# Generated by `mechregistry concat`. Do not edit; edit mech//.md. mechs: - id: ai-gene-review category: Mech layout: mech_detail name: ai-gene-review description: 'ai-gene-review is an agent-curated knowledge base of Gene Ontology annotation reviews. One record per gene product: each record takes every existing GO annotation for the gene from GOA and gives it a review action (ACCEPT, MODIFY, REMOVE, MARK_AS_OVER_ANNOTATED, KEEP_AS_NON_CORE and others) with a reason and supporting evidence. The record also holds a standalone summary of the gene, its core functions as GO-CAM-like activities, proposed new GO terms, and suggested questions and experiments for experts. Reviews cover human, mouse, worm, yeast, fly, plant and many microbial gene products. Agents fetch the UniProt record, the GOA annotations and the cited publications, add deep research and bioinformatics, and write the review, which arrives by pull request. ai-gene-review is not strictly a Mech: each record reviews annotations that another resource holds, rather than being the canonical record for its gene. It keeps the Mech practices of a LinkML schema, ontology grounding, verbatim evidence and an append-only curation history.' activity_status: active maturity: curating homepage_url: https://ai4curation.github.io/ai-gene-review repository: https://github.com/ai4curation/ai-gene-review schema_url: https://github.com/ai4curation/ai-gene-review/blob/main/src/ai_gene_review/schema/gene_review.yaml domains: - genomics - biological systems - pathways - organisms record_type: a gene product and the review of its existing GO annotations record_count: 6760 record_count_date: '2026-10-12' record_count_commit: 00d0f98ed7f4e212daf095364a8de2864f32a422 record_count_source: path: genes pattern: '*-ai-review.yaml' record_identifier_policy: Records are keyed by UniProtKB accession and named -ai-review.yaml under genes///. Organisms are a common name (human, mouse, worm, yeast) or a UniProt species code (ARATH, PSEPK). Gene symbols follow the nomenclature for the species. ontologies: - GO - ECO - NCBITaxon data_sources: - name: GOA url: https://www.ebi.ac.uk/QuickGO/ relation_type: prov:hadPrimarySource description: The existing GO annotations under review, downloaded through the QuickGO API. - name: UniProtKB url: https://www.uniprot.org/ relation_type: prov:hadPrimarySource description: The UniProt record for each gene product, which supplies the record identifier. - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:used description: Cited publications, cached as text so that supporting quotes can be checked. - name: Reactome url: https://reactome.org/ relation_type: prov:used description: Cached Reactome entries used as pathway context. - name: GO-CAM url: https://geneontology.cloud/ relation_type: prov:used description: Cached production GO-CAM models, indexed by gene product. - name: PANTHER url: https://www.pantherdb.org/ relation_type: prov:used description: Protein family membership for family-level review and propagation. license: id: https://opensource.org/licenses/BSD-3-Clause label: BSD 3-Clause License spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - dragon-ai-agent - Codex - goose evidence_policy: Each review action carries a reason. Conclusive decisions on experimental annotations are expected to cite a PMID or DOI with supporting text quoted from the paper, and validation checks reference identifiers, titles and quotes against cached publication text. Ontology term identifiers are checked against their labels to catch fabricated terms. validation: - schema - ontology_terms - references curation_history: true curation_guide_url: https://github.com/ai4curation/ai-gene-review/blob/main/CLAUDE.md features: - evidence_snippets - ontology_grounding - append_only_history - knowledge_gaps - static_browser contacts: - category: Organization label: AI4Curation contact_details: - contact_type: github value: ai4curation - category: Individual label: Christopher J. Mungall orcid: 0000-0002-6601-2165 contact_details: - contact_type: email value: cjmungall@lbl.gov - contact_type: github value: cmungall products: - id: ai-gene-review.records category: RecordCorpus name: Gene reviews description: One -ai-review.yaml file per gene product under genes///, next to the UniProt record, GOA annotations, notes and deep research it was written from. product_url: https://github.com/ai4curation/ai-gene-review/tree/main/genes format: yaml - id: ai-gene-review.schema category: DataModelProduct name: Gene review LinkML schema product_url: https://github.com/ai4curation/ai-gene-review/blob/main/src/ai_gene_review/schema/gene_review.yaml format: linkml compatibility: - linkml - id: ai-gene-review.app category: GraphicalInterface name: Gene review browser description: A searchable browser of the reviews. Review pages take thumbs-up and thumbs-down votes on individual decisions. product_url: https://ai4curation.io/ai-gene-review/app/index.html format: html - id: ai-gene-review.annotations category: OtherProduct name: Exported annotations description: One row per reviewed annotation, with the review action, reason and supporting text. product_url: https://github.com/ai4curation/ai-gene-review/blob/main/exports/exported_annotations.csv format: csv - id: ai-gene-review.stats category: DocumentationProduct name: Statistics report product_url: https://ai4curation.io/ai-gene-review/docs/stats_report.html format: html cross_references: - target: dismech relation: adopts_practice_of description: The history/ directory of append-only curation session records, with its schema, layout, scaffolder and validation, is ported from DisMech. tags: - Mech-like creation_date: '2026-10-06' last_modified_date: '2026-10-06' - id: aimech category: Mech layout: mech_detail name: AIMech description: 'AIMech extends the Mech curation workflow from biology to artificial intelligence. One record is one AI concept: a model, layer, training strategy, task, bias or the like. It holds two kinds. Imported records are a deterministic projection of the Artificial Intelligence Ontology (AIO), pinned to release 2026-07-22, and are all NOT_REVIEWED. Curated records cover concepts absent from AIO, under stable AIMech IDs with primary evidence, claim-specific citations and explicit AIO mappings, and are all DRAFT. Ontology membership is not taken as evidence of a model''s performance, safety or mechanism.' activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/AIMech/ repository: https://github.com/CultureBotAI/AIMech schema_url: https://github.com/CultureBotAI/AIMech/blob/main/src/aimech/schema/aimech.yaml collection: - x-mech-suite domains: - machine learning - information technology record_type: an artificial intelligence concept record_count: 1088 record_count_date: '2026-10-13' record_count_commit: b9b06695283c1322e58995a000f4a6b6e3e5fb07 record_count_source: path: data pattern: '*.yaml' record_identifier_policy: The AIO CURIE for imported concepts. A stable, minted AIMech CURIE for curated concepts absent from AIO. identifier_prefix: AIMech ontologies: - AIO - BFO data_sources: - name: Artificial Intelligence Ontology url: https://github.com/berkeleybop/artificial-intelligence-ontology relation_type: prov:hadPrimarySource description: The 442 named AIO classes, from a pinned release snapshot. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://opensource.org/license/bsd-3-clause label: BSD-3-Clause spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Curated concepts need inspected primary evidence, claim-specific citations, and an explicit AIO mapping or a documented no-match assessment. Scientific reviews are saved separately from records. validation: - schema - corpus_reproduction curation_history: true features: - ontology_grounding - append_only_history - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: aimech.records category: RecordCorpus name: AI concept records description: Imported AIO records under data/aio/ and curated records under data/curated/. product_url: https://github.com/CultureBotAI/AIMech/tree/main/data format: yaml - id: aimech.schema category: DataModelProduct name: AIMech LinkML schema product_url: https://github.com/CultureBotAI/AIMech/blob/main/src/aimech/schema/aimech.yaml format: linkml compatibility: - linkml - mech_shared - id: aimech.browser category: GraphicalInterface name: AIMech browser product_url: https://culturebotai.github.io/AIMech/ format: html cross_references: - target: dismech relation: follows_pattern_of description: Applies the Mech curation workflow outside biology. creation_date: '2026-10-13' last_modified_date: '2026-10-13' - id: antibioticmech category: Mech layout: mech_detail name: AntibioticMech description: AntibioticMech is a knowledge base of individual chemical structures with antimicrobial activity, harmonized from ChEBI and CARD's Antibiotic Resistance Ontology. One record is one chemical structure, keyed by its ChEBI identifier and carrying SMILES, InChI and InChIKey. A class such as macrolide antibiotic is not a record. It is a structural_class on the records it covers. Each record carries what the compound hits, how microbes resist it, and the evidence for both. activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/AntibioticMech/ repository: https://github.com/CultureBotAI/AntibioticMech schema_url: https://github.com/CultureBotAI/AntibioticMech/blob/main/src/antibioticmech/schema/antibioticmech.yaml collection: - x-mech-suite - kg-microbe domains: - chemistry and biochemistry - pharmacology - microbiology record_type: an antimicrobial chemical structure record_count: 2939 record_count_date: '2026-10-12' record_count_commit: 0611c4ed87a1d089aea7b1a1f60d3b32b9f57d32 record_count_source: path: data/antibiotics pattern: '*.yaml' record_identifier_policy: A ChEBI CURIE where the entry has a structure, otherwise a minted, content-hashed CURIE. A record with no InChIKey is never written. identifier_prefix: antibioticmech ontologies: - CHEBI - ARO - CAS - PubChem - DrugBank - NCBITaxon data_sources: - name: ChEBI url: https://www.ebi.ac.uk/chebi/ relation_type: prov:hadPrimarySource description: Structures, definitions and antimicrobial class terms. - name: CARD url: https://card.mcmaster.ca/ relation_type: prov:hadPrimarySource description: Antibiotic Resistance Ontology classification, molecular targets and resistance determinants. - name: PubChem url: https://pubchem.ncbi.nlm.nih.gov/ relation_type: prov:used description: The structures CARD's cross-references point at. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Targets and resistance determinants carry evidence. Candidate sources are ranked in a source queue and their licences verified and recorded before ingestion. validation: - schema - ontology_terms - references - corpus_reproduction curation_history: true features: - causal_mechanism_graphs - ontology_grounding - append_only_history - knowledge_gaps - static_browser - embeddings_explorer contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: antibioticmech.records category: RecordCorpus name: Antibiotic records description: One YAML file per structure under data/antibiotics//. product_url: https://github.com/CultureBotAI/AntibioticMech/tree/main/data/antibiotics format: yaml - id: antibioticmech.schema category: DataModelProduct name: AntibioticMech LinkML schema product_url: https://github.com/CultureBotAI/AntibioticMech/blob/main/src/antibioticmech/schema/antibioticmech.yaml format: linkml compatibility: - linkml - mech_shared - id: antibioticmech.browser category: GraphicalInterface name: AntibioticMech browser description: Every record by antimicrobial class, with structures, sources, CARD targets and resistance determinants. product_url: https://culturebotai.github.io/AntibioticMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: naturalproductmech relation: provides_to description: Supplies antimicrobial classification and cross-corpus links. - target: cellstructuremech relation: provides_to description: Wrote the licensed source-queue pattern that CellStructureMech adapted. creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: cellstructuremech category: Mech layout: mech_detail name: CellStructureMech description: 'CellStructureMech is a knowledge base of microbial cell structures: organelles, envelope layers, appendages, microcompartments, inclusions, cytoskeletal systems and the multi-protein complexes that build them. One record is a structure you could point to in a micrograph, from a whole organelle down to a discrete complex such as the flagellar motor. A record holds components with stoichiometry and UniProt examples, taxonomic distribution, GO functions with evidence, the TraitMech phenotypes it confers, and causal graphs of assembly, operation and regulation with every edge cited. It fills the layer between a phenotype in TraitMech and a protein in ProteinTraitsMech.' activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/CellStructureMech/ repository: https://github.com/CultureBotAI/CellStructureMech schema_url: https://github.com/CultureBotAI/CellStructureMech/blob/main/src/cellstructuremech/schema/cellstructuremech.yaml collection: - x-mech-suite - kg-microbe domains: - microbiology - biological systems - anatomy and development taxon: - NCBITaxon:2 - NCBITaxon:2157 record_type: a microbial cell structure or multi-protein complex record_count: 909 record_count_date: '2026-10-12' record_count_commit: 937ba6254eb987adcbd92e82b21b2ce8651dc5e3 record_count_source: path: data/structures pattern: '*.yaml' record_identifier_policy: A GO cellular component CURIE where one exists, otherwise a minted CURIE. ontologies: - GO - NCBITaxon - UniProt - METPO - Pfam - PDB data_sources: - name: UniProtKB url: https://www.uniprot.org/ relation_type: prov:used description: Taxon-paired protein examples for components. - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:hadPrimarySource description: Evidence on functions and on causal graph edges. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every causal graph edge and every function claim carries a citation. Candidate sources are ranked in a source queue and their licences verified before ingestion. validation: - schema - ontology_terms - references - corpus_reproduction curation_history: true curation_guide_url: https://github.com/CultureBotAI/CellStructureMech/blob/main/docs/CURATION.md features: - causal_mechanism_graphs - ontology_grounding - append_only_history - knowledge_gaps - static_browser - embeddings_explorer contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: cellstructuremech.records category: RecordCorpus name: Structure records product_url: https://github.com/CultureBotAI/CellStructureMech/tree/main/data/structures format: yaml - id: cellstructuremech.schema category: DataModelProduct name: CellStructureMech LinkML schema product_url: https://github.com/CultureBotAI/CellStructureMech/blob/main/src/cellstructuremech/schema/cellstructuremech.yaml format: linkml compatibility: - linkml - mech_shared - id: cellstructuremech.browser category: GraphicalInterface name: CellStructureMech browser description: Every record by category, with components, distribution, functions and mechanism graphs, plus a text embedding map with nearest neighbours. product_url: https://culturebotai.github.io/CellStructureMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: traitmech relation: consumes description: A structure lists the phenotypes it confers as TraitMech or METPO terms, and its causal-graph node vocabulary is TraitMech's plus a STRUCTURE node type. - target: proteintraitsmech relation: hands_off_to description: A single protein is a component of a structure, never a record of its own. It grounds to InterPro or UniProtKB and hands off to ProteinTraitsMech. - target: antibioticmech relation: adopts_practice_of description: Adapted AntibioticMech's licensed source-queue pattern. creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: cmmmech category: Mech layout: mech_detail name: CMMMech description: 'CMMMech is a knowledge base of critical minerals and materials and the microbial mechanisms that extract, transform or recover them. One record is one material: an element, a mineral species, or a secondary resource such as spent batteries or smelter dust. A record carries its chemical or mineral identity, dated criticality designations (US and EU lists), and microbial mechanisms with explicit evidence boundaries, such as missing abiotic controls. Elements, minerals and impure experimental feeds are kept distinct, and no record inherits criticality it was not designated.' activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/CMMMech/ repository: https://github.com/CultureBotAI/CMMMech schema_url: https://github.com/CultureBotAI/CMMMech/blob/main/src/cmmmech/schema/cmmmech.yaml collection: - x-mech-suite domains: - microbiology - chemistry and biochemistry - environment record_type: a critical mineral, element or secondary resource record_count: 278 record_count_date: '2026-10-13' record_count_commit: 11a0b0f8e2714f1863304faf408da4ce0e7c5b53 record_count_source: path: data/records pattern: '*.yaml' record_identifier_policy: A minted CURIE from the material name, such as cmmmech:cobalt, with ChEBI or IMA identifiers attached. identifier_prefix: cmmmech ontologies: - CHEBI - NCBITaxon data_sources: - name: ChEBI url: https://www.ebi.ac.uk/chebi/ relation_type: prov:used description: Chemical identity of elements and compounds. - name: USGS List of Critical Minerals url: https://www.usgs.gov/ relation_type: prov:hadPrimarySource description: Dated US criticality designations. - name: EU Critical Raw Materials Act url: https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32024R1252 relation_type: prov:hadPrimarySource description: Dated EU criticality designations. - name: IMA mineral list url: https://cnmnc.units.it/ relation_type: prov:used description: Mineral species identity. - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:hadPrimarySource description: Evidence on microbial mechanisms. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://opensource.org/license/bsd-3-clause label: BSD-3-Clause spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: 'Each record has a timestamped scientific review. Every microbial mechanism states its evidence boundary: what the cited experiment does not establish, such as matched abiotic controls or an isolated product yield.' validation: - schema - references curation_history: true features: - ontology_grounding - append_only_history - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: cmmmech.records category: RecordCorpus name: Material records product_url: https://github.com/CultureBotAI/CMMMech/tree/main/data/records format: yaml - id: cmmmech.schema category: DataModelProduct name: CMMMech LinkML schema product_url: https://github.com/CultureBotAI/CMMMech/blob/main/src/cmmmech/schema/cmmmech.yaml format: linkml compatibility: - linkml - mech_shared - id: cmmmech.browser category: GraphicalInterface name: CMMMech browser product_url: https://culturebotai.github.io/CMMMech/ format: html cross_references: - target: dismech relation: follows_pattern_of creation_date: '2026-10-13' last_modified_date: '2026-10-13' - id: communitymech category: Mech layout: mech_detail name: CommunityMech synonyms: - Microbial Community Mechanisms Knowledge Base description: 'CommunityMech is a knowledge base of microbial communities: their composition, ecological interactions, cultivation conditions, environments and supporting evidence. Curated YAML is the canonical record format. Validation, the static browser and the KGX export are all derived from it. Community records name the culture medium they were cultivated in by CultureMech identifier. The project is adapted from DisMech.' activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/CommunityMech/ repository: https://github.com/CultureBotAI/CommunityMech schema_url: https://github.com/CultureBotAI/CommunityMech/blob/main/src/communitymech/schema/communitymech.yaml collection: - x-mech-suite - kg-microbe domains: - microbiology - environment - organisms taxon: - NCBITaxon:2 - NCBITaxon:2157 record_type: a microbial community record_count: 458 record_count_date: '2026-10-12' record_count_commit: 80049bcc9195480a58633236169b62f86c23489a record_count_source: path: kb/communities pattern: '*.yaml' ontologies: - NCBITaxon - CHEBI - GO - ENVO - GTDB data_sources: - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:hadPrimarySource description: Literature evidence for community composition and interactions, cached in references_cache for reproducible checks. - name: GTDB url: https://gtdb.ecogenomic.org/ relation_type: prov:used description: Taxonomy for community members. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 code_license: id: https://opensource.org/license/bsd-3-clause label: BSD-3-Clause spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Interactions and cultivation claims carry evidence items with references. Cached source text in the repository makes evidence checks reproducible offline. validation: - schema - ontology_terms - references - cross_field curation_history: true features: - evidence_snippets - ontology_grounding - append_only_history - knowledge_gaps - static_browser - kgx_export contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: communitymech.records category: RecordCorpus name: Community records description: Canonical MicrobialCommunity records in kb/communities, with reusable CommonTaxon records in kb/taxa. product_url: https://github.com/CultureBotAI/CommunityMech/tree/main/kb/communities format: yaml - id: communitymech.schema category: DataModelProduct name: CommunityMech LinkML schema product_url: https://github.com/CultureBotAI/CommunityMech/blob/main/src/communitymech/schema/communitymech.yaml format: linkml compatibility: - linkml - mech_shared - id: communitymech.kgx category: GraphProduct name: KGX export description: Nodes and edges emitted by a deterministic Python emitter from the community YAML. product_url: https://github.com/CultureBotAI/CommunityMech format: kgx compatibility: - kgx - biolink - id: communitymech.browser category: GraphicalInterface name: CommunityMech browser product_url: https://culturebotai.github.io/CommunityMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: culturemech relation: consumes description: Community records name the medium they were cultivated in by CultureMech id. - target: mediaingredientmech relation: consumes description: The RelatedIngredient.mediaingredientmech_id slot is declared for MediaIngredientMech ingredient ids. No record populates it yet. creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: culturemech category: Mech layout: mech_detail name: CultureMech synonyms: - Microbial Culture Media Knowledge Graph description: 'CultureMech is a versioned knowledge base of microbial culture-media recipes from MediaDive, TogoMedium, KOMODO and the major culture collections. It combines LinkML validation, ontology grounding, provenance, deduplication, browser exports and static recipe pages. The corpus has four layers: immutable raw source payloads, mechanical source-shaped YAML, authoritative normalized records that preserve source-specific formulations, and reproducible merged records that are the deduplicated canonical output. The merged layer is what this entry counts.' activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/CultureMech/ repository: https://github.com/CultureBotAI/CultureMech schema_url: https://github.com/CultureBotAI/CultureMech/blob/main/src/culturemech/schema/culturemech.yaml collection: - x-mech-suite - kg-microbe domains: - microbiology - nutrition - chemistry and biochemistry taxon: - NCBITaxon:2 - NCBITaxon:2157 - NCBITaxon:4751 record_type: a culture-medium recipe record_count: 6320 record_count_date: '2026-10-12' record_count_commit: 9976e05b88c89c6c6b5a4c1fd60ed0d6a86033a6 record_count_source: path: data/merge_yaml/merged pattern: '*.yaml' ontologies: - CHEBI - KEGG - FOODON - UBERON - CAS - NCBITaxon data_sources: - name: MediaDive url: https://mediadive.dsmz.de/ relation_type: prov:hadPrimarySource description: DSMZ culture-media recipes and solution volumes. - name: TogoMedium url: https://togomedium.org/ relation_type: prov:hadPrimarySource - name: KOMODO url: https://komodo.modelseed.org/ relation_type: prov:hadPrimarySource description: Recipes and base volumes. - name: MediaIngredientMech url: https://github.com/CultureBotAI/MediaIngredientMech relation_type: prov:used description: Curated ingredient identity and ontology mappings synced back into recipes. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every recipe keeps its source provenance. Normalized records preserve source-specific formulations and merged records record which normalized records they combine. validation: - schema - ontology_terms - cross_field - corpus_reproduction curation_history: true curation_guide_url: https://github.com/CultureBotAI/CultureMech/blob/main/docs/DATA_LAYERS.md features: - ontology_grounding - append_only_history - knowledge_gaps - static_browser - sssom_export contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: culturemech.records category: RecordCorpus name: Merged recipe records description: Reproducible, deduplicated canonical recipes. The normalized layer holds 15,878 source-specific records behind them. product_url: https://github.com/CultureBotAI/CultureMech/tree/main/data/merge_yaml/merged format: yaml - id: culturemech.normalized category: RecordCorpus name: Normalized recipe records description: Authoritative curated and validated records, one per source formulation. product_url: https://github.com/CultureBotAI/CultureMech/tree/main/data/normalized_yaml format: yaml - id: culturemech.schema category: DataModelProduct name: CultureMech LinkML schema product_url: https://github.com/CultureBotAI/CultureMech/blob/main/src/culturemech/schema/culturemech.yaml format: linkml compatibility: - linkml - mech_shared - id: culturemech.browser category: GraphicalInterface name: CultureMech browser description: Browser-based exploration and static recipe pages. product_url: https://culturebotai.github.io/CultureMech/ format: html publications: - id: doi:10.1093/gigascience/giag077 title: 'KG-Microbe: Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences' authors: - Santangelo BE - Hegde H - Caufield JH - Reese J - Kliegr T - Hunter LE - Lozupone CA - Mungall CJ - Joachimiak MP journal: GigaScience year: '2026' doi: 10.1093/gigascience/giag077 - id: doi:10.64898/2026.06.04.729985 title: 'MicroGrowAgents: An Agentic AI System for Microbial Cultivation Engineering' authors: - Naseem S - Miller MA - Martinez-Gomez NC - Sun N - Joachimiak MP journal: bioRxiv year: '2026' doi: 10.64898/2026.06.04.729985 cross_references: - target: dismech relation: follows_pattern_of - target: mediaingredientmech relation: provides_to description: Unmapped ingredient strings and occurrence counts become MediaIngredientMech's curation backlog. - target: mediaingredientmech relation: consumes description: Vendors MediaIngredientMech's ingredient-role enums and consumes its immutable label index. - target: communitymech relation: provides_to description: Community records cite the medium they were cultivated in by CultureMech id. creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: dismech category: Mech layout: mech_detail name: DisMech synonyms: - Disorder Mechanisms Knowledge Base - Disease Mechanisms KB description: 'DisMech, the Disorder Mechanisms Knowledge Base, is a structured, evidence-backed knowledge base of disease pathophysiology. It records how diseases work: the cell types, biological processes and causal chains that link a genetic or environmental cause to its clinical phenotypes. Every claim carries a citation with a verbatim quote that is checked against the source. Each disorder is one YAML file holding pathophysiology, phenotypes, genetics, treatments, evidence and ontology term bindings. Conserved pathological processes are factored into mechanism modules that disorders declare conformance to. DisMech is the canonical Mech: the other Mechs in this registry adopt its curation pattern.' activity_status: active maturity: curating version: v0.1.39 homepage_url: https://dismech.monarchinitiative.org/ repository: https://github.com/monarch-initiative/dismech schema_url: https://github.com/monarch-initiative/dismech/blob/main/src/dismech/schema/dismech.yaml collection: - monarch domains: - biomedical - clinical - phenotype - pathways - genomics taxon: - NCBITaxon:9606 record_type: a human disorder or disorder subtype record_count: 3358 record_count_date: '2026-10-12' record_count_commit: 4cca8cef130493408e208c852c97b3b6baa9f37a record_count_source: path: kb/disorders pattern: '*.yaml' record_identifier_policy: Records are named by disorder and bound to Mondo disease identifiers where a term exists. ontologies: - MONDO - HP - GO - CL - UBERON - NCIT - CHEBI - GENO - PATO - ECTO - ENVO data_sources: - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:hadPrimarySource description: Evidence snippets are verbatim quotes from PubMed abstracts, checked at validation time. - name: ClinGen url: https://clinicalgenome.org/ relation_type: prov:used description: Gene-disease validity used for genetic factors. - name: BioModels url: https://www.ebi.ac.uk/biomodels/ relation_type: prov:used description: Source of quantitative models attached to disorders. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://opensource.org/license/bsd-3-clause label: BSD-3-Clause spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - dragon-ai-agent - goose evidence_policy: Every pathophysiological claim cites a PubMed reference with an exact quote from the abstract. The reference validator fetches the abstract and checks that the quote appears verbatim. Paraphrases, wrong PMIDs and fabricated citations fail validation. validation: - schema - ontology_terms - references - compliance curation_history: true curation_guide_url: https://dismech.monarchinitiative.org/ features: - causal_mechanism_graphs - evidence_snippets - ontology_grounding - append_only_history - knowledge_gaps - mechanism_modules - static_browser - embeddings_explorer - computational_models disclaimer: DisMech is AI-curated and AI-maintained. Most content is generated and maintained by AI curation agents, with human review as the pull-request gate. Automated validation guarantees that citations exist, quoted snippets are exact, and ontology terms are real. It does not guarantee scientific correctness. DisMech is not medical advice. If you have a health concern, consult a qualified healthcare professional. contacts: - category: Organization label: Monarch Initiative contact_details: - contact_type: url value: https://monarchinitiative.org - contact_type: github value: monarch-initiative - category: Individual label: Christopher J. Mungall orcid: 0000-0002-6601-2165 contact_details: - contact_type: github value: cmungall - category: Individual label: J. Harry Caufield orcid: 0000-0001-5705-7831 contact_details: - contact_type: email value: jhc@lbl.gov - contact_type: github value: caufieldjh products: - id: dismech.records category: RecordCorpus name: Disorder records description: One YAML file per disorder in kb/disorders, validated against the DisMech LinkML schema. product_url: https://github.com/monarch-initiative/dismech/tree/main/kb/disorders format: yaml - id: dismech.modules category: RecordCorpus name: Mechanism modules description: Conserved pathological patterns, such as the fibrotic response, that disorders declare conformance to. product_url: https://github.com/monarch-initiative/dismech/tree/main/kb/modules format: yaml - id: dismech.schema category: DataModelProduct name: DisMech LinkML schema product_url: https://github.com/monarch-initiative/dismech/blob/main/src/dismech/schema/dismech.yaml format: linkml compatibility: - linkml - id: dismech.browser category: GraphicalInterface name: Disorder browser description: Searchable browser over every disorder, with pathographs, mechanism modules, trajectories and an embeddings explorer. product_url: https://dismech.monarchinitiative.org/app/ format: html - id: dismech.docs category: DocumentationProduct name: DisMech documentation product_url: https://dismech.monarchinitiative.org/ format: html - id: dismech.models category: ModelProduct name: Computational models description: Metabolic, kinetic, Boolean and agent-based models attached to disorders, in SBML and Antimony. product_url: https://github.com/monarch-initiative/dismech/tree/main/models format: sbml publications: - id: https://zenodo.org/records/18720444 title: 'Unlocking Disease Mechanisms: Agentic AI for Clinical Knowledge' year: '2026' cross_references: [] creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: dufmech category: Mech layout: mech_detail name: DUFMech description: DUFMech is a knowledge base of protein domains of unknown function. One record is one Pfam family whose public InterPro metadata still reads like a domain or protein of unknown function (DUF or UPF), including families since renamed. Records are generated from a frozen, versioned InterPro/Pfam worklist. Scientific curation lives in separate overlays, so imported descriptions and seed labels never become functional claims. Every record is currently SEEDED. activity_status: active maturity: seeded homepage_url: https://culturebotai.github.io/DUFMech/ repository: https://github.com/CultureBotAI/DUFMech schema_url: https://github.com/CultureBotAI/DUFMech/blob/main/src/dufmech/schema/dufmech.yaml collection: - x-mech-suite domains: - genomics - microbiology record_type: a Pfam domain family of unknown function record_count: 8296 record_count_date: '2026-10-13' record_count_commit: 70a64554005fa4317a83a530e28ed217e3c3e0d2 record_count_source: path: data/families pattern: '*.yaml' record_identifier_policy: The Pfam family accession. ontologies: - Pfam - InterPro - UniProt - PDB data_sources: - name: InterPro url: https://www.ebi.ac.uk/interpro/ relation_type: prov:hadPrimarySource description: Pfam family metadata, read through the InterPro API into frozen worklists. - name: Pfam url: https://www.ebi.ac.uk/interpro/entry/pfam/ relation_type: prov:hadPrimarySource description: The families themselves, and their earlier names. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://opensource.org/license/bsd-3-clause label: BSD-3-Clause spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Imported descriptions and automated seed labels are not functional claims. Reference correspondence and Pfam/InterPro associations do not promote a SEEDED record; curation is a separate overlay. validation: - schema - ontology_terms - corpus_reproduction curation_history: true features: - ontology_grounding - append_only_history - knowledge_gaps - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: dufmech.records category: RecordCorpus name: Family records product_url: https://github.com/CultureBotAI/DUFMech/tree/main/data/families format: yaml - id: dufmech.schema category: DataModelProduct name: DUFMech LinkML schema product_url: https://github.com/CultureBotAI/DUFMech/blob/main/src/dufmech/schema/dufmech.yaml format: linkml compatibility: - linkml - mech_shared - id: dufmech.kgx category: GraphProduct name: DUFMech KGX export product_url: https://github.com/CultureBotAI/DUFMech/tree/main/exports/kgx format: kgx - id: dufmech.sssom category: MappingProduct name: DUFMech SSSOM export product_url: https://github.com/CultureBotAI/DUFMech/tree/main/exports/sssom format: sssom - id: dufmech.browser category: GraphicalInterface name: DUFMech dashboard product_url: https://culturebotai.github.io/DUFMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: proteintraitsmech relation: consumes description: A dated cross-Mech inventory lists the DUF-containing proteins that sibling Mechs hold, nearly all of them from ProteinTraitsMech. creation_date: '2026-10-13' last_modified_date: '2026-10-13' - id: habitatmech category: Mech layout: mech_detail name: HabitatMech description: HabitatMech is a knowledge base of microbial habitats and environments. Four source vocabularies that describe where microbes are found, JGI GOLD ecosystem paths, BacDive isolation sources, PREGO ontology annotations and the Madin et al. literature curation, are harmonized into records grounded in ENVO, UBERON, FOODON and BTO. Each source term becomes a source concept, each concept resolves to an identifier, and concepts that resolve to the same identifier merge into one record that keeps every source's attestation. activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/HabitatMech/ repository: https://github.com/CultureBotAI/HabitatMech schema_url: https://github.com/CultureBotAI/HabitatMech/blob/main/src/habitatmech/schema/habitatmech.yaml collection: - x-mech-suite - kg-microbe domains: - microbiology - environment taxon: - NCBITaxon:2 - NCBITaxon:2157 record_type: a microbial habitat or environment record_count: 3208 record_count_date: '2026-10-12' record_count_commit: 679a57e04cd2581aec2cfbd1cdc5a78f09ec8a4a record_count_source: path: data/habitats pattern: '*.yaml' record_identifier_policy: An ontology CURIE where one is defensible, otherwise a minted, content-hashed CURIE that can be re-grounded later. identifier_prefix: habitatmech ontologies: - ENVO - UBERON - FOODON - BTO - NCBITaxon data_sources: - name: JGI GOLD url: https://gold.jgi.doe.gov/ relation_type: prov:hadPrimarySource description: Five-level ecosystem classification paths. - name: BacDive url: https://bacdive.dsmz.de/ relation_type: prov:hadPrimarySource description: Flat isolation-source labels. - name: PREGO url: https://prego.hcmr.gr/ relation_type: prov:hadPrimarySource description: ENVO-annotated organism-environment associations. - name: Madin et al. trait database url: https://github.com/bacteria-archaea-traits/bacteria-archaea-traits relation_type: prov:hadPrimarySource description: Literature-curated habitat assignments. - name: KG-Microbe url: https://kghub.org/kg-microbe/ relation_type: prov:used description: Environmental parameters attached to records. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Records keep each source's attestation and assertion volume. Causal graphs carry evidence items with PMIDs or DOIs on every edge. validation: - schema - ontology_terms - references - corpus_reproduction curation_history: true curation_guide_url: https://github.com/CultureBotAI/HabitatMech/blob/main/docs/CURATION.md features: - causal_mechanism_graphs - ontology_grounding - append_only_history - knowledge_gaps - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - contact_type: url value: https://culturebotai.github.io/ - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: habitatmech.records category: RecordCorpus name: Habitat records description: One YAML file per habitat, filed by category (host-associated, engineered, aquatic, terrestrial, food, air, clinical, other). product_url: https://github.com/CultureBotAI/HabitatMech/tree/main/data/habitats format: yaml - id: habitatmech.schema category: DataModelProduct name: HabitatMech LinkML schema product_url: https://github.com/CultureBotAI/HabitatMech/blob/main/src/habitatmech/schema/habitatmech.yaml format: linkml compatibility: - linkml - mech_shared - id: habitatmech.browser category: GraphicalInterface name: HabitatMech browser description: Every record by category, plus the ENVO term requests the project is asking the ontology community for. product_url: https://culturebotai.github.io/HabitatMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: traitmech relation: shares_vocabulary_with description: Habitat causal graphs use a superset of TraitMech's node vocabulary, so a node may be a TraitMech or METPO trait. - target: culturemech relation: hands_off_to description: The one overlapping concept, BTO:0000316 culture medium, is handed to CultureMech rather than curated twice. creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: kg-registry category: Mech layout: mech_detail name: KG-Registry description: 'KG-Registry is a registry of knowledge graphs and the resources they are built from: data sources, ontologies, data models and aggregators. One record per resource: each record holds the resource''s description, domains, taxa, license, contacts, publications and activity status, and lists its products (graph dumps, APIs, browsers, mappings, documentation) with the upstream resources each product was derived from. Those provenance links make the registry a graph of where biomedical knowledge comes from and where it goes. Agents expand stub records and refresh stale ones with skills kept in the repository, scripted syncs pull records from the OBO Foundry, FRINK, KG-Bioportal and Translator, and every agent change arrives by pull request. KG-Registry is not strictly a Mech: its records are metadata about other resources rather than evidence-backed claims, and it keeps no append-only curation history beyond the repository''s own. It keeps the Mech practices of one record per entity in a closed LinkML schema, agent curation behind human review, and publication references checked against cached sources. MechRegistry is modeled on it.' activity_status: active maturity: curating homepage_url: https://kghub.org/kg-registry/ repository: https://github.com/Knowledge-Graph-Hub/kg-registry schema_url: https://github.com/Knowledge-Graph-Hub/kg-registry/blob/main/src/kg_registry/kg_registry_schema/schema/kg_registry_schema.yaml domains: - biomedical record_type: a knowledge resource (knowledge graph, data source, ontology, data model or aggregator) and its products record_count: 1137 record_count_date: '2026-10-12' record_count_commit: 7b84d297bb72bdf605193f1544943ed50bdabcf7 record_count_source: path: resource pattern: '*.md' exclude: - '*.*.md' - '*_eval*.md' record_identifier_policy: Records are keyed by a lowercase slug and stored as resource//.md. Products take the resource id followed by a dot and a short name, and their pages are generated next to the resource page. Many resources also carry their Biolink Information Resource (infores) identifier. ontologies: - NCBITaxon - MESH - NCIT data_sources: - name: OBO Foundry url: https://obofoundry.org/ relation_type: prov:wasDerivedFrom description: The OBO Foundry ontology registry, synced into ontology records. - name: FRINK OKN registry url: https://github.com/frink-okn/okn-registry relation_type: prov:wasDerivedFrom description: The Proto-OKN knowledge graph registry, synced into records with FRINK endpoint products. - name: KG-Bioportal url: https://github.com/ncbo/kg-bioportal relation_type: prov:wasDerivedFrom description: KGX transforms of BioPortal ontologies, added as graph products. - name: Translator url: https://kghub.org/kg-registry/resource/translator/translator.html relation_type: prov:wasDerivedFrom description: The current Translator KGX release products. - name: Biolink Information Resource Registry url: https://github.com/biolink/information-resource-registry relation_type: prov:used description: Infores identifiers for resources and stubs for resources not yet curated. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 code_license: id: https://opensource.org/licenses/BSD-3-Clause label: BSD 3-Clause License spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - dragon-ai-agent evidence_policy: Records describe resources rather than make claims, so evidence is the resource's own homepage, repository and publications. Publication titles, years, DOIs and first authors are checked against cached reference metadata, and provenance links must name registry identifiers rather than free text or URLs. validation: - schema - references curation_history: false curation_guide_url: https://kghub.org/kg-registry/docs/intro/agent-skills.html features: - static_browser contacts: - category: Organization label: Knowledge Graph Hub contact_details: - contact_type: github value: Knowledge-Graph-Hub - category: Individual label: J. Harry Caufield orcid: 0000-0001-5705-7831 contact_details: - contact_type: email value: jhc@lbl.gov - contact_type: github value: caufieldjh products: - id: kg-registry.records category: RecordCorpus name: Resource pages description: One Markdown file with a YAML header per resource under resource//, next to the generated pages for its products. product_url: https://github.com/Knowledge-Graph-Hub/kg-registry/tree/main/resource format: markdown - id: kg-registry.schema category: DataModelProduct name: KG-Registry LinkML schema product_url: https://github.com/Knowledge-Graph-Hub/kg-registry/blob/main/src/kg_registry/kg_registry_schema/schema/kg_registry_schema.yaml format: linkml compatibility: - linkml - id: kg-registry.app category: GraphicalInterface name: KG-Registry site description: A browser of every resource and product, with SQL search over the Parquet tables, a data quality dashboard and an interactive graph of resources and their sources. product_url: https://kghub.org/kg-registry/ format: html - id: kg-registry.yaml category: OtherProduct name: Registry YAML description: Every resource in one YAML file. JSON-LD and Turtle versions sit beside it. product_url: https://kghub.org/kg-registry/registry/kgs.yml format: yaml - id: kg-registry.parquet category: OtherProduct name: Registry Parquet tables description: Resources, domains, products and taxa as Parquet tables, which the read-only discovery skills query over HTTP. product_url: https://kghub.org/kg-registry/registry/parquet-downloads.html format: other - id: kg-registry.docs category: DocumentationProduct name: KG-Registry documentation product_url: https://kghub.org/kg-registry/docs/intro/ format: html tags: - Mech-like creation_date: '2026-10-10' last_modified_date: '2026-10-10' - id: mediaingredientmech category: Mech layout: mech_detail name: MediaIngredientMech synonyms: - MIM description: MediaIngredientMech is an LLM-assisted curation system for culture-media ingredient ontology mappings, with full audit trails. It manages the ingredient records aggregated from media recipes in CultureMech and owns ingredient identity for the X-Mech fleet. An ingredient record denotes a specific chemical someone can order. Where sources disagree about which form a recipe means, the record picks one by convention, preferring the term that carries the commercial CAS number, and keeps every raw form as a resolvable synonym. activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/MediaIngredientMech/ repository: https://github.com/CultureBotAI/MediaIngredientMech schema_url: https://github.com/CultureBotAI/MediaIngredientMech/blob/main/src/mediaingredientmech/schema/mediaingredientmech.yaml collection: - x-mech-suite - kg-microbe domains: - chemistry and biochemistry - nutrition - microbiology record_type: a culture-media ingredient record_count: 2953 record_count_date: '2026-10-12' record_count_commit: 1742bfd450470f5479720ace96ad2851bf4cd9d0 record_count_source: path: data/ingredients pattern: '*.yaml' ontologies: - CHEBI - CAS - NCIT - FOODON - ENVO - MESH data_sources: - name: CultureMech url: https://github.com/CultureBotAI/CultureMech relation_type: prov:wasDerivedFrom description: Unmapped ingredient strings and occurrence counts from recipes become the curation backlog. - name: ChEBI url: https://www.ebi.ac.uk/chebi/ relation_type: prov:used description: Primary mapping target for chemical ingredients. - name: FOODON url: https://foodon.org/ relation_type: prov:used description: Mapping target for complex and food-derived ingredients. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every mapping carries a MappingEvidence record and every curation action carries an event noting whether an LLM assisted. validation: - schema - ontology_terms - cross_field curation_history: true curation_guide_url: https://github.com/CultureBotAI/MediaIngredientMech/blob/main/MAPPING_SEMANTICS.md features: - ontology_grounding - append_only_history - knowledge_gaps - static_browser - sssom_export contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: mediaingredientmech.records category: RecordCorpus name: Ingredient records description: Mapped and unmapped ingredient records under data/ingredients/. product_url: https://github.com/CultureBotAI/MediaIngredientMech/tree/main/data/ingredients format: yaml - id: mediaingredientmech.schema category: DataModelProduct name: MediaIngredientMech LinkML schema product_url: https://github.com/CultureBotAI/MediaIngredientMech/blob/main/src/mediaingredientmech/schema/mediaingredientmech.yaml format: linkml compatibility: - linkml - mech_shared - id: mediaingredientmech.sssom category: MappingProduct name: Ingredient mappings (SSSOM) description: Ingredient to ontology mappings exported as SSSOM. product_url: https://github.com/CultureBotAI/MediaIngredientMech format: sssom compatibility: - sssom - id: mediaingredientmech.browser category: GraphicalInterface name: MediaIngredientMech browser product_url: https://culturebotai.github.io/MediaIngredientMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: culturemech relation: consumes description: Unmapped ingredient strings and occurrence counts become the curation backlog. Records link back to recipes by stable id with the CultureMechReference class. - target: culturemech relation: provides_to description: Curated ChEBI and FOODON mappings sync back to recipes. CultureMech vendors the ingredient-role enums and consumes the immutable label index. creation_date: '2026-09-10' last_modified_date: '2026-09-10' warnings: - The repository carries no LICENSE file as of 2026-09-10. The CC0 license recorded here is the one the X-Mech suite page states for the fleet. - id: naturalproductmech category: Mech layout: mech_detail name: NaturalProductMech description: NaturalProductMech is a knowledge base of individual natural product structures. One record is one chemical structure made by a living organism, carrying who makes it, from which biosynthetic gene cluster, what it does, and the evidence for all three. MIBiG, ChEBI, LOTUS, CyanoMetDB, NPClassifier, PubChem BioAssay and BindingDB are harmonized onto one record per InChIKey. Every record is currently SEEDED. The biosynthetic pathway and causal graph fields are empty and are the work the rest exists for. activity_status: active maturity: seeded repository: https://github.com/CultureBotAI/NaturalProductMech schema_url: https://github.com/CultureBotAI/NaturalProductMech/blob/main/src/naturalproductmech/schema/naturalproductmech.yaml collection: - x-mech-suite domains: - chemistry and biochemistry - microbiology - pathways record_type: a natural product chemical structure record_count: 3115 record_count_date: '2026-10-12' record_count_commit: e66f934111777c4ebfe69475d0520c0cfa074785 record_count_source: path: data/natural_products pattern: '*.yaml' record_identifier_policy: A ChEBI CURIE where the entry has a structure, otherwise a minted, content-hashed CURIE. A record with no InChIKey is never written. identifier_prefix: naturalproductmech ontologies: - CHEBI - NCBITaxon - MIBiG - NPAtlas - PubChem - UniProt data_sources: - name: MIBiG url: https://mibig.secondarymetabolites.org/ relation_type: prov:hadPrimarySource description: Structures, producer organisms and biosynthetic gene clusters. - name: ChEBI url: https://www.ebi.ac.uk/chebi/ relation_type: prov:hadPrimarySource description: Grounding and biological origins. - name: LOTUS url: https://lotus.naturalproducts.net/ relation_type: prov:hadPrimarySource description: Cited occurrences. - name: CyanoMetDB relation_type: prov:hadPrimarySource description: Cited occurrences for cyanobacterial metabolites. - name: NCBI Taxonomy url: https://www.ncbi.nlm.nih.gov/taxonomy relation_type: prov:used description: Name resolution for producers. - name: NPClassifier url: https://npclassifier.ucsd.edu/ relation_type: prov:used description: The filing pathway for each structure. - name: PubChem BioAssay url: https://pubchem.ncbi.nlm.nih.gov/ relation_type: prov:used description: Measured activities and targets. - name: BindingDB url: https://www.bindingdb.org/ relation_type: prov:used description: Measured activities and targets. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code evidence_policy: Producer organisms carry biosynthesis-grade evidence. Occurrences are cited. The corpus reproduces offline from committed inventories. validation: - schema - ontology_terms - corpus_reproduction curation_history: true features: - ontology_grounding - append_only_history - knowledge_gaps contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: naturalproductmech.records category: RecordCorpus name: Natural product records description: One YAML file per structure under data/natural_products//. product_url: https://github.com/CultureBotAI/NaturalProductMech/tree/main/data/natural_products format: yaml - id: naturalproductmech.schema category: DataModelProduct name: NaturalProductMech LinkML schema product_url: https://github.com/CultureBotAI/NaturalProductMech/blob/main/src/naturalproductmech/schema/naturalproductmech.yaml format: linkml compatibility: - linkml - mech_shared cross_references: - target: dismech relation: follows_pattern_of - target: antibioticmech relation: consumes description: Antimicrobial classification and cross-corpus links come from AntibioticMech. creation_date: '2026-09-10' last_modified_date: '2026-09-10' warnings: - No browser site is published yet. The GitHub repository is the only access point. - id: pathwaymech category: Mech layout: mech_detail name: PathwayMech description: 'PathwayMech is a knowledge base of pathway-level microbial mechanisms. One record is one pathway, held as a small graph: named participants, reactions, and causal edges between them, each edge citing a reference declared in the same record. It ports DisMech''s evidence modules to pathways. Importers read GO-CAM, WikiPathways, Rhea, MetaCyc, KEGG, Reactome, BiGG and a dozen other pathway resources into draft records, and identifiers are checked against frozen authority snapshots.' activity_status: active maturity: curating homepage_url: https://culturebotai.github.io/PathwayMech/ repository: https://github.com/CultureBotAI/PathwayMech schema_url: https://github.com/CultureBotAI/PathwayMech/blob/main/src/pathwaymech/schema/pathwaymech.yaml collection: - x-mech-suite domains: - pathways - microbiology - chemistry and biochemistry record_type: a microbial pathway mechanism record_count: 242 record_count_date: '2026-10-13' record_count_commit: 995b0ad9b19eaa3a46cc2898e73445cf0cce16db record_count_source: path: data/pathways pattern: '*.yaml' record_identifier_policy: The source pathway's CURIE, such as a WikiPathways or MetaCyc identifier, with an explicit prefix. ontologies: - CHEBI - RHEA - UniProt - GO - RO - ECO - NCBITaxon data_sources: - name: GO-CAM url: https://geneontology.org/docs/gocam-overview/ relation_type: prov:hadPrimarySource description: Causal activity models imported as draft pathway records. - name: WikiPathways url: https://www.wikipathways.org/ relation_type: prov:hadPrimarySource description: Pathway diagrams imported as draft records. - name: MetaCyc url: https://metacyc.org/ relation_type: prov:hadPrimarySource description: Pathway definitions and reactions. - name: Rhea url: https://www.rhea-db.org/ relation_type: prov:used description: Reaction identities and directions. - name: Reactome url: https://reactome.org/ relation_type: prov:hadPrimarySource description: Pathways read from BioPAX. - name: KEGG url: https://www.kegg.jp/ relation_type: prov:used description: Pathway maps read from KGML. - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:hadPrimarySource description: Evidence on mechanistic edges. license: id: https://creativecommons.org/licenses/by/4.0/ label: CC BY 4.0 spdx_id: CC-BY-4.0 code_license: id: https://opensource.org/license/bsd-3-clause label: BSD-3-Clause spdx_id: BSD-3-Clause curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every mechanistic edge cites a reference declared in the record, and evidence quotes are kept short enough to review. Structured source assertions carry exact source locations and are shown apart from verbatim quotations. validation: - schema - ontology_terms - references - cross_field curation_history: true features: - causal_mechanism_graphs - evidence_snippets - ontology_grounding - append_only_history - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: pathwaymech.records category: RecordCorpus name: Pathway records product_url: https://github.com/CultureBotAI/PathwayMech/tree/main/data/pathways format: yaml - id: pathwaymech.schema category: DataModelProduct name: PathwayMech LinkML schema product_url: https://github.com/CultureBotAI/PathwayMech/blob/main/src/pathwaymech/schema/pathwaymech.yaml format: linkml compatibility: - linkml - mech_shared - id: pathwaymech.browser category: GraphicalInterface name: PathwayMech browser product_url: https://culturebotai.github.io/PathwayMech/ format: html cross_references: - target: dismech relation: follows_pattern_of description: Ports DisMech's evidence modules into a pathway-specific schema. - target: traitmech relation: shares_vocabulary_with description: Inventories the UniProtKB proteins TraitMech, ProteinTraitsMech and other siblings hold, and the links they make to PathwayMech records. creation_date: '2026-10-13' last_modified_date: '2026-10-13' - id: proteintraitsmech category: Mech layout: mech_detail name: ProteinTraitsMech synonyms: - ProteinTraits description: 'ProteinTraitsMech is a knowledge base of protein sequence, structure, function and evolution traits, one YAML record per trait with optional evidence-backed causal graphs. Traits run along five axes: sequence (motifs, signal peptides, disordered regions, repeats, PTM sites), structure (folds, domains, sites, interfaces, symmetry), mixed sequence-structure (transmembrane spans, coiled coils), function (enzymatic activity, binding, cofactors, localisation) and evolution (conservation and pangenome partition). Records anchor to InterPro, Pfam, PROSITE, SMART, MEROPS, CATH, SCOP, PDB, GO, PR and UniProtKB.' activity_status: active maturity: seeded homepage_url: https://culturebotai.github.io/proteintraitsmech/ repository: https://github.com/CultureBotAI/proteintraitsmech schema_url: https://github.com/CultureBotAI/proteintraitsmech/blob/main/src/proteintraitsmech/schema/proteintraitsmech.yaml collection: - x-mech-suite - kg-microbe domains: - biological systems - chemistry and biochemistry - genomics record_type: a protein sequence, structure, function or evolution trait class record_count: 429293 record_count_date: '2026-10-12' record_count_commit: 70edd6f8458845f7d7783ac4f416df519f5e1de6 record_count_source: path: data/traits pattern: '*.yaml' record_identifier_policy: Preferably an existing InterPro, Pfam, PROSITE, CATH, SCOP, MEROPS or PR CURIE. ontologies: - InterPro - Pfam - UniProt - Rhea - GO - CHEBI - ARO - EC - CATH - SCOP - PDB - PR data_sources: - name: InterPro url: https://www.ebi.ac.uk/interpro/ relation_type: prov:wasDerivedFrom - name: Pfam url: https://www.ebi.ac.uk/interpro/entry/pfam/ relation_type: prov:wasDerivedFrom - name: Rhea url: https://www.rhea-db.org/ relation_type: prov:wasDerivedFrom - name: CATH url: https://www.cathdb.info/ relation_type: prov:wasDerivedFrom - name: SCOPe url: https://scop.berkeley.edu/ relation_type: prov:wasDerivedFrom - name: CARD url: https://card.mcmaster.ca/ relation_type: prov:wasDerivedFrom - name: UniProtKB url: https://www.uniprot.org/ relation_type: prov:used description: Release-pinned canonical example proteins and grounding assertions. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every CausalEdge must carry at least one EvidenceItem. Sources are catalogued with their licences in a download.yaml before ingestion. validation: - schema - ontology_terms - corpus_reproduction curation_history: true features: - causal_mechanism_graphs - ontology_grounding - append_only_history - knowledge_gaps - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: proteintraitsmech.records category: RecordCorpus name: Protein trait records description: One YAML file per trait under data/traits///.yaml. product_url: https://github.com/CultureBotAI/proteintraitsmech/tree/main/data/traits format: yaml - id: proteintraitsmech.schema category: DataModelProduct name: ProteinTraitsMech LinkML schema product_url: https://github.com/CultureBotAI/proteintraitsmech/blob/main/src/proteintraitsmech/schema/proteintraitsmech.yaml format: linkml compatibility: - linkml - mech_shared - id: proteintraitsmech.browser category: GraphicalInterface name: ProteinTraitsMech browser product_url: https://culturebotai.github.io/proteintraitsmech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: traitmech relation: sibling_of description: TraitMech holds organism-level ecophysiological traits. ProteinTraitsMech holds the protein-level machinery. creation_date: '2026-09-10' last_modified_date: '2026-09-10' - id: somamech category: Mech layout: mech_detail name: SOMAMech description: 'SOMAMech is a paper-extraction knowledge base for environmental health sciences. It curates publications on PM2.5, smoke and other inhaled exposures and their effects on airway biology into data that validate against the SOMA LinkML schema. One record per publication: each record is a Container that holds the paper''s study subjects, exposures, protocols, assays and measurements, linked to Key Events and Adverse Outcome Pathways. Assay classes cover ciliary function, airway surface liquid, mucociliary clearance, oxidative stress, CFTR ion transport, EGFR signaling, mucin and goblet cell biology, inflammatory markers in BALF and sputum, lung function and gene expression. Every extracted measurement carries an evidence block that quotes the paper, and the quote is checked against the paper text. Papers enter through a stub queue, are claimed one at a time by GitHub issue, and arrive by pull request. SOMAMech follows the DisMech curation pattern.' activity_status: active maturity: curating homepage_url: https://github.com/EHS-Data-Standards/somamech repository: https://github.com/EHS-Data-Standards/somamech schema_url: https://github.com/EHS-Data-Standards/somamech/blob/main/src/soma/schema/soma.yaml domains: - environment - biomedical - phenotype - biological systems taxon: - NCBITaxon:9606 - NCBITaxon:10090 record_type: a publication, extracted into its assays, measurements and Key Events record_count: 40 record_count_date: '2026-10-12' record_count_commit: d8f40d9f2ecadba8a17ba85a9365e8b8e5d2af85 record_count_source: path: kb/publications pattern: '*.yaml' record_identifier_policy: Records are named Container-.yaml and name their source paper by PMID in source_publication. KeyEvent identifiers are shared across papers. Every other entity identifier belongs to exactly one paper. ontologies: - CHEBI - GO - CL - UBERON - HP - PATO - ENVO - MONDO - NCBITaxon - OBI - UO - PR - CLO - ECTO - ExO - XCO data_sources: - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:hadPrimarySource description: The extracted publications. Evidence quotes are checked against cached abstracts and full text. - name: Zotero library relation_type: prov:used description: The seed corpus of papers and PDFs, resolved to PMIDs and DOIs in corpus.csv and turned into queue stubs. - name: SOMA url: https://github.com/EHS-Data-Standards/soma relation_type: prov:used description: The SOMA data model for Key Event and outcome assays, vendored as the schema. license: id: https://opensource.org/licenses/MIT label: MIT License spdx_id: MIT curation: agent_curated: true human_review: pull_request agents: - Claude Code evidence_policy: Every extracted measurement carries an evidence block that quotes the paper verbatim. Quotes are checked against the cached paper text. Where only the abstract can be cached, a local check against the full text writes a hash-bound verification receipt, and CI rejects any quote without one. validation: - schema - ontology_terms - references curation_history: false features: - evidence_snippets - ontology_grounding contacts: - category: Organization label: EHS-Data-Standards contact_details: - contact_type: github value: EHS-Data-Standards - category: Individual label: Sierra Moxon orcid: 0000-0002-8719-7760 contact_details: - contact_type: email value: smoxon@lbl.gov - contact_type: github value: sierra-moxon products: - id: somamech.records category: RecordCorpus name: Publication extractions description: One Container YAML file per extracted publication under kb/publications/. product_url: https://github.com/EHS-Data-Standards/somamech/tree/main/kb/publications format: yaml - id: somamech.schema category: DataModelProduct name: SOMA LinkML schema product_url: https://github.com/EHS-Data-Standards/somamech/blob/main/src/soma/schema/soma.yaml format: linkml compatibility: - linkml - id: somamech.queue category: OtherProduct name: Paper queue description: One stub per candidate paper, with screening status and decision. Stubs are the extraction queue and are not records. product_url: https://github.com/EHS-Data-Standards/somamech/tree/main/stubs format: yaml cross_references: - target: dismech relation: follows_pattern_of creation_date: '2026-09-22' last_modified_date: '2026-10-01' - id: taxonmech category: Mech layout: mech_detail name: TaxonMech description: 'TaxonMech is a knowledge base of microbial taxa and the strains behind them. One record per taxon, keyed by NCBI Taxonomy and harmonized with GTDB, LPSN, BacDive, MediaDive, GOLD, Madin et al. and BactoTraits through the kg-microbe transforms. Records are species and below. Higher taxa appear only in a record''s lineage. Each record keeps every source''s own identifier, mapping predicate and assertion count, the LPSN nomenclature with type strain designations, the GTDB species mapping with its genome count, and the BacDive strains with their culture-collection deposits. A primary focus is linking strain identifiers to genome identifiers: NCBI GenBank and RefSeq assemblies first, then GTDB, BV-BRC, IMG and AllTheBacteria records, each link carrying the source record that asserts it. Phenotypes, media and isolation sources are left to TraitMech, CultureMech and HabitatMech.' activity_status: active maturity: seeded homepage_url: https://culturebotai.github.io/TaxonMech/ repository: https://github.com/CultureBotAI/TaxonMech schema_url: https://github.com/CultureBotAI/TaxonMech/blob/main/src/taxonmech/schema/taxonmech.yaml collection: - x-mech-suite - kg-microbe domains: - microbiology - organisms - genomics taxon: - NCBITaxon:2 - NCBITaxon:2157 record_type: a microbial taxon at species rank or below record_count: 625960 record_count_date: '2026-10-12' record_count_commit: 56dcc69ed2a40f8c44a9df07242a39e36fabccf9 record_count_source: path: data/taxa pattern: '*.yaml' record_identifier_policy: Records are keyed by their NCBITaxon CURIE. Filenames are pinned by data/taxa/PATHS.tsv so a re-seed never renames an existing record. ontologies: - NCBITaxon - GTDB - BacDive - GOLD - insdc.gca - refseq - biosample - bioproject - img.taxon - brc.genome data_sources: - name: NCBI Taxonomy url: https://www.ncbi.nlm.nih.gov/taxonomy relation_type: prov:hadPrimarySource description: The identity of every record, its rank and its lineage, from a pinned snapshot. - name: GTDB url: https://gtdb.ecogenomic.org/ relation_type: prov:wasDerivedFrom description: Species mappings with the assemblies behind each, via kg-microbe. - name: LPSN url: https://lpsn.dsmz.de/ relation_type: prov:wasDerivedFrom description: Nomenclature, authority, correct-name status and type strain designations, via kg-microbe. - name: BacDive url: https://bacdive.dsmz.de/ relation_type: prov:wasDerivedFrom description: Strain records with culture-collection deposits and genome assertions. - name: GOLD url: https://gold.jgi.doe.gov/ relation_type: prov:wasDerivedFrom description: Organism, sequencing-project and analysis-project links from the public workbook. - name: AllTheBacteria url: https://allthebacteria.org/ relation_type: prov:wasDerivedFrom description: Assembly records joined through BioSample evidence. - name: StrainInfo url: https://straininfo.dsmz.de/ relation_type: prov:wasDerivedFrom description: Deposit-to-NCBI assertions and typed strain, deposit and nucleotide references. - name: MediaDive url: https://mediadive.dsmz.de/ relation_type: prov:wasDerivedFrom description: Media attestations per taxon. - name: Madin et al. url: https://doi.org/10.1038/s41597-020-0497-4 relation_type: prov:wasDerivedFrom description: Prokaryotic phenotypic trait compilation, as a source attestation. - name: BactoTraits url: https://doi.org/10.1016/j.ecolind.2021.108047 relation_type: prov:wasDerivedFrom description: Functional trait database, as a source attestation. - name: kg-microbe url: https://github.com/Knowledge-Graph-Hub/kg-microbe relation_type: prov:used description: The harmonized KGX inputs and the GTDB-to-NCBI and LPSN-to-NCBI mappings. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every causal edge must carry a citation. Seeded descriptive fields carry source attestations instead. A strain-to-genome link must name the source record that asserts it. Species membership and strain-name matching never supply a link. validation: - schema - corpus_reproduction curation_history: true features: - causal_mechanism_graphs - ontology_grounding - append_only_history - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: taxonmech.records category: RecordCorpus name: Taxon records description: One YAML file per taxon under data/taxa//.yaml. product_url: https://github.com/CultureBotAI/TaxonMech/tree/main/data/taxa format: yaml - id: taxonmech.schema category: DataModelProduct name: TaxonMech LinkML schema product_url: https://github.com/CultureBotAI/TaxonMech/blob/main/src/taxonmech/schema/taxonmech.yaml format: linkml compatibility: - linkml - mech_shared - id: taxonmech.browser category: GraphicalInterface name: TaxonMech browser product_url: https://culturebotai.github.io/TaxonMech/ format: html - id: taxonmech.strain_assemblies category: RecordCorpus name: Strain assembly inventory description: Uncapped inventory of strain-to-NCBI-assembly links, joined to BacDive strains on strain_id. Unlisted strains live here and not in the records. product_url: https://github.com/CultureBotAI/TaxonMech/blob/main/data/raw/strain_assemblies.tsv format: tsv cross_references: - target: dismech relation: follows_pattern_of - target: traitmech relation: hands_off_to description: Strain phenotypes are not held in TaxonMech. - target: culturemech relation: hands_off_to description: Growth media are not held in TaxonMech. - target: habitatmech relation: hands_off_to description: Isolation sources are not held in TaxonMech. creation_date: '2026-09-16' last_modified_date: '2026-09-16' - id: traitmech category: Mech layout: mech_detail name: TraitMech description: TraitMech is a knowledge base of microbial ecophysiological traits, seeded from METPO, the Microbial Ecophysiological Trait and Phenotype Ontology, and curated incrementally. Each trait, such as Gram type, motility, pH optimum or halophily, lives in its own YAML file with provenance back to its METPO source class and, where curated, literature evidence and a causal mechanism graph. Chemicals, microbes and enzymes are not seeded here. They belong to MediaIngredientMech and CultureMech. activity_status: active maturity: reviewed homepage_url: https://culturebotai.github.io/TraitMech/ repository: https://github.com/CultureBotAI/TraitMech schema_url: https://github.com/CultureBotAI/TraitMech/blob/main/src/traitmech/schema/traitmech.yaml collection: - x-mech-suite - kg-microbe domains: - microbiology - phenotype taxon: - NCBITaxon:2 - NCBITaxon:2157 record_type: a microbial ecophysiological trait record_count: 1105 record_count_date: '2026-10-12' record_count_commit: a57b006b32f2313579650d105d7da245a99a5b95 record_count_source: path: data/traits pattern: '*.yaml' record_identifier_policy: Records are keyed by their METPO CURIE. ontologies: - METPO - GO - NCBITaxon - CHEBI - UniProt - PATO data_sources: - name: METPO url: https://w3id.org/metpo relation_type: prov:wasDerivedFrom description: The seed. Every trait record traces to a METPO class (METPO 2025-11-25). - name: PubMed url: https://pubmed.ncbi.nlm.nih.gov/ relation_type: prov:used description: Evidence on causal graph edges. license: id: https://creativecommons.org/publicdomain/zero/1.0/ label: CC0 1.0 spdx_id: CC0-1.0 curation: agent_curated: true human_review: pull_request agents: - Claude Code - culturebotai-claw evidence_policy: Every CausalEdge carries at least one EvidenceItem with a PMID or DOI. Records carry a curation status of SEEDED, PROPOSED, REVIEWED or DEPRECATED. validation: - schema - ontology_terms - references curation_history: true features: - causal_mechanism_graphs - ontology_grounding - append_only_history - knowledge_gaps - static_browser contacts: - category: Organization label: CultureBotAI contact_details: - contact_type: github value: CultureBotAI - category: Individual label: Marcin P. Joachimiak orcid: 0000-0001-8175-045X contact_details: - contact_type: email value: mjoachimiak@lbl.gov - contact_type: github value: realmarcin products: - id: traitmech.records category: RecordCorpus name: Trait records description: One YAML file per trait under data/traits//.yaml. product_url: https://github.com/CultureBotAI/TraitMech/tree/main/data/traits format: yaml - id: traitmech.schema category: DataModelProduct name: TraitMech LinkML schema product_url: https://github.com/CultureBotAI/TraitMech/blob/main/src/traitmech/schema/traitmech.yaml format: linkml compatibility: - linkml - mech_shared - id: traitmech.browser category: GraphicalInterface name: TraitMech browser product_url: https://culturebotai.github.io/TraitMech/ format: html cross_references: - target: dismech relation: follows_pattern_of - target: proteintraitsmech relation: adopts_practice_of description: TraitMech adopted ProteinTraitsMech's licence-bearing download.yaml source catalogue, and a drift audit keeps shared trait tokens aligned. - target: mediaingredientmech relation: hands_off_to description: Chemicals are not seeded in TraitMech. - target: culturemech relation: hands_off_to description: Growth media are not seeded in TraitMech. creation_date: '2026-09-10' last_modified_date: '2026-09-10'