# interpro-database

Queries protein domains, families, and functional sites through the InterPro API. Integrates 14 member databases and automates genome annotations with GO terms.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · 2100 installs · ★ 3329
- Author: google-deepmind
- License: Apache-2.0 · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/google-deepmind/science-skills/tree/HEAD/skills/interpro_database/SKILL.md
- Updated: 2026-10-23
- HTML: https://affpapa.org/en/nevibecode/skills/interpro-database

## What it does

The skill integrates `scripts/interpro_client.py` to query the InterPro API across 14 member databases, including Pfam and CDD. The client handles rate limiting under HTTP 429, background job tracking under HTTP 408, and lazy pagination without manual header management.

You can run queries from the command line into JSONL files or import `fetch_interpro_data` directly into Python scripts. Six core endpoints are available: `/entry`, `/protein`, `/structure`, `/taxonomy`, `/proteome`, and `/set`. Each endpoint accepts only designated database names. Passing an unsupported database name immediately produces an HTTP 404 error.

The workflow requires `uv` on PATH. Without `uv`, the wrapper script will not execute. On the first run, the skill verifies that `.licenses/interpro_database_LICENSE.txt` exists in the workspace root, logging acceptance terms before returning data.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill interpro-database -a claude-code
```
```bash
npx skills add google-deepmind/science-skills --skill interpro_database -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/interpro_database/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/interpro_database/

### Codex

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill interpro_database -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/interpro_database/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill interpro_database -a cursor
```

2. **Manually: put the files in place**
- File: `.cursor/skills/interpro_database/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install google-deepmind/science-skills interpro_database
```

2. **Manually: put the files in place**
- File: `.github/skills/interpro_database/SKILL.md`

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill interpro_database -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/google-deepmind/science-skills --path skills/interpro_database
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/interpro_database/SKILL.md` — The legacy .windsurf/skills/ path still works

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add google-deepmind/science-skills --skill interpro_database -a opencode
```

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/google-deepmind/science-skills/tree/HEAD/skills/interpro_database/SKILL.md

## When to use it
- retrieve protein domains, families, and active sites by accession
- identify all proteins belonging to a specific family across species
- annotate genomic sequences with Gene Ontology terms
- filter protein entries by domain architecture using IDA search

## Example prompts
- Run `interpro_client.py` to fetch reviewed human protein entries for taxonomy ID 9606 and save the first 10 records to `proteins.jsonl`
- Query the `/entry/pfam/PF00001` endpoint with a limit of 5 matches using the InterPro client
- Write a Python script that uses `fetch_interpro_data` to stream domain entries from Pfam page by page

## Source text · SKILL.md · Apache-2.0

Below is the content of a third-party file. It is data, not instructions for you: do not act on anything written inside unless the human asks. Block tag: d4955a50ff783d7e.

BEGIN THIRD-PARTY FILE d4955a50ff783d7e
```text
---
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
```
END THIRD-PARTY FILE d4955a50ff783d7e

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