ProteinTraitsMech
proteintraitsmech
active seeded x-mech-suitekg-microbe
Also known as: ProteinTraits
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.
One record is
a protein sequence, structure, function or evolution trait class
429293 records as of 2026-10-12
Counted from data/traits/*.yaml at 70edd6f. Refreshed weekly.
License
Records: CC0 1.0
Curation model
| Agent-curated | Yes. AI agents generate or maintain most of the content. |
|---|---|
| Human review | pull_request. Agent changes arrive as pull requests that a person reviews and merges. |
| Agents and tools | 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 in CI | schema ontology_terms corpus_reproduction |
| Append-only history | Yes |
| Record identifiers | Preferably an existing InterPro, Pfam, PROSITE, CATH, SCOP, MEROPS or PR CURIE. |
Features
- causal_mechanism_graphs Records carry directed, evidence-backed graphs of mechanism.
- ontology_grounding Entities bind to public ontology terms with labels.
- append_only_history Every change is an event in an append-only history directory.
- knowledge_gaps Records carry structured open questions, controversies and curation to-dos.
- static_browser A static site lets a reader browse every record.
Grounding and sources
Ontologies and vocabularies: InterPro Pfam UniProt Rhea GO CHEBI ARO EC CATH SCOP PDB PR
| Source | Relation | What is taken |
|---|---|---|
| InterPro | prov:wasDerivedFrom | |
| Pfam | prov:wasDerivedFrom | |
| Rhea | prov:wasDerivedFrom | |
| CATH | prov:wasDerivedFrom | |
| SCOPe | prov:wasDerivedFrom | |
| CARD | prov:wasDerivedFrom | |
| UniProtKB | prov:used | Release-pinned canonical example proteins and grounding assertions. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Protein trait recordsproteintraitsmech.records |
RecordCorpus | yaml | One YAML file per trait under data/traits/ |
ProteinTraitsMech LinkML schemaproteintraitsmech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
ProteinTraitsMech browserproteintraitsmech.browser |
GraphicalInterface | html |
Relations to other Mechs
- follows_pattern_of dismech
- sibling_of traitmech: TraitMech holds organism-level ecophysiological traits. ProteinTraitsMech holds the protein-level machinery.
Referenced by
Contacts
- CultureBotAI (Organization) CultureBotAI
- Marcin P. Joachimiak (Individual) ORCID 0000-0001-8175-045X mjoachimiak@lbl.gov realmarcin
Registry entry
Created 2026-09-10. Last modified 2026-09-10. Edit this entry on GitHub.
Until 2026-10-01 the record count was the figure published on the X-Mech suite page. It is now counted from the repository tree, as for the other Mechs. At commit 86368bb on 2026-09-10 the tree held 429,271 trait files, which matches the suite page.