{ "mechs": [ { "id": "ai-gene-review", "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", "collection": [], "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_error": null, "record_count_error_date": null, "homepage_url": "https://ai4curation.github.io/ai-gene-review", "repository": "https://github.com/ai4curation/ai-gene-review", "license": "BSD 3-Clause License", "ontologies": [ "GO", "ECO", "NCBITaxon" ], "agent_curated": true, "human_review": "pull_request", "features": [ "evidence_snippets", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser" ] }, { "id": "aimech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/AIMech/", "repository": "https://github.com/CultureBotAI/AIMech", "license": "CC BY 4.0", "ontologies": [ "AIO", "BFO" ], "agent_curated": true, "human_review": "pull_request", "features": [ "ontology_grounding", "append_only_history", "static_browser" ] }, { "id": "antibioticmech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/AntibioticMech/", "repository": "https://github.com/CultureBotAI/AntibioticMech", "license": "CC BY 4.0", "ontologies": [ "CHEBI", "ARO", "CAS", "PubChem", "DrugBank", "NCBITaxon" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser", "embeddings_explorer" ] }, { "id": "cellstructuremech", "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", "collection": [ "x-mech-suite", "kg-microbe" ], "domains": [ "microbiology", "biological systems", "anatomy and development" ], "record_type": "a microbial cell structure or multi-protein complex", "record_count": 909, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/CellStructureMech/", "repository": "https://github.com/CultureBotAI/CellStructureMech", "license": "CC0 1.0", "ontologies": [ "GO", "NCBITaxon", "UniProt", "METPO", "Pfam", "PDB" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser", "embeddings_explorer" ] }, { "id": "cmmmech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/CMMMech/", "repository": "https://github.com/CultureBotAI/CMMMech", "license": "CC BY 4.0", "ontologies": [ "CHEBI", "NCBITaxon" ], "agent_curated": true, "human_review": "pull_request", "features": [ "ontology_grounding", "append_only_history", "static_browser" ] }, { "id": "communitymech", "name": "CommunityMech", "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", "collection": [ "x-mech-suite", "kg-microbe" ], "domains": [ "microbiology", "environment", "organisms" ], "record_type": "a microbial community", "record_count": 458, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/CommunityMech/", "repository": "https://github.com/CultureBotAI/CommunityMech", "license": "CC0 1.0", "ontologies": [ "NCBITaxon", "CHEBI", "GO", "ENVO", "GTDB" ], "agent_curated": true, "human_review": "pull_request", "features": [ "evidence_snippets", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser", "kgx_export" ] }, { "id": "culturemech", "name": "CultureMech", "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", "collection": [ "x-mech-suite", "kg-microbe" ], "domains": [ "microbiology", "nutrition", "chemistry and biochemistry" ], "record_type": "a culture-medium recipe", "record_count": 6320, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/CultureMech/", "repository": "https://github.com/CultureBotAI/CultureMech", "license": "CC0 1.0", "ontologies": [ "CHEBI", "KEGG", "FOODON", "UBERON", "CAS", "NCBITaxon" ], "agent_curated": true, "human_review": "pull_request", "features": [ "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser", "sssom_export" ] }, { "id": "dismech", "name": "DisMech", "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", "collection": [ "monarch" ], "domains": [ "biomedical", "clinical", "phenotype", "pathways", "genomics" ], "record_type": "a human disorder or disorder subtype", "record_count": 3358, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://dismech.monarchinitiative.org/", "repository": "https://github.com/monarch-initiative/dismech", "license": "CC BY 4.0", "ontologies": [ "MONDO", "HP", "GO", "CL", "UBERON", "NCIT", "CHEBI", "GENO", "PATO", "ECTO", "ENVO" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "evidence_snippets", "ontology_grounding", "append_only_history", "knowledge_gaps", "mechanism_modules", "static_browser", "embeddings_explorer", "computational_models" ] }, { "id": "dufmech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/DUFMech/", "repository": "https://github.com/CultureBotAI/DUFMech", "license": "CC BY 4.0", "ontologies": [ "Pfam", "InterPro", "UniProt", "PDB" ], "agent_curated": true, "human_review": "pull_request", "features": [ "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser" ] }, { "id": "habitatmech", "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", "collection": [ "x-mech-suite", "kg-microbe" ], "domains": [ "microbiology", "environment" ], "record_type": "a microbial habitat or environment", "record_count": 3208, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/HabitatMech/", "repository": "https://github.com/CultureBotAI/HabitatMech", "license": "CC0 1.0", "ontologies": [ "ENVO", "UBERON", "FOODON", "BTO", "NCBITaxon" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser" ] }, { "id": "kg-registry", "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", "collection": [], "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_error": null, "record_count_error_date": null, "homepage_url": "https://kghub.org/kg-registry/", "repository": "https://github.com/Knowledge-Graph-Hub/kg-registry", "license": "CC0 1.0", "ontologies": [ "NCBITaxon", "MESH", "NCIT" ], "agent_curated": true, "human_review": "pull_request", "features": [ "static_browser" ] }, { "id": "mediaingredientmech", "name": "MediaIngredientMech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/MediaIngredientMech/", "repository": "https://github.com/CultureBotAI/MediaIngredientMech", "license": "CC0 1.0", "ontologies": [ "CHEBI", "CAS", "NCIT", "FOODON", "ENVO", "MESH" ], "agent_curated": true, "human_review": "pull_request", "features": [ "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser", "sssom_export" ] }, { "id": "naturalproductmech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": null, "repository": "https://github.com/CultureBotAI/NaturalProductMech", "license": "CC BY 4.0", "ontologies": [ "CHEBI", "NCBITaxon", "MIBiG", "NPAtlas", "PubChem", "UniProt" ], "agent_curated": true, "human_review": "pull_request", "features": [ "ontology_grounding", "append_only_history", "knowledge_gaps" ] }, { "id": "pathwaymech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/PathwayMech/", "repository": "https://github.com/CultureBotAI/PathwayMech", "license": "CC BY 4.0", "ontologies": [ "CHEBI", "RHEA", "UniProt", "GO", "RO", "ECO", "NCBITaxon" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "evidence_snippets", "ontology_grounding", "append_only_history", "static_browser" ] }, { "id": "proteintraitsmech", "name": "ProteinTraitsMech", "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", "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_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/proteintraitsmech/", "repository": "https://github.com/CultureBotAI/proteintraitsmech", "license": "CC0 1.0", "ontologies": [ "InterPro", "Pfam", "UniProt", "Rhea", "GO", "CHEBI", "ARO", "EC", "CATH", "SCOP", "PDB", "PR" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser" ] }, { "id": "somamech", "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", "collection": [], "domains": [ "environment", "biomedical", "phenotype", "biological systems" ], "record_type": "a publication, extracted into its assays, measurements and Key Events", "record_count": 40, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://github.com/EHS-Data-Standards/somamech", "repository": "https://github.com/EHS-Data-Standards/somamech", "license": "MIT License", "ontologies": [ "CHEBI", "GO", "CL", "UBERON", "HP", "PATO", "ENVO", "MONDO", "NCBITaxon", "OBI", "UO", "PR", "CLO", "ECTO", "ExO", "XCO" ], "agent_curated": true, "human_review": "pull_request", "features": [ "evidence_snippets", "ontology_grounding" ] }, { "id": "taxonmech", "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", "collection": [ "x-mech-suite", "kg-microbe" ], "domains": [ "microbiology", "organisms", "genomics" ], "record_type": "a microbial taxon at species rank or below", "record_count": 625960, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/TaxonMech/", "repository": "https://github.com/CultureBotAI/TaxonMech", "license": "CC0 1.0", "ontologies": [ "NCBITaxon", "GTDB", "BacDive", "GOLD", "insdc.gca", "refseq", "biosample", "bioproject", "img.taxon", "brc.genome" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "ontology_grounding", "append_only_history", "static_browser" ] }, { "id": "traitmech", "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", "collection": [ "x-mech-suite", "kg-microbe" ], "domains": [ "microbiology", "phenotype" ], "record_type": "a microbial ecophysiological trait", "record_count": 1105, "record_count_date": "2026-10-12", "record_count_error": null, "record_count_error_date": null, "homepage_url": "https://culturebotai.github.io/TraitMech/", "repository": "https://github.com/CultureBotAI/TraitMech", "license": "CC0 1.0", "ontologies": [ "METPO", "GO", "NCBITaxon", "CHEBI", "UniProt", "PATO" ], "agent_curated": true, "human_review": "pull_request", "features": [ "causal_mechanism_graphs", "ontology_grounding", "append_only_history", "knowledge_gaps", "static_browser" ] } ] }