医学公开数据库查询与登记

references/interpro.md

Base URL

https://www.ebi.ac.uk/interpro/api

Authentication

None required. Fully public API.

Rate Limits

No published hard limits. EBI general guidance: be reasonable, use bulk downloads for large datasets.

Response Format

JSON by default. Some endpoints support ?format=json explicitly.

Key Endpoints

1. Entry Lookup (by accession)

GET https://www.ebi.ac.uk/interpro/api/entry/interpro/{accession}

Example:

GET https://www.ebi.ac.uk/interpro/api/entry/interpro/IPR000504

Returns JSON with entry name, type (family/domain/site/etc.), description, GO terms, literature references.

2. Entry Lookup by Member Database

GET https://www.ebi.ac.uk/interpro/api/entry/pfam/{pfam_accession}
GET https://www.ebi.ac.uk/interpro/api/entry/smart/{smart_accession}
GET https://www.ebi.ac.uk/interpro/api/entry/prosite/{prosite_accession}

Example:

GET https://www.ebi.ac.uk/interpro/api/entry/pfam/PF00076

3. Search / List Entries

GET https://www.ebi.ac.uk/interpro/api/entry/interpro?search={query}

Example:

GET https://www.ebi.ac.uk/interpro/api/entry/interpro?search=kinase

Returns paginated list of matching InterPro entries.

4. Protein Annotations — Get InterPro Entries for a Protein

GET https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/{uniprot_accession}

Example:

GET https://www.ebi.ac.uk/interpro/api/entry/interpro/protein/uniprot/P12345

Returns all InterPro entries annotating that protein.

5. Proteins with a Given Entry

GET https://www.ebi.ac.uk/interpro/api/protein/uniprot/entry/interpro/{accession}

Example:

GET https://www.ebi.ac.uk/interpro/api/protein/uniprot/entry/interpro/IPR000504

Returns paginated list of UniProt proteins annotated with that entry.

6. Structure Mappings

GET https://www.ebi.ac.uk/interpro/api/structure/pdb/entry/interpro/{accession}

Example:

GET https://www.ebi.ac.uk/interpro/api/structure/pdb/entry/interpro/IPR000504

7. Entry by Type Filter

GET https://www.ebi.ac.uk/interpro/api/entry/interpro?type=domain
GET https://www.ebi.ac.uk/interpro/api/entry/interpro?type=family
GET https://www.ebi.ac.uk/interpro/api/entry/interpro?type=homologous_superfamily

8. Taxonomy Cross-Reference

GET https://www.ebi.ac.uk/interpro/api/taxonomy/uniprot/entry/interpro/{accession}

Pagination

Responses include next and previous URLs:

{
  "count": 1234,
  "next": "https://www.ebi.ac.uk/interpro/api/entry/interpro?cursor=...&page_size=20",
  "previous": null,
  "results": [...]
}

Use ?page_size=N to control page size (default 20).

Entry Response Key Fields

{
  "metadata": {
    "accession": "IPR000504",
    "name": "RNA recognition motif domain",
    "type": "domain",
    "source_database": "interpro",
    "member_databases": {"pfam": {"PF00076": "RRM_1"}},
    "go_terms": [{"identifier": "GO:0003723", "name": "RNA binding"}],
    "description": ["<p>The RNA recognition motif...</p>"]
  }
}

Notes

• The API follows a composable URL pattern: combine entity types (entry, protein, structure, taxonomy) to create cross-reference queries.
• Member databases include pfam, smart, prosite (patterns), profile (PROSITE profiles), prints, panther, cdd, hamap, pirsf, sfld, cathgene3d, ssf, and ncbifam. tigrfams was replaced by ncbifam; discover current sources from the API root.