Shared Discussion (knowledge gaps) + Dataset module — TraitMech reference integration (claw#7 Phase 1)#119
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…aitRecord
Phase 1 of the DisMech feature adoption (culturebotai-claw#7). Introduces the
canonical, byte-identical shared LinkML module
src/traitmech/schema/mech_shared.yaml:
* Discussion — broad discourse/knowledge-gap supertype (kind enum incl.
KNOWLEDGE_GAP/OPEN_QUESTION/CONTROVERSY/CURATION_TODO/EMERGING_HYPOTHESIS/
INTERPRETATION/HUMAN_MODEL_MISMATCH; lifecycle status; free-form
`attaches_to` hash-anchor pointers; slim `proposed_experiments`; `evidence`).
* Dataset — lightweight public-data reference; canonical DatasetTypeEnum
(omics + microbial: AMPLICON/METAGENOMICS/METATRANSCRIPTOMICS/GENOMICS/…)
and DatasetRepositoryEnum (SRA/GEO/ENA/MGnify/JGI GOLD+IMG/NMDC/…).
* ProposedExperiment — domain-neutral resolution sketch.
`Discussion.evidence` / `Dataset.evidence` resolve to the IMPORTING schema's
`EvidenceItem`, so each Mech reuses its own evidence model (no duplicate class,
no collision). TraitRecord gains `discussions` + `datasets` slots; `attaches_to`
anchors into `causal_graphs#<edge>`.
TraitMech is the greenfield reference integration (no dataset migration needed).
Validated: `gen-pydantic` compiles (Discussion/Dataset/ProposedExperiment emitted,
EvidenceItem resolves); a sample TraitRecord with a KNOWLEDGE_GAP discussion +
METAGENOMICS dataset passes `linkml-validate` (No issues found).
Next (claw#7): vendor this module byte-identical + sha-pin across MIM /
CommunityMech / CultureMech, with the Dataset migration for CultureMech
(`Dataset`) and CommunityMech (`AssociatedDataset`).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…, naming Addresses the four requested adjustment areas: - Self-contained evidence: drop the `range: EvidenceItem` dependency on the importing schema; define `SupportingReference` (+ `SupportLevelEnum`) in the module. Discussion.evidence / Dataset.evidence now reference it. Module validates STANDALONE (gen-pydantic clean) and needs no per-repo reconciliation (MIM's MappingEvidence no longer matters). Each record keeps its own primary EvidenceItem; discussions/datasets carry SupportingReference citations. - Dataset enums grounded in reality: DatasetTypeEnum / DatasetRepositoryEnum are now the faithful UNION of the existing CultureMech + CommunityMech enums (plus microbial additions), with the old→new migration map documented inline so the Phase-2 migration of those two repos is loss-preserving. - Naming & constraints: field is `dataset_type` (matches both repos, was `data_type`); `accession`/`description` recommended; `url` range uri; documented `attaches_to` `<section>#<anchor>` grammar; CultureMech `dataset_id` → `accession` and CommunityMech `name` → `title` migration notes inline. - ProposedExperiment: `model_systems` is now multivalued (matches DisMech's plurality); `name` recommended. Validated: module standalone gen-pydantic (exit 0, SupportingReference + Discussion + Dataset + ProposedExperiment emitted); full traitmech schema gen-pydantic (exit 0); sample TraitRecord instance with a KNOWLEDGE_GAP discussion + METAGENOMICS dataset passes linkml-validate. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
realmarcin
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Jun 18, 2026
Completes the cross-Mech pin: TraitMech (which introduced the module in #119, before the pin recipe existed) now also pins mech_shared.yaml. All four Mechs now carry the byte-identical module (1a5e21eb) + an identical sha sidecar. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
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Phase 1 of the cross-Mech DisMech feature adoption (CultureBotAI/culturebotai-claw#7). Introduces the canonical, byte-identical shared LinkML module and wires it into TraitMech as the greenfield reference integration.
What's here
src/traitmech/schema/mech_shared.yaml(new canonical module, to be vendored byte-identical across all four Mechs):Discussion— broad knowledge-gap/discourse supertype.kind∈ {KNOWLEDGE_GAP, OPEN_QUESTION, CONTROVERSY, CURATION_TODO, EMERGING_HYPOTHESIS, INTERPRETATION, HUMAN_MODEL_MISMATCH}; lifecyclestatus; free-formattaches_tohash-anchor pointers; slimproposed_experiments;evidence.Dataset— lightweight public-data reference.DatasetTypeEnumreconciles CultureMech's omics types + microbial additions (AMPLICON/METAGENOMICS/METATRANSCRIPTOMICS/GENOMICS/…);DatasetRepositoryEnumfrom CommunityMech's orientation (SRA/GEO/ENA/MGnify/JGI GOLD+IMG/NMDC/…).ProposedExperiment— domain-neutral resolution sketch.TraitRecordgainsdiscussions+datasetsslots (attaches_to→causal_graphs#<edge>).Design note (please eyeball)
Discussion.evidence/Dataset.evidenceuserange: EvidenceItem, resolving to the importing schema'sEvidenceItem— so each Mech reuses its own evidence model, the module defines no collidingEvidenceItem/Datasetclasses, and stays byte-identical. (MIM hasMappingEvidence, notEvidenceItem— its adoption will need a small reconciliation; tracked in claw#7.)Validation
gen-pydanticcompiles with no errors;Discussion/Dataset/ProposedExperimentemitted;EvidenceItemresolves.TraitRecordwith aKNOWLEDGE_GAPdiscussion (+proposed_experiments) and aMETAGENOMICSdataset passeslinkml-validate("No issues found").Next (claw#7)
Vendor this module byte-identical + sha-pin across MIM / CommunityMech / CultureMech; do the Dataset migration for CultureMech (
Dataset) and CommunityMech (AssociatedDataset); MIMEvidenceItemreconciliation.🤖 Generated with Claude Code