/interpro_database

name: interpro-database
description: >
  Identify domains, families, and sites in proteins; find all proteins in a
  family or sharing a domain; explore species distribution for a domain;
  annotate genomes with protein families and GO terms. InterPro combines 14
  databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N
  significantly expands annotation and sequence coverage with deep learning.
  Includes domain architecture (IDA) search.

InterPro Database Access

Prerequisites

1. **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure `uv` is installed and on PATH. 2. **User Notification**: If .licenses/interpro_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.ebi.ac.uk/interpro/ and https://www.ebi.ac.uk/about/terms-of-use/, then (2) create the file recording the notification text and timestamp.

Overview

InterPro combines signatures from multiple, diverse databases into a single searchable resource, reducing redundancy and helping users interpret their sequence analysis results. By uniting these member databases (e.g., Pfam, CDD, SMART), InterPro capitalises on their individual strengths to produce a powerful diagnostic tool and integrated resource.

Use `interpro-database` to:

• Identify what domains, families, and sites are found in a particular

protein.

• Identify all proteins that belong to a protein family or contain a

particular domain, even when the names and activities of the proteins are highly variable.

• Examine the species in which a particular protein family or domain is found.
• Annotate genomes with protein family information and Gene Ontology (GO)

terms.

This skill provides a robust utility, `interpro_client.py`, to interact with the InterPro API seamlessly. It natively handles rate limiting (HTTP 429), background query sleep tracking (HTTP 408), terminal errors (HTTP 404/410), and lazy pagination.

Core Rules

• **Use the Wrapper**: ALWAYS execute the `scripts/interpro_client.py` helper

script to query the database rather than accessing the database directly. The scripts automatically enforce fair use and implement retry logic.

• **For exploratory queries**: ALWAYS use the CLI with a strict `--limit`.

This allows you to rapidly understand the data schema without polluting your context window or fetching millions of results.

• **Output to file**: Use the CLI with --output to output to a file rather

than attempting to print it all to the console. Process the output using jq or code.

• **For more complex pipelines** import the module natively into your Python

scripts to consume the generator directly, preventing the need to deserialize CLI strings in large workflows.

• **Notification**: If this skill is used, ensure this is mentioned in the

output.

Examples:

uv run ./scripts/interpro_client.py fetch protein --source_db reviewed --limit 2 --query_params tax_id=9606 --output exploratory_results.jsonl

import sys
sys.path.append('scripts')
from interpro_client import fetch_interpro_data
import itertools

# fetch_interpro_data lazily yields results page-by-page
results = fetch_interpro_data(
    endpoint="entry",
    source_db="pfam",
    query_params={"page_size": 10}
)
for match in itertools.islice(results, 10):
    print(match["metadata"]["accession"])

4 Ways to Construct Endpoints:

The arguments strictly map to the four common API path constructions. **Do not format your own `/` separated strings:**

1. **`/{endpoint}`** (e.g. `/entry`) `uv run ./scripts/interpro_client.py fetch entry --limit 10 --output entries.jsonl` 2. **`/{endpoint}/{sourceDB}`** (e.g. `/entry/pfam`) `uv run ./scripts/interpro_client.py fetch entry --source_db pfam --limit 10 --output pfam_entries.jsonl` 3. **`/{endpoint}/{sourceDB}/{accession}`** (e.g. `/entry/pfam/PF00001`) `uv run ./scripts/interpro_client.py fetch entry --source_db pfam --accession PF00001 --limit 10 --output pf00001_entry.jsonl` 4. **`/{endpoint}/{sourceDB}/{linked_endpoint}/{sourceDB}/{accession}`** (e.g. `/entry/interpro/protein/uniprot/P04637`) `uv run ./scripts/interpro_client.py fetch entry \ --source_db interpro \ --linked_endpoint protein \ --linked_source_db uniprot \ --linked_accession P04637 \ --limit 10 --output p04637_entries.jsonl`

Valid Source Databases (`--source_db`)

Each endpoint only accepts specific `source_db` values. Using an invalid value returns a 404 error.

• **`/entry`** (16 values): `interpro`, `pfam`, `cathgene3d`, `ssf`,

`panther`, `cdd`, `profile`, `smart`, `ncbifam`, `prosite`, `prints`, `hamap`, `pirsf`, `sfld`, `antifam`.

• **`/protein`** (3 values): `uniprot` (all), `reviewed` (SwissProt),

`unreviewed` (TrEMBL).

• **`/structure`** (1 value): `pdb`.
• **`/taxonomy`** (1 value): `uniprot`.
• **`/proteome`** (1 value): `uniprot`.
• **`/set`** (2 values): `pfam`, `cdd`.

Quick Reference / Core Endpoints & Parameters

**For a complete, exhaustive list of all query parameters, see the [Full API Reference](references/api_reference.md).**

The API is fully open and supports 6 core endpoints. You can combine them using the linked parameters described above. Below is a nested list of the specific query parameters available for each endpoint:

• **`/entry`** (Domain, family, active site, repeat, or homologous superfamily

entries)

• `integrated`: Filter by integrated status (e.g., `pfam`).
• `type`: Filter by type (e.g., `family`, `domain`,

`homologous_superfamily`).

• `go_term` / `go_category`: Filter by Gene Ontology.
• `ida_search` / `ida_ignore` / `exact` / `ordered`: Filter by domain

architecture (see IDA Search section).

• `extra_fields`: Request additional data (e.g., `counters` for match

coordi