "COL5A1", "stance": "supports"}, {"gene": "COL15A1", "stance": "supports"}, {"gene": "COL5A2", "stance": "supports"}, {"gene": "TIMP1", "stance": "supports"}, {"gene": "MICAL2", "stance": "supports"}, {"gene": "PXDN", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "SERPINE1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "CYGB", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}], "rationale": "The cluster shows dominant expression of numerous collagen genes (COL1A1, COL1A2, COL3A1, COL4A2, COL5A1, COL5A2, COL6A1, COL6A3, COL15A1) and prominent extracellular matrix and mesenchymal markers such as fibronectin (FN1), SPARC, and vimentin (VIM). CYGB and SFRP2 are also typical for fibroblasts and closely related populations like pancreatic stellate cells. This massive extracellular matrix gene signature overwhelmingly defines this cell population as fibroblasts."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-75516baf75"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1001106", "cell_type_label": "kidney loop of Henle thick ascending limb epithelial cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}], "rationale": "The cluster expresses classic and highly specific markers of the thick ascending limb (TAL) of the loop of Henle, most notably UMOD (uromodulin, or Tamm-Horsfall protein) and SLC12A1 (NKCC2), which are canonical for TAL epithelial cells. The presence of Na+/K+ ATPase subunits (ATP1A1, ATP1B1) and multiple mitochondrial genes (MT-*) further corroborates this cell type, as these cells are highly metabolically active to support extensive active ion transport."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-7954bd765f"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}], "rationale": "The cluster is defined by extremely high expression of hemoglobin genes (HBB, HBA2, HBA1, HBD, HBM), which are the main functional components of red blood cells. It also expresses mitochondrial carriers essential for heme biosynthesis (SLC25A37, SLC25A39) and the erythrocyte membrane protein GYPC. This expression profile strongly and uniquely identifies the cluster as erythrocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-838e09fefd"} +{"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": "MYL9", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}], "rationale": "The cluster highly expresses classic structural and functional markers of smooth muscle cells, including TAGLN, MYL9, ACTA2, TPM2, CALD1, and the highly specific MYH11. It also expresses RGS5, which is typically found in mural cells like pericytes and vascular smooth muscle cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-884f62d6f1"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'type A intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). 'type A intercalated cell' is the name of CL:0005011 (renal alpha-intercalated 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:0005010", "cell_type_label": "type A intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "This cluster expresses strong and specific markers of intercalated cells of the collecting duct, most notably multiple subunits of the vacuolar H+-ATPase (ATP6V0D2, ATP6V1G3, ATP6V0B, ATP6V1B1, ATP6AP2) which are critical for their proton secretion function. It also expresses carbonic anhydrase 12 (CA12) and the rhesus blood group family type C ammonia transporter (RHCG). Crucially, the presence of the basolateral anion exchangers SLC4A1 (AE1) and SLC26A7 unambiguously identifies this cluster as type A intercalated cells (alpha-intercalated cells), distinguishing them from type B intercalated cells which would instead express SLC26A4 (pendrin)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.8}, {"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "This cluster expresses strong and specific markers of intercalated cells of the collecting duct, most notably multiple subunits of the vacuolar H+-ATPase (ATP6V0D2, ATP6V1G3, ATP6V0B, ATP6V1B1, ATP6AP2) which are critical for their proton secretion function. It also expresses carbonic anhydrase 12 (CA12) and the rhesus blood group family type C ammonia transporter (RHCG). Crucially, the presence of the basolateral anion exchangers SLC4A1 (AE1) and SLC26A7 unambiguously identifies this cluster as renal alpha-intercalated cells (type A intercalated cells), distinguishing them from beta-intercalated cells which would instead express SLC26A4 (pendrin)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'type A intercalated cell' is not the name of CL:0005010 ('renal intercalated cell'). 'type A intercalated cell' is the name of CL:0005011 (renal alpha-intercalated cell)."], "seconds": 22.4}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-90023ca6ff"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000160", "cell_type_label": "goblet cell", "decision": "annotate", "markers": [{"gene": "TFF3", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}, {"gene": "MUC2", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}], "rationale": "The cluster is characterized by the strong expression of well-known markers of goblet cells, most notably the primary intestinal mucin MUC2. It also expresses a host of other goblet cell-associated secretory proteins and markers including TFF3, SPINK4, CLCA1, ZG16, REG4, and ITLN1, clearly identifying this cluster as goblet cells."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.6}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-9ce2902282"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002275", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "PAX6", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}], "rationale": "This cluster represents pancreatic PP cells (also known as gamma cells). The most definitive marker is PPY (pancreatic polypeptide), which has a very high log fold change and is the characteristic hormone secreted by this cell type. Furthermore, the cluster expresses general pancreatic endocrine markers such as PAX6, NEUROD1, SCG2, CHGB, and PCSK2, which confirm its neuroendocrine islet identity. There are no contradicting markers suggesting a mixed population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 24.6}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-a26635e6cd"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}], "rationale": "The cluster expresses classic myeloid and macrophage lineage markers, including TYROBP, FCER1G, AIF1, LYZ, and CTSS. It also expresses various pro-inflammatory cytokines and chemokines (IL1B, CXCL8, CCL3) and S100A9, which are characteristic of infiltrating inflammatory macrophages or monocytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-b2d44d2eda"} +{"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": "NKG7", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}], "rationale": "The high expression of TRDC (T cell receptor delta constant) definitively identifies this as a cluster of gamma-delta T cells, distinguishing it from conventional alpha-beta T cells and Natural Killer (NK) cells. The co-expression of innate-like and cytotoxic markers such as granzymes (GZMK, GZMA), chemokines (CCL3, CCL4, CCL5, XCL1, XCL2), and NK-associated receptors and molecules (NKG7, KLRB1/CD161, KLRC1/NKG2A, IL2RB, TYROBP) is highly characteristic of tissue-resident gamma-delta T cells found in the lung."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.8}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-bb928b569a"} +{"attempts": [{"codes": ["BEV017"], "evidence": 17, "findings": [{"message": "The label 'Kupffer cell' is not the name of CL:0000312 ('keratinocyte'). 'Kupffer cell' is the name of CL:0000091 (Kupffer cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 17, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "The cluster is characterized by the robust expression of genes typical of macrophages, including complement components (C1QA, C1QB, C1QC), scavenger receptors (CD163, MARCO), MHC class II molecules (HLA-DRA, CD74), and various myeloid markers (AIF1, TYROBP, MS4A6A, MS4A7, FCER1G). Given that this dataset is from the liver, the combination of macrophage identity and strong expression of genes involved in heme and iron recycling (HMOX1, SLC40A1, FTL) specifically points to Kupffer cells, which are the resident specialized macrophages of the liver."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.8}, {"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CTSB", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "FTL", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "The cluster is characterized by the robust expression of genes typical of macrophages, including complement components (C1QA, C1QB, C1QC), scavenger receptors (CD163, MARCO), MHC class II molecules (HLA-DRA, CD74), and various myeloid markers (AIF1, TYROBP, MS4A6A, MS4A7, FCER1G). Given that this dataset is from the liver, the combination of macrophage identity and strong expression of genes involved in heme and iron recycling (HMOX1, SLC40A1, FTL) specifically points to Kupffer cells, which are the resident specialized macrophages of the liver."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'Kupffer cell' is not the name of CL:0000312 ('keratinocyte'). 'Kupffer cell' is the name of CL:0000091 (Kupffer cell)."], "seconds": 17.8}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-c12bd3b011"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}], "rationale": "The cluster expresses high levels of SLC12A3, which encodes the thiazide-sensitive sodium-chloride cotransporter (NCC), a definitive and canonical marker for the distal convoluted tubule (DCT) in the kidney. It also expresses WNK1, a kinase known to regulate SLC12A3 in the DCT. Other top markers include DEFB1, TMEM52B, and KNG1, which are known to be highly enriched in distal convoluted tubule cells. Furthermore, the presence of ion pumps (ATP1B1, ATP1A1) and abundant mitochondrial genes (MT-ND1, MT-CO1, etc.) reflects the high metabolic activity and active ion transport roles characteristic of DCT cells. No markers present suggest a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-c7858eb46a"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "endothelial cell of lymphatic vessel", "decision": "annotate", "markers": [{"gene": "CCL21", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "ECSCR", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "FABP4", "stance": "supports"}], "rationale": "The cluster strongly expresses classic, definitive markers for lymphatic endothelial cells. Most notably, PROX1 is the master transcriptional regulator for lymphatic endothelial specification, LYVE1 is a highly specific hyaluronan receptor found on lymphatic endothelium, and CCL21 is a chemokine abundantly secreted by lymphatic endothelial cells to attract CCR7-expressing immune cells. The cluster also expresses MMRN1, another established marker for lymphatic endothelial cells, along with a suite of general endothelial markers including CLDN5, ECSCR, RAMP2, and TFPI. Together, this expression profile unambiguously identifies the cluster as endothelial cells of lymphatic vessels. There are no contradicting marker genes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-cc1cfcedd3"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}, {"gene": "APOLD1", "stance": "supports"}], "rationale": "The cluster highly expresses RGS5, which is a canonical and well-established marker for pericytes (as well as some vascular smooth muscle cells) across many tissues including the kidney. Additionally, it expresses C11orf96, IGFBP5, TIMP3, and APOLD1, which are commonly enriched in pericyte and stromal populations. A large proportion of the top upregulated genes (e.g., CCL2, JUN, JUNB, SOCS3, HSPA1A, DNAJB1, CDKN1A) are immediate-early genes, heat shock proteins, and stress response genes. This indicates a strong stress signature, likely induced by the enzymatic tissue dissociation process typical of scRNA-seq protocols, but the underlying cell type identity remains clearly recognizable as pericytes."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 31.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-d9bc81cfff"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'enterocyte' is not the name of CL:0002071 ('enterocyte of epithelium of large intestine'). 'enterocyte' is the name of CL:0000584 (enterocyte).", "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:0002071", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}], "rationale": "This cluster represents BEST4+ enterocytes (also known as BEST4/OTOP2 cells), a distinct subtype of intestinal epithelial cells. They are robustly characterized by the co-expression of BEST4, SPIB, CFTR, CA7, CPA2, and members of the guanylin family (GUCA2A, GUCA2B). While LYZ is traditionally considered a Paneth cell marker, it is also highly expressed in this specific BEST4+ lineage. Since a specific and universally used Cell Ontology term for the BEST4+ subpopulation may be lacking or highly granular, they fall under the broader classification of enterocytes (CL:0002071)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.0}, {"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}], "rationale": "This cluster represents BEST4+ enterocytes (also known as BEST4/OTOP2 cells), a distinct subtype of intestinal epithelial cells found in the duodenum. They are robustly characterized by the co-expression of BEST4, SPIB, CFTR, CA7, CPA2, and members of the guanylin family (GUCA2A, GUCA2B). LYZ is also highly expressed in this specific BEST4+ lineage. They fall under the classification of enterocytes (CL:0000584)."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'enterocyte' is not the name of CL:0002071 ('enterocyte of epithelium of large intestine'). 'enterocyte' is the name of CL:0000584 (enterocyte)."], "seconds": 17.0}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-daa29fa7c3"} +{"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": "GZMB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "The cluster exhibits strong expression of canonical natural killer (NK) cell markers, including cytolytic effector molecules (GNLY, GZMB, GZMA, CST7), NK cell-associated receptors and signaling molecules (KLRD1, HCST), and FGFBP2, which is highly specific for mature (CD56dim) NK cells. Chemokines CCL4 and CCL5 also strongly support an NK cell or cytotoxic T cell identity. The absence of canonical T cell lineage markers (such as CD3) among the top highly enriched genes further supports a natural killer cell classification."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.2}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-def3067099"} +{"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": "IL7R", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "The cluster displays high expression of PTPRC (CD45), a pan-leukocyte marker, along with specific T cell markers including IL7R, CD2, and CD52. Additional immune and lymphoid markers like CXCR4 and SRGN further support the T cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.5}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-e0c7aa5d8b"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "EMCN", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "PLPP3", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}], "rationale": "The prominent expression of classic vascular markers such as EMCN (Endomucin), RAMP2, PLAT, PLPP3, and RNASE1 strongly identifies this cluster as endothelial cells. Furthermore, human kidney microvascular endothelial cells are well known to constitutively express MHC class II molecules (such as CD74 and HLA-DRB1) alongside MHC class I molecules, which explains their robust presence in this cluster. The high expression of other factors like IGFBP5 and CRHBP is also highly characteristic of the renal endothelial cell transcriptome."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.7}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-e6fd6bbd15"} +{"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": "CD3D", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "The cluster shows strong expression of the pan-leukocyte marker PTPRC (CD45) and the specific T cell marker CD3D, indicating it is a T cell population. Additionally, it expresses IL32 and CD52 (which are highly expressed in T cells) as well as the tissue-residency/activation marker CD69, consistent with T cells residing in the skin."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 19.2}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-e76b10ee43"} +{"attempts": [{"codes": [], "evidence": 6, "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": "CTLA4", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}], "rationale": "The expression profile includes general T cell markers such as CD3E, CD2, and TRAC. The cluster also shows strong, specific expression of FOXP3, the master transcriptional regulator of regulatory T cells (Tregs), and CTLA4, a key immune checkpoint receptor characteristically highly expressed on Tregs, confirming its identity as a regulatory T cell cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.3}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-f3161764a6"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000898", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}], "rationale": "The cluster exhibits clear expression of the pan-T cell marker CD3E, identifying it as a T cell population. The high expression of key transcription factors TCF7 and LEF1, along with homing receptors CCR7 and SELL (CD62L), strongly points to a naive T cell (or central memory) phenotype. Additional markers such as IL7R, LRRN3, and CD27 further support a naive/resting T cell state. CD40LG suggests this is likely a naive CD4+ T cell subpopulation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.9}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-f5c625b34c"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "LUM", "stance": "supports"}, {"gene": "DCN", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "VIM", "stance": "supports"}, {"gene": "TCF21", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MFAP4", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "ADAMDEC1", "stance": "supports"}], "rationale": "The cluster shows robust expression of classic structural extracellular matrix genes (COL1A2, COL3A1, LUM, DCN) as well as the intermediate filament vimentin (VIM), all of which are hallmark markers of fibroblasts. The expression of TCF21 and MFAP4 further confirms its identity as a mesenchymal/fibroblast population in the intestinal stroma. ADAMDEC1 and CXCL14 are also prominently expressed in these intestinal fibroblasts."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 21.0}], "model": "gemini-pro", "protocol": 2, "task_id": "ct-f7c13b08bb"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}], "rationale": "The combination of NK receptors KLRD1 and KLRC1, signaling adaptors TYROBP and FCER1G, and strong NKG7, GNLY, and cytotoxic effector expression supports natural killer cells. No listed markers clearly contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.1}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-0bcb90ea26"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}], "rationale": "Most consistent with inflammatory, antigen-presenting macrophages: TYROBP and AIF1 support myeloid identity, strong CD74/HLA-II expression indicates antigen presentation, and IL1B/CCL3 indicate inflammatory activation. These markers overlap with monocytes and dendritic cells, so the macrophage assignment is provisional; no listed marker clearly contradicts it."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 58.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-0c19dd5456"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "epithelial cell of proximal tubule", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "RBP5", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}], "rationale": "The coordinated metabolic markers, particularly ALDOB, MIOX, GATM and FABP1, strongly support kidney proximal tubule epithelial identity. Elevated metallothioneins suggest a stress-response state and do not contradict this annotation. No listed markers clearly establish a competing cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.4}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-0f7cfea7f3"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}], "rationale": "Strong enrichment of TRDV2, together with CD3E, supports a Vδ2 gamma-delta T-cell identity. IL7R, KLRB1, GZMK and IL23R support its functional phenotype. SLC4A10 is associated with MAIT cells but does not alone establish a conflicting identity or mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.7}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-1161617d72"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD3E", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}], "rationale": "CD3E expression in 96.9% of cells, together with CD247, LCK and CD7, supports T-cell identity. KLRB1, GZMA and NKG7 suggest an innate-like or cytotoxic phenotype, but do not distinguish conventional cytotoxic T, MAIT or NKT cells. These markers do not clearly indicate a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.8}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-13d48ee1d6"} +{"attempts": [{"codes": [], "evidence": 5, "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": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}], "rationale": "CD79A and IGKC strongly support B-cell identity, accompanied by the antigen-presentation markers CD74 and HLA-DRA and the lymphocyte-associated marker CD52. These markers support a general B-cell annotation but do not establish a specific subtype. No listed markers clearly contradict this identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.1}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-18ce9fb955"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}], "rationale": "Strong, coordinated C1QA/C1QB/C1QC expression together with myeloid markers TYROBP, AIF1, MS4A6A, FCER1G and LYZ identifies macrophages. SELENOP supports a tissue-resident intestinal macrophage phenotype. High HLA class II expression is consistent with antigen-presenting macrophages; no listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-1fcb853772"} +{"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:0000623", "cell_type_label": "natural killer cell", "decision": "annotate", "markers": [{"gene": "GNLY", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "IGKC", "stance": "contradicts"}], "rationale": "The combined GNLY, KLRD1, FGFBP2 and cytotoxic effector signature supports natural killer cells. IGKC suggests a B-lineage contribution, potentially from ambient RNA, doublets or cluster mixing; these possibilities cannot be distinguished from the marker table alone."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.5}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-20d7fe4cf5"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}], "rationale": "The strong cytotoxic program together with FCGR3A, TYROBP and FCER1G supports natural killer cells. FGFBP2 and CX3CR1 further suggest a mature CD16-positive, CD56-dim phenotype. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.2}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-2e16bde736"} +{"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": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}], "rationale": "CD79A, CD79B and MS4A1 establish B-cell identity, supported by immunoglobulin light chains and 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": 34.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-33d5498243"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002543", "cell_type_label": "vein endothelial cell", "decision": "annotate", "markers": [{"gene": "ACKR1", "stance": "supports"}, {"gene": "SELE", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}], "rationale": "The combined endothelial signature and strong ACKR1 expression support venous, particularly postcapillary venular, endothelial cells. SELE suggests endothelial activation. CD74 can reflect endothelial antigen presentation and does not by itself indicate a mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.2}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-3875326824"} +{"attempts": [{"codes": [], "evidence": 6, "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": "RORC", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The combined RORC, IL7R, KIT, IL23R and CCR6 signature strongly supports ILC3 identity, particularly a CCR6-positive, lymphoid tissue inducer-like phenotype. Although several markers overlap with Th17 cells, KIT expression and the overall signature favor ILC3. No listed marker clearly establishes a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 60.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-3ec5acbb2d"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000488", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "KRT7", "stance": "supports"}, {"gene": "ANXA4", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}], "rationale": "The strong KRT7, ANXA4, FXYD2, SPP1, and CD24 signature, together with epithelial keratins KRT8/KRT18, identifies liver bile duct epithelial cells (cholangiocytes). No listed markers clearly establish a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 50.4}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-4163a3b864"} +{"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": "MZB1", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}], "rationale": "Strong MZB1 and JCHAIN expression, abundant immunoglobulin transcripts, and the XBP1/DERL3/FKBP11 secretory program identify antibody-secreting plasma cells. Multiple immunoglobulin isotypes can reflect different plasma cells within the cluster and do not independently indicate doublets. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.6}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-41fb1f6e39"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "PTPRB", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "DNASE1L3", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}], "rationale": "The coherent PTPRB/ENG/RNASE1/RAMP3 signature identifies endothelial cells. DNASE1L3, FCN3 and INMT further favor liver sinusoidal endothelial identity. TAGLN suggests a contractile or mesenchymal program but alone does not establish a separate lineage or doublets; the conservative ontology assignment is endothelial cell."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.2}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-4d4de5c13f"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT1", "stance": "supports"}, {"gene": "KRT10", "stance": "supports"}, {"gene": "DMKN", "stance": "supports"}, {"gene": "KRTDAP", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "KRT14", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "DSP", "stance": "supports"}], "rationale": "Strong KRT1/KRT10 expression together with DMKN and KRTDAP identifies differentiating epidermal keratinocytes, consistent with a suprabasal/spinous phenotype. KRT14 supports keratinocyte identity and does not by itself indicate a mixed cluster. No listed markers clearly support a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.4}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-506f19166c"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000173", "cell_type_label": "pancreatic D cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "LEPR", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "ISL1", "stance": "supports"}], "rationale": "Strong SST enrichment together with HHEX supports pancreatic delta (D) cells, which produce somatostatin. RBP4 and LEPR reinforce this identity; PCSK1 and ISL1 support endocrine differentiation. Despite widespread SST detection outside the cluster, its large expression enrichment is compelling. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-50ec79996f"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000798", "cell_type_label": "gamma-delta T cell", "decision": "annotate", "markers": [{"gene": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}], "rationale": "TRDV2 enrichment strongly supports a Vδ2-bearing gamma-delta T-cell population, with CD3E and CD3D establishing T-cell identity. GZMK, CD27 and XCL1 support its functional phenotype. No listed markers clearly indicate a conflicting lineage; the broader gamma-delta T-cell annotation is more secure than a specific functional subtype."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.1}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-52a80b5c6b"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "AQP2", "stance": "supports"}, {"gene": "FXYD4", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}, {"gene": "KRT19", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}], "rationale": "Strong enrichment of AQP2, FXYD4 and AQP3 identifies collecting duct principal cells. CDH16 supports renal tubular identity, while KRT19 and KRT18 support epithelial identity. None of the listed markers clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-54741cc370"} +{"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": "TNFRSF17", "stance": "supports"}, {"gene": "JCHAIN", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGLL5", "stance": "supports"}], "rationale": "MZB1 and TNFRSF17, together with strong JCHAIN expression and the XBP1/DERL3/FKBP11 secretory program, identify antibody-secreting plasma cells. CD79A and IGLL5 support B-lineage identity. No listed markers clearly suggest a conflicting cell type; immunoglobulin isotype cannot be determined from this list."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.4}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-560d5829d2"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002187", "cell_type_label": "basal cell of epidermis", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}], "rationale": "Near-universal KRT14 and KRT5 expression, supported by KRT15, DST and S100A2, identifies basal epidermal keratinocytes. AQP3 and CCL27 reinforce epidermal identity. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-5633d2ce11"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002201", "cell_type_label": "type B intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC26A4", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}], "rationale": "The intercalated-cell proton-pump signature (ATP6V1B1, ATP6V1G3, ATP6V0D2), together with highly cluster-specific SLC26A4 (pendrin), supports type B intercalated cells. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-6807a1005a"} +{"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": "LYZ", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}], "rationale": "Strong S100A8/S100A9 and LYZ enrichment together with LST1 and other myeloid markers favors monocytes. C1QA suggests some macrophage-associated differentiation, but does not alone establish a separate population or doublets; a finer subtype is not securely resolved."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-6846a2fbd5"} +{"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": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}], "rationale": "CD3E with CD8A/CD8B establishes CD8 T-cell identity. Strong CCR7, SELL, TCF7, LEF1 and LRRN3 expression favors a naive phenotype, although central memory cells can share several of these markers. No listed marker clearly establishes a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.2}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-6b9f55ce2e"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "AHSP", "stance": "supports"}, {"gene": "ALAS2", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "GYPA", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}], "rationale": "Strong, widespread hemoglobin expression together with erythroid heme-synthesis genes (ALAS2, AHSP) and red-cell membrane markers (GYPA, SLC4A1) identifies erythrocytes. RNA-bearing reticulocytes may contribute, but these markers do not establish a precise maturation stage. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.6}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-73d8984fbc"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002410", "cell_type_label": "pancreatic stellate cell", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "COL6A1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "CYGB", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}], "rationale": "The strong collagen and extracellular-matrix expression program, together with CYGB and SFRP2, supports pancreatic stellate cells with an activated, matrix-producing phenotype. No listed markers clearly indicate a conflicting cell lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.7}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-75516baf75"} +{"attempts": [{"codes": ["BEV017"], "evidence": 4, "findings": [{"message": "The label 'epithelial cell of thick ascending limb of loop of Henle' is not the name of CL:0002304 ('non-pigmented ciliary epithelial cell').", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002304", "cell_type_label": "epithelial cell of thick ascending limb of loop of Henle", "decision": "annotate", "markers": [{"gene": "SLC12A1", "stance": "supports"}, {"gene": "UMOD", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}], "rationale": "Strong enrichment of SLC12A1 (96.0% inside versus 5.3% outside) and UMOD (84.7% versus 17.5%) identifies thick ascending limb epithelium. KNG1 and DEFB1 provide additional support. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.3}, {"answer": {"cell_type_id": "CL:1001106", "cell_type_label": "kidney loop of Henle thick ascending limb epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A1", "stance": "supports"}, {"gene": "UMOD", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}], "rationale": "SLC12A1 (96.0% inside versus 5.3% outside) and UMOD (84.7% versus 17.5%) strongly support thick ascending limb epithelium. KNG1 and DEFB1 provide additional support. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'epithelial cell of thick ascending limb of loop of Henle' is not the name of CL:0002304 ('non-pigmented ciliary epithelial cell')."], "seconds": 30.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-7954bd765f"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}], "rationale": "Strong, widespread globin expression together with the erythrocyte membrane gene GYPC and supporting heme-related genes identifies an erythrocyte cluster. These markers do not resolve maturation stage reliably; none clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.5}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-838e09fefd"} +{"attempts": [{"codes": [], "evidence": 8, "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": "MYL9", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TPM2", "stance": "supports"}, {"gene": "CALD1", "stance": "supports"}, {"gene": "MYH11", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}], "rationale": "Strong expression of contractile genes, especially MYH11 together with ACTA2, TAGLN and MYL9, supports vascular smooth muscle identity. RGS5 supports a vascular mural-cell phenotype and is shared with pericytes; it does not independently indicate a mixed cluster. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.6}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-884f62d6f1"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}], "rationale": "SLC4A1 and SLC26A7 strongly identify acid-secreting alpha-intercalated (type A) cells. Their high prevalence, together with proton-pump subunits ATP6V1B1, ATP6V1G3 and ATP6V0D2 and the ammonia transporter RHCG, supports this annotation. No listed markers clearly indicate a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-90023ca6ff"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000160", "cell_type_label": "goblet cell", "decision": "annotate", "markers": [{"gene": "MUC2", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "ST6GALNAC1", "stance": "supports"}], "rationale": "The strong, broadly expressed MUC2–TFF3–CLCA1 signature, supported by SPINK4 and ZG16, identifies intestinal mucus-secreting goblet cells. No listed marker clearly establishes a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.8}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-9ce2902282"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002275", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "PAX6", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "PAM", "stance": "supports"}], "rationale": "Strong PPY enrichment (logfc 6.381), with expression in all cluster cells, identifies pancreatic polypeptide-producing PP (gamma) cells. The accompanying endocrine transcription factors and secretory-processing genes support this identity. No listed markers clearly contradict it."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.8}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-a26635e6cd"} +{"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": "IL1B", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}], "rationale": "The coordinated myeloid markers LST1, TYROBP, FCER1G, AIF1 and LYZ, together with strong S100A9, IL1B and CXCL8, support inflammatory monocytes. These markers establish monocyte identity more confidently than a specific subtype; none clearly indicates a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.7}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-b2d44d2eda"} +{"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": "NKG7", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "The coordinated NK receptor, TYROBP adaptor, and cytotoxic/chemokine signature supports natural killer cells. TRDC raises a gamma-delta T-cell alternative, but can also be expressed in NK cells; without accompanying T-cell receptor/CD3 evidence, it does not clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-bb928b569a"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "MARCO", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "HMOX1", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}], "rationale": "The strong C1QA/B/C and CD163 macrophage signature, together with MARCO and the iron-handling genes SLC40A1 and HMOX1 in liver tissue, supports Kupffer cells (liver-resident macrophages). No listed markers clearly indicate a conflicting cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-c12bd3b011"} +{"attempts": [{"codes": [], "evidence": 5, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "SLC12A3", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}], "rationale": "SLC12A3, encoding the characteristic distal convoluted tubule sodium–chloride cotransporter, is expressed in 97.5% of cluster cells versus 3.6% outside. WNK1 and the accompanying epithelial markers reinforce this identity. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.8}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-c7858eb46a"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "endothelial cell of lymphatic vessel", "decision": "annotate", "markers": [{"gene": "CCL21", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "TFF3", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "ECSCR", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}], "rationale": "CCL21, PROX1, and LYVE1 together strongly identify lymphatic endothelial cells. MMRN1 and TFF3 reinforce this identity, while CLDN5, ECSCR, and RAMP2 support endothelial lineage. No listed markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.1}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-cc1cfcedd3"} +{"attempts": [{"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "TIMP3", "stance": "supports"}], "rationale": "Strong, enriched RGS5 expression supports a pericyte identity, reinforced by IGFBP5, IGFBP7 and TIMP3. CCL2 and stress-response genes suggest an activated state. The listed markers do not clearly establish a competing cell identity."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.2}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-d9bc81cfff"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000584", "cell_type_label": "enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}], "rationale": "The combined BEST4, CA7, CFTR and guanylin-family signature identifies BEST4-positive enterocytes, an intestinal epithelial subtype specialized in ion transport and pH regulation. Enterocyte is the broader Cell Ontology annotation used here. LYZ and SPIB alone do not establish a conflicting lineage or mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.7}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-daa29fa7c3"} +{"attempts": [{"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": "FGFBP2", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "Strong GNLY and NKG7 expression together with KLRD1, FGFBP2 and cytotoxic granule genes supports natural killer cells. Some markers are shared with cytotoxic T cells, but the supplied markers show no clear conflicting lineage signal."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 55.9}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-def3067099"} +{"attempts": [{"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000084", "cell_type_label": "T cell", "decision": "annotate", "markers": [{"gene": "CD2", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}], "rationale": "CD2 and IL7R enrichment supports T-cell identity, with CD52 and PTPRC supporting leukocyte identity. The markers suggest an IL7R-positive T-cell population but do not establish a specific subtype. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 62.4}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-e0c7aa5d8b"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "EMCN", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "PLPP3", "stance": "supports"}], "rationale": "EMCN, RAMP2, RNASE1 and GNG11 form a coherent vascular endothelial signature, consistent with renal microvascular endothelium. The markers support endothelial identity more confidently than a specific vascular subtype. CD74 and HLA-DRB1 can reflect endothelial antigen presentation and do not independently establish immune-cell contamination."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.6}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-e6fd6bbd15"} +{"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": "CD3D", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}], "rationale": "CD3D identifies T-cell lineage, supported by IL32 and LTB expression within a leukocyte signature (PTPRC, CD52). CD69 suggests activation or tissue residency. These markers do not reliably distinguish CD4, CD8, or specific resident-memory subsets. No listed markers clearly contradict the T-cell annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.5}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-e76b10ee43"} +{"attempts": [{"codes": [], "evidence": 7, "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": "CTLA4", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD5", "stance": "supports"}], "rationale": "Strong enrichment of FOXP3 (59.3% inside versus 0.5% outside) and CTLA4 (61.3% versus 1.0%), together with TNFRSF1B and clear T-cell lineage markers, identifies regulatory T cells. No listed markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.4}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-f3161764a6"} +{"attempts": [{"codes": [], "evidence": 9, "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": "CD3E", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}], "rationale": "CD3E supports T-cell identity; strong TCF7, LEF1, SELL, CCR7 and LRRN3 expression favors a naive phenotype. CD40LG and IL7R favor the CD4 helper lineage. Central memory CD4 T cells remain a close alternative, but the combined naive program favors this annotation. No listed marker clearly establishes a contradictory lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.3}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-f5c625b34c"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "LUM", "stance": "supports"}, {"gene": "DCN", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "TCF21", "stance": "supports"}, {"gene": "MFAP4", "stance": "supports"}, {"gene": "CXCL14", "stance": "supports"}, {"gene": "ADAMDEC1", "stance": "supports"}], "rationale": "The coherent extracellular-matrix signature (LUM, DCN, COL1A2, COL3A1), together with TCF21, strongly supports fibroblasts. CXCL14 and ADAMDEC1 are consistent with intestinal stromal fibroblasts. No listed markers clearly indicate a conflicting lineage."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.5}], "model": "gpt-astra", "protocol": 2, "task_id": "ct-f7c13b08bb"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}], "rationale": "The cluster shows a coherent cytotoxic NK-cell program: near-universal NKG7, high GNLY, KLRD1, KLRC1, FCGR3A, PRF1, GZMB, and XCL1/XCL2 expression. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.4}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-0bcb90ea26"} +{"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": "CD74", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DRB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}, {"gene": "HLA-DQA1", "stance": "supports"}, {"gene": "GPR183", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}], "rationale": "The cluster shows a strong antigen-presenting dendritic-cell program (HLA-DRA, CD74, HLA-DP/DQ genes) together with TYROBP, AIF1, GPR183 and inflammatory cytokine/chemokine expression (CXCL8, IL1B, CCL3), consistent with an activated inflammatory dendritic-cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.0}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-0c19dd5456"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002306", "cell_type_label": "kidney proximal tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "ALDOB", "stance": "supports"}, {"gene": "PDZK1IP1", "stance": "supports"}, {"gene": "GATM", "stance": "supports"}, {"gene": "GSTA1", "stance": "supports"}, {"gene": "MIOX", "stance": "supports"}, {"gene": "FABP1", "stance": "supports"}, {"gene": "HPD", "stance": "supports"}, {"gene": "RBP5", "stance": "supports"}, {"gene": "UGT2B7", "stance": "supports"}, {"gene": "ASS1", "stance": "supports"}, {"gene": "GPX3", "stance": "supports"}, {"gene": "CYB5A", "stance": "supports"}], "rationale": "The cluster shows a strong proximal tubule epithelial program, including ALDOB, GATM, GSTA1, MIOX, FABP1, HPD, RBP5, UGT2B7, and ASS1. These markers support proximal tubule identity; no marker clearly indicates a distinct cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.9}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-0f7cfea7f3"} +{"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": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "KLRB1", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "SLC4A10", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "TC2N", "stance": "supports"}], "rationale": "The cluster is clearly a T-cell population, with TRDV2 strongly supporting Vδ2 gamma-delta T-cell identity. KLRB1, IL23R, SLC4A10, IL7R, GZMK, and CD3E support an activated/memory mucosal-like gamma-delta T-cell phenotype. No marker clearly indicates a conflicting cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.1}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-1161617d72"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"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": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000945", "cell_type_label": "mucosal invariant T cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}], "rationale": "The cluster shows a T-cell program (CD3E, CD7, CD247, LCK) together with strong KLRB1, NKG7, GZMA, and HCST expression, consistent with mucosal invariant T cells, including the MAIT-like population commonly found in intestinal tissue. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.3}, {"answer": {"cell_type_id": "CL:0000940", "cell_type_label": "mucosal-associated invariant T cell", "decision": "annotate", "markers": [{"gene": "KLRB1", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD7", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}, {"gene": "CD247", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "LCK", "stance": "supports"}], "rationale": "The cluster has a clear T-cell program (CD3E, CD7, CD247, LCK) combined with KLRB1, NKG7, GZMA, and HCST, supporting a mucosal-associated invariant T-cell identity. No marker clearly indicates a conflicting cell type."}, "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": 51.1}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-13d48ee1d6"} +{"attempts": [{"codes": [], "evidence": 6, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000236", "cell_type_label": "B cell", "decision": "annotate", "markers": [{"gene": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "CD79A, CD74, HLA-DRA, and IGKC indicate an antigen-presenting immunoglobulin-expressing B-cell population. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.8}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-18ce9fb955"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "SELENOP", "stance": "supports"}, {"gene": "HLA-DPA1", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "The cluster shows a coherent macrophage antigen-presentation and phagocyte program: C1Q genes, TYROBP, AIF1, LYZ, MS4A6A, FCER1G, SELENOP, and high MHC-II genes. No markers clearly indicate a different cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 36.8}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-1fcb853772"} +{"attempts": [{"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": "GZMB", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CORO1A", "stance": "supports"}, {"gene": "CYBA", "stance": "supports"}], "rationale": "The cluster shows a strong cytotoxic NK-cell program, including GNLY, NKG7, GZMB, FGFBP2, KLRD1, CCL5, and CCL4. The high FGFBP2 and GZMB expression is consistent with mature cytotoxic NK cells. IGKC may reflect ambient RNA or minor contamination but does not outweigh the coherent NK-cell marker profile."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 37.7}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-20d7fe4cf5"} +{"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": "NKG7", "stance": "supports"}, {"gene": "GNLY", "stance": "supports"}, {"gene": "GZMB", "stance": "supports"}, {"gene": "PRF1", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "GZMH", "stance": "supports"}, {"gene": "FCGR3A", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "CX3CR1", "stance": "supports"}, {"gene": "TBX21", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}], "rationale": "The cluster shows a strong cytotoxic natural-killer program, including NKG7, GNLY, GZMB, PRF1, GZMH, FGFBP2, and CCL5. FCGR3A, CX3CR1, TBX21, TYROBP, and FCER1G further support a mature, effector CD16-positive NK phenotype. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 32.7}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-2e16bde736"} +{"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": "CD74", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}, {"gene": "CD79B", "stance": "supports"}, {"gene": "MS4A1", "stance": "supports"}, {"gene": "CD37", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}, {"gene": "IGLC2", "stance": "supports"}, {"gene": "HLA-DPB1", "stance": "supports"}, {"gene": "HLA-DQB1", "stance": "supports"}], "rationale": "The cluster shows a coherent B-cell antigen-presentation and B-cell receptor program: CD79A, CD79B, MS4A1, CD74, multiple HLA class II genes, CD37, and immunoglobulin light chains. No clearly contradictory lineage markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 38.9}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-33d5498243"} +{"attempts": [{"codes": ["BEV016"], "evidence": 10, "findings": [{"message": "CL:0002542 is not in the pinned CL release (releases/2026-06-08). 'venous endothelial cell' is the name of CL:0002543 (vein endothelial cell).", "rule_id": "BEV016", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002542", "cell_type_label": "venous endothelial cell", "decision": "annotate", "markers": [{"gene": "TM4SF1", "stance": "supports"}, {"gene": "SELE", "stance": "supports"}, {"gene": "ACKR1", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "PCAT19", "stance": "supports"}, {"gene": "MCTP1", "stance": "supports"}], "rationale": "The cluster shows a strong vascular endothelial program (TM4SF1, SPARCL1, AQP1, GNG11, CLDN5, RAMP2) with ACKR1 and SELE specifically supporting venous/post-capillary venular endothelial identity. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 51.4}, {"answer": {"cell_type_id": "CL:0002543", "cell_type_label": "vein endothelial cell", "decision": "annotate", "markers": [{"gene": "TM4SF1", "stance": "supports"}, {"gene": "SELE", "stance": "supports"}, {"gene": "ACKR1", "stance": "supports"}, {"gene": "SPARCL1", "stance": "supports"}, {"gene": "AQP1", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "PCAT19", "stance": "supports"}, {"gene": "MCTP1", "stance": "supports"}], "rationale": "The cluster has a strong vascular endothelial program, including TM4SF1, SPARCL1, AQP1, GNG11, CLDN5, RAMP2, PCAT19, and MCTP1. ACKR1 and SELE specifically support venous/post-capillary venular endothelial identity. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0002542 is not in the pinned CL release (releases/2026-06-08). 'venous endothelial cell' is the name of CL:0002543 (vein endothelial cell)."], "seconds": 36.0}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-3875326824"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'group 3 innate lymphoid cell' is not the name of CL:0001068 ('ILC1'). '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": 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:0001068", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "IL4I1", "stance": "supports"}, {"gene": "JAML", "stance": "supports"}], "rationale": "The combination of IL7R, CCR6, RORC, IL23R, and KIT is characteristic of human group 3 innate lymphoid cells (ILC3), particularly CCR6-positive ILC3. LTB, IL4I1, and JAML further support an activated type-3 lymphoid profile. LST1 is atypical but is not sufficient on its own to establish a myeloid mixed cluster."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 56.0}, {"answer": {"cell_type_id": "CL:0001071", "cell_type_label": "group 3 innate lymphoid cell", "decision": "annotate", "markers": [{"gene": "IL7R", "stance": "supports"}, {"gene": "CCR6", "stance": "supports"}, {"gene": "RORC", "stance": "supports"}, {"gene": "IL23R", "stance": "supports"}, {"gene": "KIT", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "JAML", "stance": "supports"}, {"gene": "LST1", "stance": "contradicts"}], "rationale": "IL7R, CCR6, RORC, IL23R, and KIT form a characteristic human ILC3, especially CCR6-positive ILC3, marker combination. LTB and JAML are also compatible with this lymphoid profile. Strong LST1 expression is atypical for ILC3 and may indicate myeloid contamination or a mixed/doublet component."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'group 3 innate lymphoid cell' is not the name of CL:0001068 ('ILC1'). 'group 3 innate lymphoid cell' is the name of CL:0001071 (group 3 innate lymphoid cell)."], "seconds": 51.6}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-3ec5acbb2d"} +{"attempts": [{"codes": ["BEV017"], "evidence": 13, "findings": [{"message": "The label 'cholangiocyte' is not the name of CL:0000646 ('basal cell'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte).", "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:0000646", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "ANXA4", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}, {"gene": "GSTP1", "stance": "supports"}], "rationale": "The cluster shows a cholangiocyte/ductal epithelial signature: KRT7, KRT8, KRT18, ANXA4, SPP1, TM4SF4, DEFB1, CD24, LGALS4, and SLPI. SPP1 and KRT7 are particularly characteristic of activated or mature cholangiocytes. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 33.5}, {"answer": {"cell_type_id": "CL:1000488", "cell_type_label": "cholangiocyte", "decision": "annotate", "markers": [{"gene": "ANXA4", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}, {"gene": "FXYD2", "stance": "supports"}, {"gene": "TM4SF4", "stance": "supports"}, {"gene": "SPP1", "stance": "supports"}, {"gene": "CD24", "stance": "supports"}, {"gene": "KRT8", "stance": "supports"}, {"gene": "KRT18", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}, {"gene": "LGALS4", "stance": "supports"}, {"gene": "SLPI", "stance": "supports"}, {"gene": "ELF3", "stance": "supports"}, {"gene": "GSTP1", "stance": "supports"}], "rationale": "The cluster has a clear cholangiocyte/ductal epithelial signature, including KRT7, KRT8, KRT18, ANXA4, TM4SF4, DEFB1, CD24, LGALS4, SLPI, and SPP1. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'cholangiocyte' is not the name of CL:0000646 ('basal cell'). 'cholangiocyte' is the name of CL:1000488 (cholangiocyte)."], "seconds": 39.1}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-4163a3b864"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'plasma cell' is not the name of CL:0000988 ('hematopoietic 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:0000988", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "The cluster shows a strong antibody-secreting plasma-cell program: nearly ubiquitous MZB1, JCHAIN, FKBP11, XBP1, DERL3, and abundant immunoglobulin transcripts. The mixture of IgM, IgG, and IgA isotypes is compatible with a plasma-cell population rather than indicating a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 29.7}, {"answer": {"cell_type_id": "CL:0000786", "cell_type_label": "plasma cell", "decision": "annotate", "markers": [{"gene": "JCHAIN", "stance": "supports"}, {"gene": "MZB1", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "DERL3", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "IGHM", "stance": "supports"}, {"gene": "IGHG1", "stance": "supports"}, {"gene": "IGHA1", "stance": "supports"}, {"gene": "IGKC", "stance": "supports"}], "rationale": "The cluster has a strong antibody-secreting plasma-cell program, with abundant immunoglobulin transcripts and highly prevalent MZB1, JCHAIN, FKBP11, XBP1, DERL3, and SEC11C. Multiple immunoglobulin isotypes are compatible with plasma-cell heterogeneity and do not indicate a distinct cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'plasma cell' is not the name of CL:0000988 ('hematopoietic cell'). 'plasma cell' is the name of CL:0000786 (plasma cell)."], "seconds": 31.5}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-41fb1f6e39"} +{"attempts": [{"codes": ["BEV017"], "evidence": 11, "findings": [{"message": "The label 'liver sinusoidal endothelial cell' is not the name of CL:0002145 ('multiciliated columnar cell of tracheobronchial tree'). 'liver sinusoidal endothelial cell' is the name of CL:1000398 (endothelial cell of hepatic sinusoid).", "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:0002145", "cell_type_label": "liver sinusoidal endothelial cell", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "PLAC8", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}], "rationale": "The cluster is best annotated as liver sinusoidal endothelial cells. Strong endothelial markers include PTPRB, ENG, RNASE1, RAMP3, and HSPG2, while hepatic vascular/sinusoidal-associated markers such as DNASE1L3, FCN3, INMT, and PLAC8 support a liver sinusoidal endothelial identity. TAGLN may reflect an activated or specialized vascular endothelial state; the overall marker profile does not require a mixed-cell or doublet interpretation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 40.5}, {"answer": {"cell_type_id": "CL:1000398", "cell_type_label": "endothelial cell of hepatic sinusoid", "decision": "annotate", "markers": [{"gene": "DNASE1L3", "stance": "supports"}, {"gene": "RAMP3", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "INMT", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "ENG", "stance": "supports"}, {"gene": "PTPRB", "stance": "supports"}, {"gene": "FCN3", "stance": "supports"}, {"gene": "PLAC8", "stance": "supports"}, {"gene": "HSPG2", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}], "rationale": "The cluster is best annotated as an endothelial cell of the hepatic sinusoid. PTPRB, ENG, RNASE1, RAMP3, and HSPG2 support endothelial identity, while DNASE1L3, FCN3, INMT, and PLAC8 are characteristic of hepatic sinusoidal endothelial cells. TAGLN may indicate a specialized or activated vascular state, but no marker clearly requires a different cell type or doublet interpretation."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'liver sinusoidal endothelial cell' is not the name of CL:0002145 ('multiciliated columnar cell of tracheobronchial tree'). 'liver sinusoidal endothelial cell' is the name of CL:1000398 (endothelial cell of hepatic sinusoid)."], "seconds": 35.3}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-4d4de5c13f"} +{"attempts": [{"codes": [], "evidence": 16, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT1", "stance": "supports"}, {"gene": "DMKN", "stance": "supports"}, {"gene": "KRT10", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "KRTDAP", "stance": "supports"}, {"gene": "LY6D", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "LYPD3", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "DSP", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "SERPINB5", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "CLDN1", "stance": "supports"}], "rationale": "The cluster is a differentiated epidermal keratinocyte population, supported by near-universal KRT1 and KRT10 expression together with DMKN, KRTDAP, SFN, PERP, LGALS7B, SERPINB5, and epidermal junction/barrier genes. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 26.7}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-506f19166c"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'pancreatic delta cell' is not the name of CL:0002275 ('pancreatic PP cell'). 'pancreatic delta cell' is the name of CL:0000173 (pancreatic D 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:0002275", "cell_type_label": "pancreatic delta cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "ISL1", "stance": "supports"}, {"gene": "CASR", "stance": "supports"}, {"gene": "UCHL1", "stance": "supports"}, {"gene": "GABRG2", "stance": "supports"}], "rationale": "The cluster is best annotated as a pancreatic delta cell, supported by strong SST expression together with endocrine markers PCSK1 and ISL1, and delta-cell-associated genes HHEX, RBP4, CASR, and GABRG2. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.4}, {"answer": {"cell_type_id": "CL:0000173", "cell_type_label": "pancreatic D cell", "decision": "annotate", "markers": [{"gene": "SST", "stance": "supports"}, {"gene": "RBP4", "stance": "supports"}, {"gene": "PCSK1", "stance": "supports"}, {"gene": "HHEX", "stance": "supports"}, {"gene": "ISL1", "stance": "supports"}, {"gene": "CASR", "stance": "supports"}, {"gene": "GABRG2", "stance": "supports"}], "rationale": "Near-universal SST expression identifies a pancreatic delta/D cell, with endocrine markers PCSK1 and ISL1 and supporting delta-cell-associated markers HHEX, RBP4, CASR, and GABRG2. No marker clearly indicates a separate cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic delta cell' is not the name of CL:0002275 ('pancreatic PP cell'). 'pancreatic delta cell' is the name of CL:0000173 (pancreatic D cell)."], "seconds": 29.3}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-50ec79996f"} +{"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": "TRDV2", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD3D", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "ZNF683", "stance": "supports"}, {"gene": "CXCR3", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}], "rationale": "The cluster is a gamma-delta T-cell population, strongly supported by TRDV2 together with the T-cell receptor genes CD3D/CD3E. GZMK, CD8A, CXCR3, XCL1 and ZNF683 indicate an activated, cytotoxic/ tissue-associated gamma-delta T-cell state."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.6}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-52a80b5c6b"} +{"attempts": [{"codes": ["BEV017"], "evidence": 4, "findings": [{"message": "The label 'kidney collecting duct principal cell' is not the name of CL:0002349 ('CD27-high, CD11b-low natural killer cell, mouse'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 4, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002349", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "FXYD4", "stance": "supports"}, {"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}], "rationale": "Strong AQP2, AQP3, and FXYD4 expression is characteristic of collecting duct principal cells. CDH16 supports renal tubular epithelial identity; the additional epithelial/stress markers do not clearly indicate a distinct cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.5}, {"answer": {"cell_type_id": "CL:1001431", "cell_type_label": "kidney collecting duct principal cell", "decision": "annotate", "markers": [{"gene": "FXYD4", "stance": "supports"}, {"gene": "AQP2", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "CDH16", "stance": "supports"}], "rationale": "The strong combination of FXYD4, AQP2, and AQP3 is characteristic of kidney collecting duct principal cells. CDH16 further supports renal tubular epithelial identity; the other epithelial markers do not clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney collecting duct principal cell' is not the name of CL:0002349 ('CD27-high, CD11b-low natural killer cell, mouse'). 'kidney collecting duct principal cell' is the name of CL:1001431 (kidney collecting duct principal cell)."], "seconds": 29.3}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-54741cc370"} +{"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": "DERL3", "stance": "supports"}, {"gene": "FKBP11", "stance": "supports"}, {"gene": "XBP1", "stance": "supports"}, {"gene": "TNFRSF17", "stance": "supports"}, {"gene": "SEC11C", "stance": "supports"}, {"gene": "DNAJB9", "stance": "supports"}, {"gene": "CD79A", "stance": "supports"}], "rationale": "The cluster shows a strong antibody-secreting plasma-cell program: JCHAIN, MZB1, DERL3, FKBP11, XBP1, TNFRSF17, SEC11C, and DNAJB9, together with near-universal expression of immunoglobulin-related genes. No markers clearly indicate a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.3}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-560d5829d2"} +{"attempts": [{"codes": [], "evidence": 19, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000312", "cell_type_label": "keratinocyte", "decision": "annotate", "markers": [{"gene": "KRT14", "stance": "supports"}, {"gene": "S100A2", "stance": "supports"}, {"gene": "KRT5", "stance": "supports"}, {"gene": "SFN", "stance": "supports"}, {"gene": "DST", "stance": "supports"}, {"gene": "MIR205HG", "stance": "supports"}, {"gene": "SERPINB2", "stance": "supports"}, {"gene": "PERP", "stance": "supports"}, {"gene": "AQP3", "stance": "supports"}, {"gene": "S100A14", "stance": "supports"}, {"gene": "TACSTD2", "stance": "supports"}, {"gene": "LGALS7B", "stance": "supports"}, {"gene": "ERRFI1", "stance": "supports"}, {"gene": "SERPINB5", "stance": "supports"}, {"gene": "AREG", "stance": "supports"}, {"gene": "RND3", "stance": "supports"}, {"gene": "FGFBP1", "stance": "supports"}, {"gene": "CCL27", "stance": "supports"}, {"gene": "KRT15", "stance": "supports"}], "rationale": "The cluster is a basal-like epidermal keratinocyte population, strongly supported by the KRT5/KRT14 program together with S100A2, SFN, MIR205HG, SERPINB5, KRT15, TACSTD2, and related epithelial keratinocyte markers. No marker clearly indicates a distinct contaminating cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.6}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-5633d2ce11"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'kidney intercalated cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:0005010 (renal intercalated cell); CL:1000500 (kidney interstitial cell); CL:1000606 (kidney nerve 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:0002306", "cell_type_label": "kidney intercalated cell", "decision": "annotate", "markers": [{"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}], "rationale": "The cluster is a kidney intercalated-cell population, likely enriched for beta-intercalated features. The combination of vacuolar H+-ATPase genes (ATP6V1B1, ATP6V1G3, ATP6V0D2), SLC26A4, CA12, and TMEM213 strongly supports intercalated-cell identity; WFDC2 and KRT7 are also characteristic of this distal nephron/collecting-duct epithelial population. No clear contradictory markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 47.7}, {"answer": {"cell_type_id": "CL:0005010", "cell_type_label": "renal intercalated cell", "decision": "annotate", "markers": [{"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "SLC26A4", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "WFDC2", "stance": "supports"}, {"gene": "KRT7", "stance": "supports"}], "rationale": "The cluster is a renal intercalated-cell population. ATP6V1B1, ATP6V1G3, ATP6V0D2, SLC26A4, CA12, and TMEM213 strongly support intercalated-cell identity, with epithelial markers WFDC2 and KRT7 consistent with a collecting-duct/distal nephron epithelial population. No clear contradictory markers are present."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney intercalated cell' is not the name of CL:0002306 ('epithelial cell of proximal tubule'). Closest names: CL:0005010 (renal intercalated cell); CL:1000500 (kidney interstitial cell); CL:1000606 (kidney nerve cell)."], "seconds": 32.9}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-6807a1005a"} +{"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": "TYROBP", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "C1QA", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "CST3", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "S100A8", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}], "rationale": "The cluster shows a strong myeloid/macrophage program (TYROBP, LYZ, AIF1, FCER1G, LST1, CST3) with macrophage-associated C1QA and antigen-presentation genes HLA-DRA, CD74, and CTSS. High S100A8/S100A9 suggests an inflammatory state, but does not by itself establish a separate cell type or a doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 56.4}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-6846a2fbd5"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'naive T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-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:0000900", "cell_type_label": "naive T cell", "decision": "annotate", "markers": [{"gene": "CD8B", "stance": "supports"}, {"gene": "CD8A", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster is a naive, lymphoid-homing CD8 T-cell population. CD8A/CD8B indicate CD8 lineage, while CCR7, SELL, LEF1, TCF7, IL7R, and CD27 support a naive or central-memory-like state rather than effector or cytotoxic differentiation. No markers clearly contradict this annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 41.0}, {"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": "LEF1", "stance": "supports"}, {"gene": "TCF7", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "CD8A and CD8B support CD8 T-cell identity, while CCR7, SELL, LEF1, TCF7, IL7R, and CD27 indicate a naive lymphoid-homing state. The markers do not clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'naive T cell' is not the name of CL:0000900 ('naive thymus-derived CD8-positive, alpha-beta T cell'). 'naive T cell' is the name of CL:0000898 (naive T cell)."], "seconds": 38.6}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-6b9f55ce2e"} +{"attempts": [{"codes": [], "evidence": 10, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "AHSP", "stance": "supports"}, {"gene": "CA1", "stance": "supports"}, {"gene": "SLC4A1", "stance": "supports"}, {"gene": "ALAS2", "stance": "supports"}, {"gene": "GYPA", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}], "rationale": "The cluster shows a coherent erythroid/erythrocyte program: highly abundant globins (HBB, HBA1, HBA2, HBD), erythroid heme synthesis and maturation markers (AHSP, ALAS2, SLC25A37, HBM), and erythrocyte membrane/anion-exchange genes (SLC4A1, GYPA, GYPC)."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.5}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-73d8984fbc"} +{"attempts": [{"codes": [], "evidence": 13, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000057", "cell_type_label": "fibroblast", "decision": "annotate", "markers": [{"gene": "COL1A1", "stance": "supports"}, {"gene": "COL3A1", "stance": "supports"}, {"gene": "COL1A2", "stance": "supports"}, {"gene": "COL6A1", "stance": "supports"}, {"gene": "COL6A3", "stance": "supports"}, {"gene": "COL4A2", "stance": "supports"}, {"gene": "COL5A1", "stance": "supports"}, {"gene": "COL5A2", "stance": "supports"}, {"gene": "COL15A1", "stance": "supports"}, {"gene": "SPARC", "stance": "supports"}, {"gene": "FN1", "stance": "supports"}, {"gene": "SFRP2", "stance": "supports"}, {"gene": "CYGB", "stance": "supports"}], "rationale": "The strong, coherent extracellular-matrix program—COL1A1/COL1A2, COL3A1, COL5A1/COL5A2, COL6A1/COL6A3, SPARC, FN1, COL15A1 and SFRP2—is characteristic of pancreatic fibroblasts/stellate cells. No clear competing lineage marker is present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.4}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-75516baf75"} +{"attempts": [{"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'thick ascending limb cell' is not the name of CL:0002205 ('brush cell of lobular bronchiole'). Closest names: CL:1001131 (vasa recta ascending limb cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV016"], "evidence": 7, "findings": [{"message": "CL:1001130 is not in the pinned CL release (releases/2026-06-08).", "rule_id": "BEV016", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": ["BEV017"], "evidence": 7, "findings": [{"message": "The label 'kidney loop of Henle thick ascending limb epithelial cell' is not the name of CL:1001107 ('kidney loop of Henle thin ascending limb epithelial cell'). 'kidney loop of Henle thick ascending limb epithelial cell' is the name of CL:1001106 (kidney loop of Henle thick ascending limb epithelial cell).", "rule_id": "BEV017", "where": "object label"}], "status": "rejected", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002205", "cell_type_label": "thick ascending limb cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}], "rationale": "The strong combination of UMOD and SLC12A1, with KNG1 and CA12, is characteristic of kidney thick ascending limb epithelial cells. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 23.8}, {"answer": {"cell_type_id": "CL:1001130", "cell_type_label": "kidney thick ascending limb cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}], "rationale": "UMOD and SLC12A1 are highly characteristic markers of kidney thick ascending limb epithelial cells. KNG1, CA12, ATP1A1, ATP1B1, and DEFB1 provide additional support for this nephron segment. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'thick ascending limb cell' is not the name of CL:0002205 ('brush cell of lobular bronchiole'). Closest names: CL:1001131 (vasa recta ascending limb cell)."], "seconds": 35.7}, {"answer": {"cell_type_id": "CL:1001107", "cell_type_label": "kidney loop of Henle thick ascending limb epithelial cell", "decision": "annotate", "markers": [{"gene": "UMOD", "stance": "supports"}, {"gene": "SLC12A1", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}, {"gene": "DEFB1", "stance": "supports"}], "rationale": "UMOD and SLC12A1 are highly characteristic of thick ascending limb epithelial cells, with KNG1, CA12, ATP1A1, ATP1B1, and DEFB1 providing additional epithelial nephron-segment support. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:1001130 is not in the pinned CL release (releases/2026-06-08)."], "seconds": 37.4}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-7954bd765f"} +{"attempts": [{"codes": [], "evidence": 8, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000232", "cell_type_label": "erythrocyte", "decision": "annotate", "markers": [{"gene": "HBB", "stance": "supports"}, {"gene": "HBA1", "stance": "supports"}, {"gene": "HBA2", "stance": "supports"}, {"gene": "HBD", "stance": "supports"}, {"gene": "HBM", "stance": "supports"}, {"gene": "GYPC", "stance": "supports"}, {"gene": "SLC25A37", "stance": "supports"}, {"gene": "SLC25A39", "stance": "supports"}], "rationale": "The cluster is strongly defined by erythroid hemoglobin genes (HBB, HBA1, HBA2, HBD, HBM), with erythrocyte-associated GYPC and heme/mitochondrial iron transport genes SLC25A37 and SLC25A39. No markers clearly indicate a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 28.1}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-838e09fefd"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "ACTA2", "stance": "supports"}, {"gene": "TAGLN", "stance": "supports"}, {"gene": "MYL9", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "RGS5", "stance": "supports"}], "rationale": "The combination of RGS5, ACTA2, TAGLN, MYL9, CALD1, TPM2, and C11orf96 indicates a contractile mural-cell population, with RGS5 being particularly characteristic of pericytes. The ACTA2/MYH11 program reflects contractile pericyte differentiation rather than requiring a separate smooth-muscle annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 48.0}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-884f62d6f1"} +{"attempts": [{"codes": ["BEV017"], "evidence": 10, "findings": [{"message": "The label 'kidney alpha-intercalated cell' is not the name of CL:0005013 ('single ciliated epithelial cell'). Closest names: CL:0005011 (renal alpha-intercalated cell); CL:0005010 (renal intercalated cell); CL:4030015 (kidney collecting duct alpha-intercalated 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:0005013", "cell_type_label": "kidney alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ADGRF5", "stance": "supports"}], "rationale": "The strong combination of SLC4A1, ATP6V1B1, ATP6V1G3, ATP6V0D2, SLC26A7, RHCG, CA12, and TMEM213 is characteristic of renal acid-secreting alpha-intercalated cells. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 39.4}, {"answer": {"cell_type_id": "CL:0005011", "cell_type_label": "renal alpha-intercalated cell", "decision": "annotate", "markers": [{"gene": "SLC4A1", "stance": "supports"}, {"gene": "ATP6V1B1", "stance": "supports"}, {"gene": "ATP6V1G3", "stance": "supports"}, {"gene": "ATP6V0D2", "stance": "supports"}, {"gene": "SLC26A7", "stance": "supports"}, {"gene": "RHCG", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "TMEM213", "stance": "supports"}, {"gene": "ATP6V0B", "stance": "supports"}, {"gene": "ATP6AP2", "stance": "supports"}, {"gene": "ADGRF5", "stance": "supports"}], "rationale": "The coordinated expression of SLC4A1, ATP6V1B1, ATP6V1G3, ATP6V0D2, SLC26A7, RHCG, CA12, and TMEM213 is characteristic of renal alpha-intercalated cells. No marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney alpha-intercalated cell' is not the name of CL:0005013 ('single ciliated epithelial cell'). Closest names: CL:0005011 (renal alpha-intercalated cell); CL:0005010 (renal intercalated cell); CL:4030015 (kidney collecting duct alpha-intercalated cell)."], "seconds": 42.3}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-90023ca6ff"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000160", "cell_type_label": "goblet cell", "decision": "annotate", "markers": [{"gene": "TFF3", "stance": "supports"}, {"gene": "SPINK4", "stance": "supports"}, {"gene": "CLCA1", "stance": "supports"}, {"gene": "MUC2", "stance": "supports"}, {"gene": "REG4", "stance": "supports"}, {"gene": "ITLN1", "stance": "supports"}, {"gene": "AGR2", "stance": "supports"}, {"gene": "ZG16", "stance": "supports"}, {"gene": "ST6GALNAC1", "stance": "supports"}], "rationale": "The cluster is a goblet-cell population. Uniform expression of MUC2, CLCA1, TFF3, SPINK4, AGR2, REG4 and ITLN1 supports intestinal mucin production, secretory differentiation, and goblet-cell identity. No markers clearly indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 49.5}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-9ce2902282"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'pancreatic PP cell' is not the name of CL:0002278 ('GIP cell'). 'pancreatic PP cell' is the name of CL:0002275 (pancreatic PP 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:0002278", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "PAX6", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PAM", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "SERTM1", "stance": "supports"}, {"gene": "GAD2", "stance": "supports"}], "rationale": "The defining marker is PPY, expressed in every cell, together with pancreatic endocrine/neuroendocrine markers PAX6, PCSK2, SCG2, CHGB, PAM, and NEUROD1. SERTM1 and GAD2 further support a pancreatic PP/gamma endocrine identity. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 42.3}, {"answer": {"cell_type_id": "CL:0002275", "cell_type_label": "pancreatic PP cell", "decision": "annotate", "markers": [{"gene": "PPY", "stance": "supports"}, {"gene": "PAX6", "stance": "supports"}, {"gene": "PCSK2", "stance": "supports"}, {"gene": "SCG2", "stance": "supports"}, {"gene": "CHGB", "stance": "supports"}, {"gene": "PAM", "stance": "supports"}, {"gene": "NEUROD1", "stance": "supports"}, {"gene": "SERTM1", "stance": "supports"}], "rationale": "PPY is the defining marker and is expressed in all cluster cells. The accompanying endocrine/neuroendocrine markers PAX6, PCSK2, SCG2, CHGB, PAM, NEUROD1, and SERTM1 support a pancreatic PP (gamma) cell identity. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'pancreatic PP cell' is not the name of CL:0002278 ('GIP cell'). 'pancreatic PP cell' is the name of CL:0002275 (pancreatic PP cell)."], "seconds": 29.0}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-a26635e6cd"} +{"attempts": [{"codes": [], "evidence": 11, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000576", "cell_type_label": "monocyte", "decision": "annotate", "markers": [{"gene": "TYROBP", "stance": "supports"}, {"gene": "IL1B", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "LST1", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "S100A9", "stance": "supports"}, {"gene": "CXCL8", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "BCL2A1", "stance": "supports"}], "rationale": "The cluster shows a coherent inflammatory monocyte program: TYROBP, FCER1G, LST1, AIF1, LYZ and CTSS indicate mononuclear phagocytes, while IL1B, S100A9, CXCL8, CCL3 and BCL2A1 support an activated/inflammatory state. No markers clearly indicate a different cell type or a mixed doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 44.6}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-b2d44d2eda"} +{"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": "KLRB1", "stance": "supports"}, {"gene": "IL2RB", "stance": "supports"}, {"gene": "NKG7", "stance": "supports"}, {"gene": "GZMK", "stance": "supports"}, {"gene": "CCL3", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "XCL1", "stance": "supports"}, {"gene": "XCL2", "stance": "supports"}, {"gene": "KLRC1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "TRDC provides strong evidence for a gamma-delta T-cell identity. The cytotoxic and NK-like program (NKG7, GZMA, GZMK, CCL3/CCL4, CCL5, XCL1/XCL2, KLRC1, TYROBP) is consistent with an activated cytotoxic gamma-delta T-cell subset."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 43.7}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-bb928b569a"} +{"attempts": [{"codes": ["BEV016"], "evidence": 15, "findings": [{"message": "CL:0002739 is not in the pinned CL release (releases/2026-06-08). 'Kupffer cell' is the name of CL:0000091 (Kupffer cell).", "rule_id": "BEV016", "where": "object id"}], "status": "rejected", "to_expert": false}, {"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002739", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "CTSS", "stance": "supports"}, {"gene": "AIF1", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "NPC2", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}], "rationale": "The combination of C1QA/B/C, CD163, MARCO, SLC40A1, MS4A6A/MS4A7, FCER1G and TYROBP strongly supports a resident hepatic macrophage (Kupffer cell) identity. HLA-DRA and CD74 indicate antigen presentation, consistent with Kupffer cells. No markers clearly indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 52.9}, {"answer": {"cell_type_id": "CL:0000091", "cell_type_label": "Kupffer cell", "decision": "annotate", "markers": [{"gene": "C1QA", "stance": "supports"}, {"gene": "C1QB", "stance": "supports"}, {"gene": "C1QC", "stance": "supports"}, {"gene": "CD163", "stance": "supports"}, {"gene": "MARCO", "stance": "supports"}, {"gene": "SLC40A1", "stance": "supports"}, {"gene": "MS4A6A", "stance": "supports"}, {"gene": "MS4A7", "stance": "supports"}, {"gene": "FCER1G", "stance": "supports"}, {"gene": "TYROBP", "stance": "supports"}, {"gene": "HLA-DRA", "stance": "supports"}, {"gene": "CD74", "stance": "supports"}], "rationale": "The strong C1QA/C1QB/C1QC, CD163, MARCO, and SLC40A1 signal supports a resident hepatic macrophage identity, i.e. Kupffer cell. MS4A6A, MS4A7, FCER1G, TYROBP, HLA-DRA, and CD74 further support macrophage and antigen-presenting functions. No markers clearly indicate a distinct contaminating cell type."}, "cli_tools": [], "error": null, "feedback": ["object id: CL:0002739 is not in the pinned CL release (releases/2026-06-08). 'Kupffer cell' is the name of CL:0000091 (Kupffer cell)."], "seconds": 35.5}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-c12bd3b011"} +{"attempts": [{"codes": ["BEV017"], "evidence": 8, "findings": [{"message": "The label 'kidney distal convoluted tubule epithelial cell' is not the name of CL:0002308 ('epithelial cell of skin gland'). 'kidney distal convoluted tubule epithelial cell' is the name of CL:1000849 (kidney distal convoluted tubule epithelial 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:0002308", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "SLC12A3", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}], "rationale": "The strong SLC12A3 and WNK1 expression is characteristic of distal convoluted tubule cells, with CA12, DEFB1, TMEM52B, KNG1, and Na+/K+-ATPase genes providing additional renal tubular support. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 46.8}, {"answer": {"cell_type_id": "CL:1000849", "cell_type_label": "kidney distal convoluted tubule epithelial cell", "decision": "annotate", "markers": [{"gene": "DEFB1", "stance": "supports"}, {"gene": "SLC12A3", "stance": "supports"}, {"gene": "TMEM52B", "stance": "supports"}, {"gene": "KNG1", "stance": "supports"}, {"gene": "WNK1", "stance": "supports"}, {"gene": "CA12", "stance": "supports"}, {"gene": "ATP1A1", "stance": "supports"}, {"gene": "ATP1B1", "stance": "supports"}], "rationale": "SLC12A3 is a defining marker of distal convoluted tubule cells, supported by WNK1, CA12, DEFB1, TMEM52B, KNG1, and Na+/K+-ATPase genes. The correct Cell Ontology term is CL:1000849."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'kidney distal convoluted tubule epithelial cell' is not the name of CL:0002308 ('epithelial cell of skin gland'). 'kidney distal convoluted tubule epithelial cell' is the name of CL:1000849 (kidney distal convoluted tubule epithelial cell)."], "seconds": 26.8}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-c7858eb46a"} +{"attempts": [{"codes": [], "evidence": 12, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0002138", "cell_type_label": "lymphatic endothelial cell", "decision": "annotate", "markers": [{"gene": "CCL21", "stance": "supports"}, {"gene": "CLDN5", "stance": "supports"}, {"gene": "MMRN1", "stance": "supports"}, {"gene": "PROX1", "stance": "supports"}, {"gene": "LYVE1", "stance": "supports"}, {"gene": "CAVIN2", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "ECSCR", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "TFPI", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "FABP4", "stance": "supports"}], "rationale": "The combination of endothelial markers (CLDN5, GNG11, TFPI, ECSCR, RAMP2, TM4SF1) with lymphatic endothelial markers (CCL21, PROX1, LYVE1, MMRN1, CAVIN2) identifies a lymphatic endothelial cell population. No markers clearly indicate a competing cell type or doublet."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 25.2}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-cc1cfcedd3"} +{"attempts": [{"codes": [], "evidence": 7, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000669", "cell_type_label": "pericyte", "decision": "annotate", "markers": [{"gene": "RGS5", "stance": "supports"}, {"gene": "C11orf96", "stance": "supports"}, {"gene": "TM4SF1", "stance": "supports"}, {"gene": "IGFBP7", "stance": "supports"}, {"gene": "APOLD1", "stance": "supports"}, {"gene": "CCL2", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}], "rationale": "The combination of strong RGS5, C11orf96, TM4SF1, APOLD1, IGFBP5 and IGFBP7 expression is characteristic of kidney pericytes. CCL2 suggests an activated or inflammatory pericyte state; no marker clearly indicates a distinct competing cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 34.8}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-d9bc81cfff"} +{"attempts": [{"codes": ["BEV017"], "evidence": 9, "findings": [{"message": "The label 'BEST4+ enterocyte' is not the name of CL:0002075 ('brush cell of tracheobronchial tree'). 'BEST4+ enterocyte' is the name of CL:4030026 (BEST4+ enterocyte).", "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:0002075", "cell_type_label": "BEST4+ enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}, {"gene": "KRT20", "stance": "supports"}], "rationale": "The combination of BEST4, GUCA2A/B, CA7, CFTR, SPIB, and CPA2 is characteristic of BEST4+ absorptive enterocytes in the small intestine. LYZ is also commonly expressed in this enterocyte subtype. CL:0002075 is the Cell Ontology term for enterocyte; BEST4+ enterocyte is the more specific biological annotation."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.8}, {"answer": {"cell_type_id": "CL:4030026", "cell_type_label": "BEST4+ enterocyte", "decision": "annotate", "markers": [{"gene": "BEST4", "stance": "supports"}, {"gene": "GUCA2A", "stance": "supports"}, {"gene": "GUCA2B", "stance": "supports"}, {"gene": "CA7", "stance": "supports"}, {"gene": "CFTR", "stance": "supports"}, {"gene": "SPIB", "stance": "supports"}, {"gene": "CPA2", "stance": "supports"}, {"gene": "LYZ", "stance": "supports"}], "rationale": "BEST4, GUCA2A/B, CA7, CFTR, SPIB, and CPA2 form a characteristic BEST4+ enterocyte marker combination in the human small intestine. LYZ is also compatible with this absorptive enterocyte subtype. The correct Cell Ontology term is CL:4030026, BEST4+ enterocyte."}, "cli_tools": [], "error": null, "feedback": ["object label: The label 'BEST4+ enterocyte' is not the name of CL:0002075 ('brush cell of tracheobronchial tree'). 'BEST4+ enterocyte' is the name of CL:4030026 (BEST4+ enterocyte)."], "seconds": 24.6}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-daa29fa7c3"} +{"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": "GZMB", "stance": "supports"}, {"gene": "CCL5", "stance": "supports"}, {"gene": "CCL4", "stance": "supports"}, {"gene": "CST7", "stance": "supports"}, {"gene": "FGFBP2", "stance": "supports"}, {"gene": "KLRD1", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "GZMA", "stance": "supports"}], "rationale": "The cluster shows a strong mature cytotoxic NK-cell program: GNLY, NKG7, GZMB, FGFBP2, KLRD1, CST7, CCL5, and CCL4 are highly enriched and broadly expressed within the cluster. No markers clearly indicate a different cell type or a mixed/doublet population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.7}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-def3067099"} +{"attempts": [{"codes": [], "evidence": 6, "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": "CXCR4", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD52", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "SRGN", "stance": "supports"}], "rationale": "IL7R and CXCR4, together with CD2, CD52, PTPRC, and SRGN, support a CD4-positive alpha-beta T-cell identity. No listed marker clearly indicates a conflicting cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 59.2}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-e0c7aa5d8b"} +{"attempts": [{"codes": [], "evidence": 9, "findings": [], "status": "admitted", "to_expert": false}], "calls": [{"answer": {"cell_type_id": "CL:0000115", "cell_type_label": "endothelial cell", "decision": "annotate", "markers": [{"gene": "EMCN", "stance": "supports"}, {"gene": "PLAT", "stance": "supports"}, {"gene": "GNG11", "stance": "supports"}, {"gene": "PLPP3", "stance": "supports"}, {"gene": "RAMP2", "stance": "supports"}, {"gene": "RNASE1", "stance": "supports"}, {"gene": "MGP", "stance": "supports"}, {"gene": "IGFBP5", "stance": "supports"}, {"gene": "SOST", "stance": "supports"}], "rationale": "The cluster shows a strong endothelial transcriptional program: EMCN, PLAT, GNG11, PLPP3, RAMP2, RNASE1, MGP, and IGFBP5. SOST and CRHBP are consistent with a specialized kidney endothelial subtype. CD74 and HLA-DRB1 likely indicate endothelial MHC-II expression or activation rather than a separate immune cell population."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 45.4}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-e6fd6bbd15"} +{"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": "CD52", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "PTPRCAP", "stance": "supports"}, {"gene": "PTPRC", "stance": "supports"}, {"gene": "CD69", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "HCST", "stance": "supports"}, {"gene": "S100A4", "stance": "supports"}, {"gene": "CXCR4", "stance": "supports"}], "rationale": "The cluster shows a coherent T-cell program, including CD3D, PTPRC, PTPRCAP, CD52, IL32, LTB, and HCST. CD69 and CXCR4 suggest activation or tissue-associated state, but the markers do not robustly distinguish CD4, CD8, or another specific T-cell subtype. No clear contradictory lineage markers are present."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 30.9}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-e76b10ee43"} +{"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": "CTLA4", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "TRAC", "stance": "supports"}, {"gene": "CD2", "stance": "supports"}, {"gene": "CD5", "stance": "supports"}, {"gene": "IL32", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}, {"gene": "TNFRSF1B", "stance": "supports"}], "rationale": "The cluster is clearly a T-cell population (CD3E, TRAC, CD2, CD5) with strong regulatory T-cell markers FOXP3 and CTLA4, together with CD27 and TNFRSF1B. No marker clearly indicates a different cell type."}, "cli_tools": [], "error": null, "feedback": [], "seconds": 35.2}], "model": "gpt-luna", "protocol": 2, "task_id": "ct-f3161764a6"} +{"attempts": [{"codes": [], "evidence": 11, "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": "TCF7", "stance": "supports"}, {"gene": "LEF1", "stance": "supports"}, {"gene": "SELL", "stance": "supports"}, {"gene": "IL7R", "stance": "supports"}, {"gene": "CCR7", "stance": "supports"}, {"gene": "RGS10", "stance": "supports"}, {"gene": "LRRN3", "stance": "supports"}, {"gene": "CD3E", "stance": "supports"}, {"gene": "CD27", "stance": "supports"}, {"gene": "CD40LG", "stance": "supports"}, {"gene": "LTB", "stance": "supports"}], "rationale": "The cluster shows a coherent naive/central-memory CD4 T-cell program: TCF7, LEF1, CCR7, SELL, IL7R, LRRN3, CD27 and CD40LG, together with the pan-T-cell marker CD3E. 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b/evaluation/llm_benchmark/results/celltype-test/summary.md @@ -0,0 +1,31 @@ +# Single-cell cell-type annotation (test set, protocol 2) + +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) | 46/46 | 26/46 | 4/46 | 7/46 | 9/46 | 0/46 | 4/46 | 0/46 | +| Claude Opus 5.5 | Model + bioevidence gate (first answer) | 38/46 | 25/46 | 3/46 | 6/46 | 4/46 | 0/46 | 0/38 | 8/46 | +| Claude Opus 5.5 | Model + bioevidence feedback loop (last answer) | 42/46 | 27/46 | 3/46 | 7/46 | 5/46 | 0/46 | 0/42 | 4/46 | +| GPT-6-Astra | Model alone (first answer) | 46/46 | 24/46 | 6/46 | 6/46 | 10/46 | 0/46 | 1/46 | 0/46 | +| GPT-6-Astra | Model + bioevidence gate (first answer) | 44/46 | 24/46 | 6/46 | 6/46 | 8/46 | 0/46 | 0/44 | 2/46 | +| GPT-6-Astra | Model + bioevidence feedback loop (last answer) | 45/46 | 25/46 | 6/46 | 6/46 | 8/46 | 0/46 | 0/45 | 1/46 | +| Gemini 3.1 Pro | Model alone (first answer) | 46/46 | 20/46 | 9/46 | 3/46 | 14/46 | 0/46 | 10/46 | 0/46 | +| Gemini 3.1 Pro | Model + bioevidence gate (first answer) | 33/46 | 18/46 | 8/46 | 1/46 | 6/46 | 0/46 | 0/33 | 13/46 | +| Gemini 3.1 Pro | Model + bioevidence feedback loop (last answer) | 43/46 | 22/46 | 8/46 | 6/46 | 7/46 | 0/46 | 0/43 | 3/46 | +| Claude Haiku 4.5 | Model alone (first answer) | 46/46 | 13/46 | 3/46 | 2/46 | 27/46 | 1/46 | 23/46 | 0/46 | +| Claude Haiku 4.5 | Model + bioevidence gate (first answer) | 20/46 | 13/46 | 2/46 | 1/46 | 4/46 | 0/46 | 0/20 | 26/46 | +| Claude Haiku 4.5 | Model + bioevidence feedback loop (last answer) | 41/46 | 20/46 | 4/46 | 4/46 | 13/46 | 0/46 | 0/41 | 5/46 | +| GPT-5.6-Luna | Model alone (first answer) | 46/46 | 13/46 | 5/46 | 3/46 | 23/46 | 2/46 | 16/46 | 0/46 | +| GPT-5.6-Luna | Model + bioevidence gate (first answer) | 30/46 | 13/46 | 4/46 | 2/46 | 11/46 | 0/46 | 0/30 | 16/46 | +| GPT-5.6-Luna | Model + bioevidence feedback loop (last answer) | 44/46 | 19/46 | 6/46 | 6/46 | 13/46 | 0/46 | 0/44 | 2/46 | +| Gemini 3.8 Flash | Model alone (first answer) | 46/46 | 21/46 | 6/46 | 5/46 | 14/46 | 0/46 | 9/46 | 0/46 | +| Gemini 3.8 Flash | Model + bioevidence gate (first answer) | 33/46 | 20/46 | 4/46 | 5/46 | 4/46 | 0/46 | 0/33 | 13/46 | +| Gemini 3.8 Flash | Model + bioevidence feedback loop (last answer) | 40/46 | 25/46 | 4/46 | 7/46 | 4/46 | 0/46 | 0/40 | 6/46 | +| All models | Model alone (first answer) | 276/276 | 117/276 | 33/276 | 26/276 | 97/276 | 3/276 | 63/276 | 0/276 | +| All models | Model + bioevidence gate (first answer) | 198/276 | 113/276 | 27/276 | 21/276 | 37/276 | 0/276 | 0/198 | 78/276 | +| All models | Model + bioevidence feedback loop (last answer) | 255/276 | 138/276 | 31/276 | 36/276 | 50/276 | 0/276 | 0/255 | 21/276 | + +Errors in the models' first answers (all models): label mismatch 59/276, marker not in data 1/276, no markers 0/276, not a cell type 0/276, obsolete id 1/276, unapproved symbol 0/276, unknown id 2/276. + +276 episodes, 344 model calls (0 failed), 63 revised after feedback. Rule codes raised across all records: BEV004 21, BEV016 4, BEV017 65, BEV023 1. diff --git a/examples/singlecell_celltype/README.md b/examples/singlecell_celltype/README.md new file mode 100644 index 0000000..55cce4d --- /dev/null +++ b/examples/singlecell_celltype/README.md @@ -0,0 +1,67 @@ +# Real-source case: single-cell cell-type annotation + +The third real-data case, after ontology names (`vbo_canine`) and clinical genetics (`clinvar_germline`), +moves to data: a cluster of a single-cell RNA-seq dataset, the marker genes that characterise it, and the +Cell Ontology term an annotator gives it. It asks what bioevidence adds when a model annotates clusters: +which of the model's errors can be caught without knowing the answer, and which cannot. + +**Not a benchmark of cell-type annotation methods.** Author labels are the reference; they are themselves +judgments (see Limits). + +## Sources + +Six normal human datasets from [CZ CELLxGENE Discover](https://cellxgene.cziscience.com/) (CC BY 4.0), each +annotated by its authors with Cell Ontology terms: liver, kidney, adult duodenum, pancreas, skin, and the T, +NK and ILC compartment of a fetal lung atlas (a fine-grained immune subset). Reference releases: the Cell +Ontology (2026-06-08, full `cl.obo`, which keeps the disjointness axioms), the HGNC complete set +(2026-09-30) and the HuBMAP ASCT+B tables for liver, kidney, pancreas, skin and lung (CCF v2.0). See +[`sources/ATTRIBUTION.md`](sources/ATTRIBUTION.md). + +`prepare_source.py` derives, from files downloaded once and recorded with their SHA-256 in +`sources/manifest.json`: + +- **Marker tables.** Each author cell type with at least 30 cells is a "cluster". From raw counts + (normalised to 10,000 per cell, log1p), each gene gets `logfc` (mean inside minus mean outside the + cluster), `pct_in` and `pct_out`. The 50 genes with the highest positive `logfc` among those expressed in + at least a quarter of the cluster form its table, named by current HGNC symbols. One table per dataset. +- **Truth.** The authors' term for each cluster (`truth.jsonl`), never shown to a model. +- **Reference.** ASCT+B biomarker genes as `gene marker_of cell type` assertions (1,027). +- **Tasks.** 70 clusters, one task each, showing the tissue, the assay and the top 20 markers with their + statistics. Four per dataset (24) form the pilot split; the other 46 are held out. + +The derived tables, the two reference releases and the ASCT+B projection are committed as gzip-compressed +snapshots named by their SHA-256; the expression matrices are not. + +## Records and grounders + +An annotation is a record under [`profile.yaml`](profile.yaml): `cluster has_cell_type `, with one +`marker_gene` evidence item per cited gene, located as `cluster=c03;gene=CD8A` in the dataset's marker +table, in a supporting or contradicting evidence line. Five grounders check it, all generic: + +| Grounder | What it checks here | +|---|---| +| `TableGrounder` | Each cited marker is one of this cluster's markers in the pinned table (BEV016 otherwise, naming the closest genes). A marker counts as verified only then, and the profile requires a verified marker. | +| `OntologyGrounder` | The term exists (BEV016), is current (BEV023), is a cell type under CL:0000000 (BEV024) and matches its label (BEV017, naming the term the label belongs to). | +| `GeneGrounder` | Cited genes are approved HGNC symbols (aliases and previous symbols: BEV023, naming the approved one). | +| `ReferenceGrounder` | A supporting marker that ASCT+B lists only for cell types the Cell Ontology declares disjoint from the claimed one (e.g. a B cell marker for a T cell) sends the record to an expert (BEV025). Used in protocol 1 (the pilot) only: ASCT+B biomarker lists are not specificity statements, and the pilot showed its alarms to be mostly spurious. | +| `SourceBytesGrounder` | The marker table's bytes hash to the record's frozen hash. | + +The AI experiment is in [`evaluation/llm_benchmark/celltype_loop.py`](../../evaluation/llm_benchmark/celltype_loop.py), +with results in the [benchmark README](../../evaluation/llm_benchmark/README.md#scenario-3-single-cell-cell-type-annotation). + +On the 46 held-out clusters, six models working alone gave a Cell Ontology ID that does not match its label +in about one answer in five. Bioevidence admitted none of these errors. In its feedback loop: +- answers compatible with the authors' term rose from 176 to 205 of 276; +- 8% of the annotations went to a person. + +## Limits + +- Author labels are the reference, at the granularity each study chose ("myeloid leukocyte", "stem cell"). + Some are debatable from the markers alone (a duodenal "B cell" cluster led by JCHAIN and MZB1 looks like + plasma cells). Scoring is ontology-aware (exact, coarser, finer, wrong), not an expert judgment. +- The marker table holds the top 50 upregulated genes of each cluster. A claim that a gene is absent + cannot be checked against it, and is reported as not in the table. +- ASCT+B covers some organs and some cell types, and a gene it does not list is never reported. The + disjointness axioms of the Cell Ontology cover major lineages only (e.g. epithelial cell and leukocyte, + T cell and B cell lineage, lymphocyte and myeloid leukocyte), so a marker cited for the wrong type within + a lineage is not caught this way. diff --git a/examples/singlecell_celltype/prepare_source.py b/examples/singlecell_celltype/prepare_source.py new file mode 100644 index 0000000..3df2573 --- /dev/null +++ b/examples/singlecell_celltype/prepare_source.py @@ -0,0 +1,184 @@ +"""Build the pinned single-cell cell-type annotation case (run once, offline, from downloaded files). + + uv run --frozen --with anndata==0.11.4 python examples/singlecell_celltype/prepare_source.py --data DIR + +DIR holds what was downloaded beforehand (see README): `selected.json` (the CELLxGENE Discover metadata of the +six datasets), `h5ad/.h5ad`, `ref/cl.obo` (the full release: it keeps the disjointness axioms), `ref/hgnc_complete_set.txt`, `asctb/asct-b-vh-.csv`. +None of it is committed except as the derived, content-addressed snapshots below. + +1. Markers. For each dataset, each cell type its authors annotated (a Cell Ontology term, not "unknown", with + at least MIN_CELLS cells) is one "cluster". Raw counts are normalised to 10,000 per cell and log1p-transformed; for + each cluster and gene, `logfc` is the mean in the cluster minus the mean in all other cells, `pct_in` and + `pct_out` the fractions of cells with a non-zero count. Genes expressed in at least a quarter of the + cluster are ranked by `logfc`; the top TOP_GENES with a positive `logfc` form the cluster's marker table. + Genes are named by their current HGNC approved symbol, mapped from their Ensembl ID; genes without an + HGNC entry are left out. +2. Truth. The authors' term for each cluster, updated to its replacement when the pinned Cell Ontology release + has obsoleted it. It is kept apart from the tasks, which never show it. +3. Reference. HuBMAP ASCT+B biomarker genes, as `gene marker_of cell type` assertions: each row's most specific + 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. + +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`. +""" +from __future__ import annotations + +import argparse +import csv +import gzip +import hashlib +import io +import json +from pathlib import Path + +import anndata +import numpy as np +import scipy.sparse as sp + +from bioevidence_validator.identifiers import Genes, Ontology + +ROOT = Path(__file__).resolve().parent +SOURCES = ROOT / "sources" +KEY = "bioai-singlecell-celltype-v1" +MIN_CELLS, TOP_GENES, PROMPT_GENES, MIN_PCT, PILOT_PER_DATASET = 30, 50, 20, 0.25, 4 +ORGANS = {"liver": "liver", "kidney": "kidney", "pancreas": "pancreas", "skin": "skin", "lung_t_nk_ilc": "lung"} + + +def sha256(data: bytes) -> str: + return hashlib.sha256(data).hexdigest() + + +def pin(data: bytes, suffix: str) -> str: + """Write a gzip-compressed snapshot named by the SHA-256 of its uncompressed bytes.""" + digest = sha256(data) + (SOURCES / "snapshots").mkdir(parents=True, exist_ok=True) + (SOURCES / "snapshots" / f"{digest}.{suffix}.gz").write_bytes(gzip.compress(data, mtime=0)) + return digest + + +def tsv(columns: list[str], rows: list[dict]) -> bytes: + out = io.StringIO() + writer = csv.DictWriter(out, columns, delimiter="\t", lineterminator="\n") + writer.writeheader() + writer.writerows(rows) + return out.getvalue().encode() + + +def markers(path: Path, genes: Genes, ontology: Ontology) -> tuple[list[dict], list[dict]]: + """(marker rows, clusters) 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 + matrix = sp.csr_matrix(counts, dtype=np.float64) + ensembl = {row.get("ensembl_gene_id"): symbol for symbol, row in + ((r["symbol"], r) for r in genes.by_id.values()) if row.get("ensembl_gene_id")} + keep, symbols = [], [] + for column, gene_id in enumerate(var.index): + symbol = ensembl.get(str(gene_id).split(".")[0]) + if symbol and symbol not in symbols: + keep.append(column) + symbols.append(symbol) + matrix = matrix[:, keep] + size = np.asarray(matrix.sum(axis=1)).ravel() + normalised = sp.diags(1e4 / np.where(size > 0, size, 1)) @ matrix + normalised.data = np.log1p(normalised.data) + expressed = (matrix > 0).astype(np.float64) + terms = data.obs["cell_type_ontology_term_id"].astype(str).to_numpy() + 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 = [], [] + 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 + inside = mask.sum() + mean_in = np.asarray(normalised[mask].sum(axis=0)).ravel() / inside + mean_out = (total - mean_in * inside) / (cells - inside) + pct_in = np.asarray(expressed[mask].sum(axis=0)).ravel() / inside + pct_out = (total_expressed - pct_in * inside) / (cells - inside) + logfc = mean_in - mean_out + 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}" + 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, "" + if term in ontology.terms and ontology.terms[term].obsolete: + replacement = ontology.terms[term].replaced_by + truth, note = (replacement[0], f"obsolete {term} replaced") if replacement else (term, "obsolete, no replacement") + 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 + + +def asctb(directory: Path, genes: Genes) -> list[dict]: + """gene marker_of cell type, from the ASCT+B biomarker gene columns.""" + found = {} + for organ in sorted(set(ORGANS.values())): + lines = (directory / f"asct-b-vh-{organ}.csv").read_text(encoding="utf-8-sig").splitlines() + start = next(i for i, line in enumerate(lines) if line.startswith("AS/1,")) + for row in csv.DictReader(lines[start:]): + cell_types = [(row[k], row.get(k.replace("/ID", "/LABEL")) or row.get(k.replace("/ID", "")) or "") + for k in row if k and k.startswith("CT/") and k.endswith("/ID") and (row[k] or "").startswith("CL:")] + if not cell_types: + continue + cell_type, label = cell_types[-1] + for key in (k for k in row if k and k.startswith("BGene/") and k.endswith("/ID")): + gene = genes.by_id.get((row[key] or "").strip()) + if gene: + found[(gene["symbol"], cell_type)] = {"subject": gene["symbol"], "predicate": "marker_of", + "object": cell_type, "object_label": label.strip(), + "organ": organ} + return [found[k] for k in sorted(found)] + + +def main(argv: list[str] | None = None) -> int: + parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("--data", type=Path, required=True) + args = parser.parse_args(argv) + 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) + 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")}, + "hgnc": {"file": "hgnc_complete_set.txt", "retrieved": "2026-09-30", "sha256": pin(hgnc_bytes, "tsv")}, + "datasets": []} + reference = asctb(data / "asctb", genes) + 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) + table = pin(tsv(["cluster", "gene", "rank", "logfc", "pct_in", "pct_out"], 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)}) + 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", + "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, + "markers": [{k: r[k] for k in ("gene", "logfc", "pct_in", "pct_out")} for r in top]}) + truth.append({"task_id": task_id, "dataset": meta["name"], **c}) + for name, rows in (("tasks.jsonl", tasks), ("truth.jsonl", truth)): + (SOURCES / name).write_text("".join(json.dumps(r, sort_keys=True) + "\n" for r in rows), encoding="utf-8", + 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") + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/examples/singlecell_celltype/profile.yaml b/examples/singlecell_celltype/profile.yaml new file mode 100644 index 0000000..9967175 --- /dev/null +++ b/examples/singlecell_celltype/profile.yaml @@ -0,0 +1,28 @@ +id: singlecell-celltype +version: 0.1.0 +description: Cell-type annotation of a single-cell RNA-seq cluster from its marker genes. A marker gene counts only + when a grounder has found it among the cluster's markers in the pinned marker table; model-cited markers are + allowed for a research summary on that condition, while a reference annotation needs a human's acceptance. +predicates: +- has_cell_type +subject_types: +- cell_cluster +object_types: +- cell_type +uses: + research_summary: + required_evidence_types: + - marker_gene + verified_evidence_types: + - marker_gene + require_human_acceptance: false + allow_llm_only: true + allow_string_match_only: false + reference_annotation: + required_evidence_types: + - marker_gene + verified_evidence_types: + - marker_gene + require_human_acceptance: true + allow_llm_only: true + allow_string_match_only: false diff --git a/examples/singlecell_celltype/sources/ATTRIBUTION.md b/examples/singlecell_celltype/sources/ATTRIBUTION.md new file mode 100644 index 0000000..04e50c6 --- /dev/null +++ b/examples/singlecell_celltype/sources/ATTRIBUTION.md @@ -0,0 +1,35 @@ +# Attribution + +The marker tables in `snapshots/` are derived by `prepare_source.py` from the datasets below, as curated +and distributed by [CZ CELLxGENE Discover](https://cellxgene.cziscience.com/) under +[CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). The expression matrices themselves are not +redistributed; `manifest.json` records each file's SHA-256 and dataset version. The cell-type labels in +`truth.jsonl` are the datasets' own author annotations. + +| Name | Dataset | Publication | +|---|---|---| +| liver | Liver, in *Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations* | *Nat Commun* 2018, [10.1038/s41467-018-06318-7](https://doi.org/10.1038/s41467-018-06318-7) | +| kidney | normal, in *Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response* | *PNAS* 2021, [10.1073/pnas.2103240118](https://doi.org/10.1073/pnas.2103240118) | +| duodenum | Adult duodenum, in *Charting human development using a multi-endodermal organ atlas and organoid models* | *Cell* 2021, [10.1016/j.cell.2021.04.028](https://doi.org/10.1016/j.cell.2021.04.028) | +| pancreas | A Single-Cell Transcriptome Atlas of the Human Pancreas (Muraro Pancreas) | *Cell Systems* 2016, [10.1016/j.cels.2016.09.002](https://doi.org/10.1016/j.cels.2016.09.002) | +| 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) | + +Reference releases, redistributed unchanged (gzip-compressed) in `snapshots/`: + +- **Cell Ontology**, release 2026-06-08, full `cl.obo` + ([obophenotype/cell-ontology](https://github.com/obophenotype/cell-ontology)), CC BY 4.0. +- **HGNC complete set**, retrieved 2026-09-30 from [genenames.org](https://www.genenames.org/), CC0. + +The ASCT+B reference (`gene marker_of cell type`) is derived from the HuBMAP ASCT+B Tables, CCF release +v2.0 ([hubmapconsortium/ccf-releases](https://github.com/hubmapconsortium/ccf-releases)), CC BY 4.0. +Overall citation: Quardokus E, Herr BW II, Record L, Börner K. *HuBMAP ASCT+B Tables*, +[humanatlas.io/asctb-tables](https://humanatlas.io/asctb-tables). + +| Organ | Table | +|---|---| +| liver | Masci AM, Kendall T, Suzuki A. HuBMAP ASCT+B Tables. Liver v1.2, [10.48539/HBM449.XCGD.289](https://doi.org/10.48539/HBM449.XCGD.289) | +| kidney | Jain S, Valerius MT, He Y, El-Achkar T, Eadon M, Spraggins J. HuBMAP ASCT+B Tables. Kidney v1.4, [10.48539/HBM636.MXKP.682](https://doi.org/10.48539/HBM636.MXKP.682) | +| pancreas | Campbell-Thompson M, Eskaros A, Saunders D. HuBMAP ASCT+B Tables. Pancreas v1.3, [10.48539/HBM336.TBNP.923](https://doi.org/10.48539/HBM336.TBNP.923) | +| skin | Ginty F, Ho J, Sunshine J, Karunamurthy A. HuBMAP ASCT+B Tables. Skin v1.3, [10.48539/HBM785.XBPB.444](https://doi.org/10.48539/HBM785.XBPB.444) | +| lung | Pryhuber G. HuBMAP ASCT+B Tables. Lung v1.4, [10.48539/HBM823.VZGJ.394](https://doi.org/10.48539/HBM823.VZGJ.394) | diff --git a/examples/singlecell_celltype/sources/manifest.json b/examples/singlecell_celltype/sources/manifest.json new file mode 100644 index 0000000..00022e8 --- /dev/null +++ b/examples/singlecell_celltype/sources/manifest.json @@ -0,0 +1,159 @@ +{ + "asctb": { + "assertions": 1027, + "organs": [ + "kidney", + "liver", + "lung", + "pancreas", + "skin" + ], + "release": "ccf-releases v2.0", + "sha256": "351dbaacdd372af704594f4a36d889c324f807c12fd2cbc307aeba9cffcb3302" + }, + "cell_ontology": { + "sha256": "7e19b4aef8e7fe7720b0c4474c6a5b8713c904ea9ab7b7d5d96f2cb28b8fc51f", + "version": "releases/2026-06-08" + }, + "datasets": [ + { + "assay": [ + "10x 3' v2" + ], + "cell_count": 8444, + "clusters": 12, + "collection_doi": "10.1038/s41467-018-06318-7", + "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", + "h5ad_sha256": "9d9c24983830f1948033c4fcf0c139e735e35e05db50e3778f64c7f8b3db7bee", + "markers_sha256": "fe2ff2cb67d700473d6285d4b052a1d892278cfc5377937a37152123c8c6b98d", + "name": "liver", + "tissue": { + "label": "caudate lobe of liver", + "ontology_term_id": "UBERON:0001117", + "tissue_type": "tissue" + }, + "title": "Liver", + "url": "https://datasets.cellxgene.cziscience.com/9681a962-f2d0-4d53-8127-7ac87f2bd799.h5ad" + }, + { + "assay": [ + "10x 3' v2" + ], + "cell_count": 6044, + "clusters": 18, + "collection_doi": "10.1073/pnas.2103240118", + "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", + "h5ad_sha256": "3215543bd2dc490db5ef247d082632aaa12392cac536e6cad41dd7f991b33f49", + "markers_sha256": "a8bc60d1f3d0c6496eba01eb18f3f2ec0226f329ff4fdc52033e41486fc3a58b", + "name": "kidney", + "tissue": { + "label": "kidney", + "ontology_term_id": "UBERON:0002113", + "tissue_type": "tissue" + }, + "title": "normal - Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response", + "url": "https://datasets.cellxgene.cziscience.com/5f0b9675-aed8-4870-8ad8-7a3f38037486.h5ad" + }, + { + "assay": [ + "10x 3' v2" + ], + "cell_count": 5200, + "clusters": 10, + "collection_doi": "10.1016/j.cell.2021.04.028", + "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", + "h5ad_sha256": "c42a9fcf76fbc2905d8fe1fc24d29e88677298dea722fa1d7c2a268f0ad41b89", + "markers_sha256": 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"https://datasets.cellxgene.cziscience.com/ac56150b-add4-4336-9059-6d3d3ce17f3b.h5ad" + }, + { + "assay": [ + "10x 3' v2" + ], + "cell_count": 15457, + "clusters": 10, + "collection_doi": "10.1038/s42003-020-0922-4", + "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", + "h5ad_sha256": "0968cb3ccad509198e0aa37541c3f2301abcbfe81eefeec781abac80c15bc8ad", + "markers_sha256": "1dacf640d2c4d41b43f2b7e7d3b7a1fc13fe72ac383760d336886501afacfa1b", + "name": "skin", + "tissue": { + "label": "zone of skin", + "ontology_term_id": "UBERON:0000014", + "tissue_type": "tissue" + }, + "title": "Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming", + "url": "https://datasets.cellxgene.cziscience.com/1a6bbe2b-4eed-477a-97c9-f7a74d4874d7.h5ad" + }, + { + "assay": [ + "10x 5' v1" + ], + 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"dataset": "skin", "label": "pericyte", "note": "", "task_id": "ct-22fc152fbd", "term": "CL:0000669"} +{"author_label": "endothelial cell of lymphatic vessel", "author_term": "CL:0002138", "cells": 294, "cluster": "c07", "dataset": "skin", "label": "endothelial cell of lymphatic vessel", "note": "", "task_id": "ct-cc1cfcedd3", "term": "CL:0002138"} +{"author_label": "endothelial cell of vascular tree", "author_term": "CL:0002139", "cells": 1467, "cluster": "c08", "dataset": "skin", "label": "endothelial cell of vascular tree", "note": "", "task_id": "ct-3875326824", "term": "CL:0002139"} +{"author_label": "skin fibroblast", "author_term": "CL:0002620", "cells": 5948, "cluster": "c09", "dataset": "skin", "label": "skin fibroblast", "note": "", "task_id": "ct-5e18af843a", "term": "CL:0002620"} +{"author_label": "stem cell of epidermis", "author_term": "CL:1000428", "cells": 1187, "cluster": "c10", "dataset": "skin", "label": "stem cell of epidermis", "note": "", "task_id": "ct-5633d2ce11", "term": "CL:1000428"} +{"author_label": "T cell", "author_term": "CL:0000084", "cells": 46, "cluster": "c01", "dataset": "lung_t_nk_ilc", "label": "T cell", "note": "", "task_id": "ct-c8e68f267e", "term": "CL:0000084"} +{"author_label": "natural killer cell", "author_term": "CL:0000623", "cells": 1184, "cluster": "c02", "dataset": "lung_t_nk_ilc", "label": "natural killer cell", "note": "", "task_id": "ct-0bcb90ea26", "term": "CL:0000623"} +{"author_label": "CD8-positive, alpha-beta T cell", "author_term": "CL:0000625", "cells": 405, "cluster": "c03", "dataset": "lung_t_nk_ilc", "label": "CD8-positive, alpha-beta T cell", "note": "", "task_id": "ct-6b9f55ce2e", "term": "CL:0000625"} +{"author_label": "regulatory T cell", "author_term": "CL:0000815", "cells": 253, "cluster": "c04", "dataset": "lung_t_nk_ilc", "label": "regulatory T cell", "note": "", "task_id": "ct-f3161764a6", "term": "CL:0000815"} +{"author_label": "CD4-positive, alpha-beta memory T cell", "author_term": "CL:0000897", "cells": 638, "cluster": "c05", "dataset": "lung_t_nk_ilc", "label": "CD4-positive, alpha-beta memory T cell", "note": "", "task_id": "ct-f5c625b34c", "term": "CL:0000897"} +{"author_label": "T-helper 17 cell", "author_term": "CL:0000899", "cells": 167, "cluster": "c06", "dataset": "lung_t_nk_ilc", "label": "T-helper 17 cell", "note": "", "task_id": "ct-c84f57496a", "term": "CL:0000899"} +{"author_label": "type I NK T cell", "author_term": "CL:0000921", "cells": 123, "cluster": "c07", "dataset": "lung_t_nk_ilc", "label": "type I NK T cell", "note": "", "task_id": "ct-1161617d72", "term": "CL:0000921"} +{"author_label": "type II NK T cell", "author_term": "CL:0000922", "cells": 147, "cluster": "c08", "dataset": "lung_t_nk_ilc", "label": "type II NK T cell", "note": "", "task_id": "ct-52a80b5c6b", "term": "CL:0000922"} +{"author_label": "CD16-negative, CD56-bright natural killer cell, human", "author_term": "CL:0000938", "cells": 752, "cluster": "c09", "dataset": "lung_t_nk_ilc", "label": "CD16-negative, CD56-bright natural killer cell, human", "note": "", "task_id": "ct-bb928b569a", "term": "CL:0000938"} +{"author_label": "CD16-positive, CD56-dim natural killer cell, human", "author_term": "CL:0000939", "cells": 687, "cluster": "c10", "dataset": "lung_t_nk_ilc", "label": "CD16-positive, CD56-dim natural killer cell, human", "note": "", "task_id": "ct-2e16bde736", "term": "CL:0000939"} +{"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"} diff --git a/tests/test_singlecell_case.py b/tests/test_singlecell_case.py new file mode 100644 index 0000000..dc7eee3 --- /dev/null +++ b/tests/test_singlecell_case.py @@ -0,0 +1,138 @@ +"""The single-cell cell-type annotation case: pinned sources, tasks, records and scoring.""" +import importlib.util +import json +from collections import Counter +from pathlib import Path + +import pytest + +from bioevidence_validator.feedback import reasons, to_expert + +ROOT = Path(__file__).resolve().parents[1] +CASE = ROOT / "examples" / "singlecell_celltype" + + +def load(name): + spec = importlib.util.spec_from_file_location(f"bench_{name}", ROOT / "evaluation" / "llm_benchmark" / f"{name}.py") + module = importlib.util.module_from_spec(spec) + spec.loader.exec_module(module) + return module + + +loop = load("celltype_loop") + + +@pytest.fixture(scope="module") +def case(): + return loop.Case() + + +def jsonl(path): + return [json.loads(line) for line in path.read_text(encoding="utf-8").splitlines()] + + +def test_snapshots_match_the_manifest(case): + manifest = case.manifest + hashes = [manifest["cell_ontology"]["sha256"], manifest["hgnc"]["sha256"], manifest["asctb"]["sha256"], + *(d["markers_sha256"] for d in manifest["datasets"])] + assert all(case.store.verified(h) for h in hashes) + assert case.ontology.prefix == "CL" and manifest["cell_ontology"]["version"] == case.ontology.version + assert len(case.genes.approved) > 40_000 and manifest["asctb"]["assertions"] > 1000 + + +def test_tasks_hide_the_answer_and_split_per_dataset(case): + tasks, truth = jsonl(CASE / "sources/tasks.jsonl"), jsonl(CASE / "sources/truth.jsonl") + assert [t["task_id"] for t in tasks] == [t["task_id"] for t in truth] and len({t["task_id"] for t in tasks}) == len(tasks) + assert all(not {"term", "label", "author_term", "author_label"} & set(t) for t in tasks) + assert set(Counter(t["dataset"] for t in tasks if t["split"] == "pilot").values()) == {4} + for task, answer in zip(tasks, truth, strict=True): + text = json.dumps(task).casefold() + assert answer["term"].casefold() not in text and answer["label"].casefold() not in text + assert answer["term"] in case.ontology.terms and not case.ontology.terms[answer["term"]].obsolete + + +def test_task_markers_are_the_top_rows_of_the_pinned_table(case): + for task in case.tasks.values(): + rows = [r for r in case.tables[task["markers_sha256"]] if r["cluster"] == task["cluster"]] + assert [m["gene"] for m in task["markers"]] == [r["gene"] for r in rows[:20]] + assert all(g in case.genes.approved for g in (r["gene"] for r in rows)) + + +def hepatocytes(case): + return next(t for t in case.tasks.values() if t["dataset"] == "liver" and t["cluster"] == "c01") + + +def answer(term, label, *genes, against=()): + return {"decision": "annotate", "cell_type_id": term, "cell_type_label": label, "rationale": "", + "markers": [{"gene": g, "stance": "supports"} for g in genes] + [{"gene": g, "stance": "contradicts"} + for g in against]} + + +def test_validator_admits_a_grounded_answer_and_explains_errors(case): + validator, task = case.validator(), hepatocytes(case) + report = validator.validate(loop.record(case, task, answer("CL:0000182", "hepatocytes", "APOC3", "TTR"))) + assert report["overall_status"] == "admitted" + record = loop.record(case, task, answer("CL:0000092", "hepatocyte", "APOC3", "CD20")) + report = validator.validate(record) + assert report["overall_status"] == "rejected" + text = " ".join(reasons(record, report)) + assert "'hepatocyte' is the name of CL:0000182" in text and "alias of MS4A1" in text and "No row" in text + lymphocyte = loop.record(case, task, answer("CL:0000084", "T cell", "APOC3", against=["TTR"])) + assert to_expert(validator.validate(lymphocyte)) # its own evidence disagrees + assert loop.record(case, task, {**answer("", "", "APOC3"), "decision": "uncertain"}) is None + + +def test_reference_cross_check_uses_disjointness(case): + validator, task = case.validator(protocol=1), hepatocytes(case) + grounder = next(g for g in validator.grounders if g.name == "reference:ASCT+B") + record = loop.record(case, task, answer("CL:0000182", "hepatocyte", "APOC3")) + listed = {row["subject"] for row in grounder.assertions if row["object"] == "CL:0000236"} # B cell markers + assert "MS4A1" in listed or "CD19" in listed or "CD79A" in listed + record["evidence_items"][0]["locator"] = "cluster=c01;gene=" + sorted(listed & {"MS4A1", "CD19", "CD79A"})[0] + assert [f.rule_id for f in grounder.check(record)] == ["BEV025"] # a B cell marker for an epithelial cell + + +@pytest.mark.parametrize("term,expected", [("CL:0000182", "exact"), ("CL:0000066", "coarser"), ("CL:0000084", "wrong"), + ("CL:9999999", "invalid"), ("UBERON:0002107", "invalid")]) +def test_outcomes_follow_the_ontology(case, term, expected): + assert loop.outcome(case, "CL:0000182", answer(term, "x")) == expected + assert loop.outcome(case, "CL:0000625", answer("CL:0000084", "T cell")) == "coarser" + assert loop.outcome(case, "CL:0000084", answer("CL:0000625", "CD8-positive, alpha-beta T cell")) == "finer" + + +def test_problems_are_looked_up_directly(case): + task = hepatocytes(case) + assert loop.problems(case, task, answer("CL:0000182", "hepatocyte", "APOC3")) == [] + assert loop.problems(case, task, answer("CL:0000182", "liver cell", "CD20", "APOC3")) == [ + "label_mismatch", "unapproved_symbol", "marker_not_in_data"] + assert loop.problems(case, task, answer("CL:9999999", "x")) == ["unknown_id", "no_markers"] + with pytest.raises(ValueError): + loop.check_answer({"decision": "annotate"}) + assert loop.gene_token(" CD3E;x=1 ") == "CD3E_x_1" + + +@pytest.mark.parametrize("folder", ["celltype-pilot", "celltype-test"]) +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()) + loop.score(tmp_path) + for name in ("summary.json", "summary.md"): + assert (tmp_path / name).read_bytes() == (committed / name).read_bytes(), name + + +def test_views_follow_the_attempts(): + row = {"calls": [{"answer": answer("CL:0000084", "B cell", "CD3E")}, {"answer": answer("CL:0000084", "T cell", "CD3E")}], + "attempts": [{"status": "rejected", "to_expert": False}, {"status": "admitted", "to_expert": False}]} + assert loop.view(row, "model")["answer"]["cell_type_label"] == "B cell" + assert loop.view(row, "gate") == {"answer": None, "routed": True, "expert": False} + assert loop.view(row, "loop")["answer"]["cell_type_label"] == "T cell" + assert loop.view({"calls": [{"answer": None}], "attempts": []}, "gate") == {"answer": None, "routed": False, + "expert": False} + + +def test_protocol_2_drops_the_reference_check_and_narrows_contradicting_markers(case): + task = hepatocytes(case) + assert [g.name for g in case.validator(protocol=1).grounders][-1] == "reference:ASCT+B" + 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]