DisMech
dismech
active curating monarch version v0.1.39
Also known as: Disorder Mechanisms Knowledge Base, Disease Mechanisms KB
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.
One record is
a human disorder or disorder subtype
3358 records as of 2026-10-12
Counted from kb/disorders/*.yaml at 4cca8ce. 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, 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 in CI | schema ontology_terms references compliance |
| Append-only history | Yes |
| Record identifiers | Records are named by disorder and bound to Mondo disease identifiers where a term exists. |
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.
- knowledge_gaps Records carry structured open questions, controversies and curation to-dos.
- mechanism_modules Recurring mechanisms are factored into reusable modules that records declare conformance to.
- static_browser A static site lets a reader browse every record.
- embeddings_explorer The site offers an embedding map or nearest-neighbour view of records.
- computational_models The Mech carries quantitative or executable models alongside records.
Grounding and sources
Ontologies and vocabularies: MONDO HP GO CL UBERON NCIT CHEBI GENO PATO ECTO ENVO
| Source | Relation | What is taken |
|---|---|---|
| PubMed | prov:hadPrimarySource | Evidence snippets are verbatim quotes from PubMed abstracts, checked at validation time. |
| ClinGen | prov:used | Gene-disease validity used for genetic factors. |
| BioModels | prov:used | Source of quantitative models attached to disorders. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Disorder recordsdismech.records |
RecordCorpus | yaml | One YAML file per disorder in kb/disorders, validated against the DisMech LinkML schema. |
Mechanism modulesdismech.modules |
RecordCorpus | yaml | Conserved pathological patterns, such as the fibrotic response, that disorders declare conformance to. |
DisMech LinkML schemadismech.schema |
DataModelProduct | linkml
linkml |
|
Disorder browserdismech.browser |
GraphicalInterface | html | Searchable browser over every disorder, with pathographs, mechanism modules, trajectories and an embeddings explorer. |
DisMech documentationdismech.docs |
DocumentationProduct | html | |
Computational modelsdismech.models |
ModelProduct | sbml | Metabolic, kinetic, Boolean and agent-based models attached to disorders, in SBML and Antimony. |
Relations to other Mechs
Referenced by
- ai-gene-review adopts_practice_of
- AIMech follows_pattern_of
- AntibioticMech follows_pattern_of
- CellStructureMech follows_pattern_of
- CMMMech follows_pattern_of
- CommunityMech follows_pattern_of
- CultureMech follows_pattern_of
- DUFMech follows_pattern_of
- HabitatMech follows_pattern_of
- MediaIngredientMech follows_pattern_of
- NaturalProductMech follows_pattern_of
- PathwayMech follows_pattern_of
- ProteinTraitsMech follows_pattern_of
- SOMAMech follows_pattern_of
- TaxonMech follows_pattern_of
- TraitMech follows_pattern_of
Publications
- Unlocking Disease Mechanisms: Agentic AI for Clinical Knowledge. 2026. https://zenodo.org/records/18720444
Contacts
- Monarch Initiative (Organization) https://monarchinitiative.org monarch-initiative
- Christopher J. Mungall (Individual) ORCID 0000-0002-6601-2165 cmungall
- J. Harry Caufield (Individual) ORCID 0000-0001-5705-7831 jhc@lbl.gov caufieldjh
Registry entry
Created 2026-09-10. Last modified 2026-09-10. Edit this entry on GitHub.
DisMech is the reference implementation of the Mech pattern. The X-Mech suite
vendors two of its record sections, Discussion and Dataset, through the shared
mech_shared.yaml module.