terraphim / terraphim/terraphim-ai

Feature Request: Integrate external ontologies (UniProt, ChEBI)

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Dominant language
Rust
Stars
62
Forks
5
Avg merge
2h 27m
Merged PRs (30d)
1

Description

Summary

Integrate external ontology sources (starting with UniProt and ChEBI) into the dynamic ontology pipeline.

Context

Dynamic ontology currently works with local/domain terms; external ontology enrichment is listed as follow-up work.

Problem

Domain coverage can remain low for biomedical/scientific terms without external canonical vocabularies.

Proposed Scope

  • Add import/normalization adapters for UniProt and ChEBI.
  • Add source provenance metadata to grounded terms.
  • Handle versioning/sync strategy for external updates.
  • Define conflict-resolution policy between local and external terms.

Acceptance Criteria

  • External source adapters implemented behind feature flags/config
  • Provenance included in grounded term metadata
  • Conflicts resolved deterministically
  • Integration tests cover import + grounding paths

References

  • docs/handovers/dynamic-ontology-handover.md
  • docs/src/dynamic-ontology.md

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with docs/handovers/dynamic-ontology-handover.md and docs/src/dynamic-ontology.md to understand the existing dynamic ontology pipeline and its grounding paths. Then identify where import, metadata, configuration, and integration tests belong. Done means UniProt and ChEBI adapters, provenance, deterministic conflict handling, configurable synchronization, and passing import-to-grounding integration tests.

Written by the indexing model from the issue text.

Assessment

Tech stack
rust
Domain
ai, data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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