PathwayMech
pathwaymech
active curating x-mech-suite
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.
One record is
a microbial pathway mechanism
242 records as of 2026-10-13
Counted from data/pathways/*.yaml at 995b0ad. Refreshed weekly.
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 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 in CI | schema ontology_terms references cross_field |
| Append-only history | Yes |
| Record identifiers | The source pathway's CURIE, such as a WikiPathways or MetaCyc identifier, with an explicit prefix. |
Features
- causal_mechanism_graphs Records carry directed, evidence-backed graphs of mechanism.
- evidence_snippets Evidence items quote the cited source verbatim.
- ontology_grounding Entities bind to public ontology terms with labels.
- append_only_history Every change is an event in an append-only history directory.
- static_browser A static site lets a reader browse every record.
Grounding and sources
Ontologies and vocabularies: CHEBI RHEA UniProt GO RO ECO NCBITaxon
| Source | Relation | What is taken |
|---|---|---|
| GO-CAM | prov:hadPrimarySource | Causal activity models imported as draft pathway records. |
| WikiPathways | prov:hadPrimarySource | Pathway diagrams imported as draft records. |
| MetaCyc | prov:hadPrimarySource | Pathway definitions and reactions. |
| Rhea | prov:used | Reaction identities and directions. |
| Reactome | prov:hadPrimarySource | Pathways read from BioPAX. |
| KEGG | prov:used | Pathway maps read from KGML. |
| PubMed | prov:hadPrimarySource | Evidence on mechanistic edges. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Pathway recordspathwaymech.records |
RecordCorpus | yaml | |
PathwayMech LinkML schemapathwaymech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
PathwayMech browserpathwaymech.browser |
GraphicalInterface | html |
Relations to other Mechs
- follows_pattern_of dismech: Ports DisMech's evidence modules into a pathway-specific schema.
- shares_vocabulary_with traitmech: Inventories the UniProtKB proteins TraitMech, ProteinTraitsMech and other siblings hold, and the links they make to PathwayMech records.
Contacts
- CultureBotAI (Organization) CultureBotAI
- Marcin P. Joachimiak (Individual) ORCID 0000-0001-8175-045X mjoachimiak@lbl.gov realmarcin
Registry entry
Created 2026-10-13. Last modified 2026-10-13. Edit this entry on GitHub.
Joined the X-Mech fleet manifest on 2026-09-28. Of 242 records, 99 carry a curation history as of 2026-10-13.