Uniprot Access

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

Audit 0.4.1 · source sha c8c1fc3a2b13 · 19 Oct 2026Report an issue or request a re-scan

• PublisherGPTomics GitHub organizationOwner of the repository this skill is read from
• Source folderGPTomics/bioSkills/database-access/uniprot-accessThe exact folder we audited
• LicenceMITAs the repository states it
• Commit pinned for this verdictc8c1fc3a2b13A new audit runs when the source changes
• Repository statusArchivedLast push 65 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON…

---
name: bio-uniprot-access
description: Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.
tool_type: python
primary_tool: requests
---

## Version Compatibility

Reference examples tested with: requests 2.31+, pandas 2.2+; UniProt REST API as of 2024_06 release

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show requests pandas`
- API surface: confirm endpoint URLs match https://www.uniprot.org/help/api

The REST API JSON schema is stable within a release; major schema changes are documented at https://www.uniprot.org/release-notes. The 2022 migration broke the legacy `https://www.uniprot.org/uniprot/...` endpoints.

# UniProt Access

**"Get protein information from UniProt"** -> Two facts dominate every UniProt workflow in 2026: (1) **the API endpoint migrated in 2022** from `https://www.uniprot.org/uniprot/...` to `https://rest.uniprot.org/uniprotkb/...` with a substantially different JSON schema; pre-2022 code does not work as-is. (2) **`?fields=`** is essential — default JSON returns the full entry (~20-30 KB each); for bulk pulls, request only the fields actually needed.

The major databases under the UniProt umbrella have different scopes:

- **UniProtKB**: the curated knowledgebase — Swiss-Prot (manually reviewed, ~570K entries as of 2024) + TrEMBL (auto-annotated, ~250M). Always specify `reviewed:true` for high-quality reference work.
- **UniRef**: clustered sequences at 100%, 90%, 50% identity. UniRef50 is the standard for redundancy reduction.
- **UniParc**: archival "every unique sequence ever seen" — for provenance and historical lookup.
- **Proteomes**: organism-level groupings; reference proteomes (one per species) are the canonical subset.

- Python: `requests.get('https://rest.uniprot.org/uniprotkb/...')` (REST API)
- Python: `Bio.ExPASy.get_sprot_raw()` (BioPython; legacy SwissProt format)
- CLI: `curl https://rest.uniprot.org/uniprotkb/P04637.json`

## Required Setup

```python
import requests
import pandas as pd
import time
```

No API key required. Rate limit is generous (~200 req/sec tolerated empirically); ID-mapping has its own job queue.

## Endpoint reference

Base: `https://rest.uniprot.org/`

| Resource | Endpoint | Use |
|---|---|---|
| Single entry | `/uniprotkb/{accession}` | One protein record |
| Search | `/uniprotkb/search` | Query with up to 500 results per page |
| Stream | `/uniprotkb/stream` | No 500-result limit; for bulk |
| Batch by accession | `/uniprotkb/accessions` | Multiple specific accessions |
| ID Mapping (run) | `/idmapping/run` | Submit conversion job |
| ID Mapping (status) | `/idmapping/status/{jobId}` | Poll |
| ID Mapping (results) | `/idmapping/results/{jobId}` | Retrieve |
| UniRef entry | `/uniref/{cluster_id}` | One cluster |
| UniRef search | `/uniref/search` | UniRef cluster queries |
| Proteome | `/proteomes/{upid}` | Organism proteome |
| Proteome FASTA | `/proteomes/{upid}.fasta.gz` | Download whole proteome |
| Taxonomy | `/taxonomy/{taxid}` | Taxonomy info |

Append `.json`, `.fasta`, `.tsv`, `.xml`, `.txt`, or `.gff` to single-entry URLs to control format.

## Search query syntax

UniProt search queries use a Lucene-like syntax distinct from Entrez:

| Query | Means |
|---|---|
| `gene:TP53` | Gene name TP53 |
| `gene_exact:TP53` | Exact gene name (no wildcard match) |
| `organism_id:9606` | Human (NCBI taxonomy ID) |
| `organism_name:"Homo sapiens"` | By name (slower than taxid) |
| `reviewed:true` | Swiss-Prot only |
| `reviewed:false` | TrEMBL only |
| `length:[100 TO 500]` | Sequence length range |
| `go:0006915` | GO term (apoptosis) |
| `keyword:KW-0067` | UniProt keyword |
| `ec:2.7.1.1` | Enzyme classification |
| `database:pdb` | Has PDB cross-ref |
| `xref:pdb` | Same as above |
| `existence:1` | Evidence at protein level (1 = strongest) |

Combine: `organism_id:9606 AND reviewed:true AND keyword:KW-0067 AND xref:pdb`.

## `?fields=` for bulk pulls

Default JSON entry is ~20-30 KB. For batch work, restrict fields:

```python
fields = 'accession,id,gene_names,protein_name,length,sequence,xref_pdb,xref_alphafolddb'
url = 'https://rest.uniprot.org/uniprotkb/search'
params = {'query': 'organism_id:9606 AND reviewed:true', 'fields': fields, 'format': 'tsv', 'size': 500}
```

Common field selectors:
| Field | Returns |
|---|---|
| `accession`, `id` | Primary accession (P04637), entry name (P53_HUMAN) |
| `gene_names` | All gene names |
| `gene_primary` | Primary gene name only |
| `protein_name` | Recommended name |
| `organism_name`, `organism_id` | Species |
| `length`, `mass` | Sequence stats |
| `sequence` | The actual sequence |
| `cc_function`, `cc_subcellular_location` | Function and localization comments |
| `ft_domain`, `ft_binding`, `ft_active_site` | Domain/site features |
| `go_p`, `go_c`, `go_f` | GO biological process / cellular component / molecular function |
| `xref_pdb`, `xref_alphafolddb`, `xref_ensembl`, `xref_refseq` | Cross-references |
| `keyword` | UniProt keywords |
| `ec` | Enzyme classification |
| `reviewed` | Swiss-Prot vs TrEMBL flag |
| `cc_alternative_products` | Isoforms |

## Stream vs search vs accessions

| Endpoint | When | Limit |
|---|---|---|
| `/uniprotkb/{acc}` | One accession | 1 entry |
| `/uniprotkb/accessions?accessions=...` | Several known accessions | Up to ~100 per call |
| `/uniprotkb/search?query=...` | Query-driven; need pagination | 500 results per page; `cursor=` for paging |
| `/uniprotkb/stream?query=...

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

1. 2026-10-19
   ✓SAFE B 89 / 100

   first audit · source c8c1fc3a2b13

Questions about Uniprot Access

• github.com/GPTomics/bioSkills/tree/main/database-access/uniprot- — the audited source at commit c8c1fc3a2b13 and every finding aboveObserved · 19 Oct 2026

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