DUFMech
dufmech
active seeded x-mech-suite
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.
One record is
a Pfam domain family of unknown function
8296 records as of 2026-10-13
Counted from data/families/*.yaml at 70a6455. Refreshed weekly.
Domains
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 | 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 in CI | schema ontology_terms corpus_reproduction |
| Append-only history | Yes |
| Record identifiers | The Pfam family accession. |
Features
- 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: Pfam InterPro UniProt PDB
| Source | Relation | What is taken |
|---|---|---|
| InterPro | prov:hadPrimarySource | Pfam family metadata, read through the InterPro API into frozen worklists. |
| Pfam | prov:hadPrimarySource | The families themselves, and their earlier names. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Family recordsdufmech.records |
RecordCorpus | yaml | |
DUFMech LinkML schemadufmech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
DUFMech KGX exportdufmech.kgx |
GraphProduct | kgx | |
DUFMech SSSOM exportdufmech.sssom |
MappingProduct | sssom | |
DUFMech dashboarddufmech.browser |
GraphicalInterface | html |
Relations to other Mechs
- follows_pattern_of dismech
- consumes proteintraitsmech: A dated cross-Mech inventory lists the DUF-containing proteins that sibling Mechs hold, nearly all of them from ProteinTraitsMech.
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.
The worklist was first frozen on 2026-10-01 with 6,532 families. The current snapshot,
interpro-pfam-duf-2026-10-10, holds 8,296, including families Pfam has renamed away from
DUF or UPF names.