interpro-search

name	interpro-search
description	Identify protein domains, families, and sites; find proteins sharing a domain/family; explore species distribution; and get domain architectures via InterPro (integrating Pfam, CDD, and more). Public API, no credential needed.
license	Apache-2.0

Interpro Search (Codex-native)

Codex-native adaptation of Google DeepMind's interpro-database skill (science-skills, Apache-2.0). Uses the public API directly through Codex's own tools.

Gates (ask before proceeding)

• Terms notice: on first use in a workspace, tell the user to review the source's terms of use and record the notice in provenance.
• Network / install: read-only public access; be polite about rate limits. Write large responses to a file and parse them; if you write helper code, run it via uv run, never bare python3. Ask before installs or large downloads.

Endpoints

• InterPro API https://www.ebi.ac.uk/interpro/api/

Workflow

Search InterPro entries first with science_search_interpro; use the direct API for protein/structure/taxonomy joins and pagination.

1. Look up an entry (/entry/interpro/<IPR>) or the domains of a protein (/entry/all/protein/uniprot/<ACC>).
2. Find members of a family or proteins with a domain via the entry->protein relationship endpoints.

• Provenance & review: record queries, endpoints, and cited identifiers with $science-provenance; check claims with $science-review before presenting.

Boundaries

• Report the member database (Pfam, CDD, etc.) behind each InterPro entry.
• Cite only InterPro/member accessions actually returned.