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references/uniprot.md

Base URL

https://rest.uniprot.org

Identifier handling

UniProtKB accessions contain 6 or 10 alphanumeric characters under the official accession patterns; do not restrict them to P/Q plus five digits. Preserve the submitted accession and record the resolved primary accession when a secondary accession redirects. Isoform identifiers such as P04637-2 add a suffix and require an endpoint that supports isoforms; do not silently strip it and return the canonical sequence.

Authentication

No API key required. All endpoints are public.

Key Endpoints

1. Search proteins

GET /uniprotkb/search

Parameters:

Parameter	Type	Description
`query`	string	Required. Search query using UniProt query syntax (field:value pairs, boolean operators).
`format`	string	`json` (default), `tsv`, `fasta`, `xml`, `list`, `xlsx`, `obo`
`fields`	string	Comma-separated list of columns to return. Key fields: `accession`, `id`, `protein_name`, `gene_names`, `organism_name`, `organism_id`, `length`, `sequence`, `cc_function`, `go_id`, `go`, `xref_pdb`, `reviewed`, `ec`, `cc_subcellular_location`, `ft_domain`, `lineage`
`size`	int	Results per page (max 500, default 25)
`cursor`	string	Pagination cursor (returned in `Link` response header)
`sort`	string	Sort field and direction, e.g. `gene asc`, `length desc`, `annotation_score desc`

Example calls:

Search for reviewed human TP53:

https://rest.uniprot.org/uniprotkb/search?query=(gene:TP53) AND (organism_id:9606) AND (reviewed:true)&format=json&fields=accession,protein_name,gene_names,organism_name,length,cc_function&size=10

Search by protein name keyword:

https://rest.uniprot.org/uniprotkb/search?query=(protein_name:insulin) AND (reviewed:true)&format=json&size=5

Search by EC number (enzyme classification):

https://rest.uniprot.org/uniprotkb/search?query=(ec:2.7.11.1) AND (organism_id:9606)&format=json&size=25

Search by Gene Ontology:

https://rest.uniprot.org/uniprotkb/search?query=(go:0006915) AND (organism_id:9606) AND (reviewed:true)&format=json&size=25

Response (JSON):

{
  "results": [
    {
      "entryType": "UniProtKB reviewed (Swiss-Prot)",
      "primaryAccession": "P04637",
      "uniProtkbId": "P53_HUMAN",
      "organism": {
        "scientificName": "Homo sapiens",
        "taxonId": 9606
      },
      "proteinDescription": {
        "recommendedName": {
          "fullName": { "value": "Cellular tumor antigen p53" }
        }
      },
      "genes": [
        {
          "geneName": { "value": "TP53" },
          "synonyms": [{ "value": "P53" }]
        }
      ],
      "sequence": {
        "value": "MEEPQSDP...",
        "length": 393,
        "molWeight": 43653,
        "crc64": "..."
      },
      "comments": [...],
      "features": [...],
      "references": [...]
    }
  ]
}

Pagination: The Link response header contains the next page URL with the cursor parameter. Follow it to get subsequent pages.

2. Fetch single entry by accession

GET /uniprotkb/{accession}

Parameters:

Parameter	Type	Description
`format`	string	`json`, `tsv`, `fasta`, `xml`, `gff`

Example calls:

https://rest.uniprot.org/uniprotkb/P04637?format=json
https://rest.uniprot.org/uniprotkb/P04637.fasta

3. FASTA sequence retrieval

Append .fasta to the accession or use format=fasta:

https://rest.uniprot.org/uniprotkb/P04637.fasta

Batch FASTA from search:

https://rest.uniprot.org/uniprotkb/search?query=(gene:BRCA1) AND (organism_id:9606) AND (reviewed:true)&format=fasta

4. ID Mapping (convert between ID types)

ID mapping is a two-step async process.

Step 1: Submit job

POST /idmapping/run
Content-Type: application/x-www-form-urlencoded

from={dbFrom}&to={dbTo}&ids={comma-separated-ids}

Common from/to database names:

UniProtKB_AC-ID (UniProt accession)
Gene_Name
GeneID (NCBI Gene / Entrez Gene)
Ensembl, Ensembl_Genomes
RefSeq_Protein
PDB
ChEMBL
EMBL-GenBank-DDBJ
STRING

Returns:

{ "jobId": "abc123def456" }

Step 2: Poll and retrieve results

GET /idmapping/status/{jobId}

Poll the status response until no longer running. Then request GET /idmapping/details/{jobId} and follow its redirectURL for the correct result resource. A typical result path is:

GET /idmapping/results/{jobId}?format=json&size=500

Example:

Map Ensembl gene IDs to UniProt accessions:

POST /idmapping/run
from=Ensembl&to=UniProtKB&ids=ENSG00000141510,ENSG00000012048

Map UniProt to PDB:

POST /idmapping/run
from=UniProtKB_AC-ID&to=PDB&ids=P04637,P38398

Response (results):

{
  "results": [
    {
      "from": "ENSG00000141510",
      "to": {
        "primaryAccession": "P04637",
        "uniProtkbId": "P53_HUMAN",
        ...
      }
    }
  ]
}

5. UniRef (clustered sequences)

GET /uniref/search?query={query}&format=json
GET /uniref/{id}

Cluster IDs: UniRef100_P04637, UniRef90_P04637, UniRef50_P04637

6. UniParc (sequence archive)

GET /uniparc/search?query={query}&format=json
GET /uniparc/{upi}

7. Proteomes

GET /proteomes/search?query=(organism_id:9606)&format=json
GET /proteomes/{upid}

Example — human reference proteome:

https://rest.uniprot.org/proteomes/UP000005640?format=json

8. Taxonomy

GET /taxonomy/search?query={query}&format=json
GET /taxonomy/{taxonId}

Query Syntax

UniProt search queries support field:value syntax with boolean operators:

(gene:TP53) -- gene name
(organism_id:9606) -- NCBI taxonomy ID (9606 = human, 10090 = mouse)
(organism_name:"Homo sapiens") -- organism name
(reviewed:true) -- Swiss-Prot only (manually reviewed)
(protein_name:kinase) -- protein name contains keyword
(ec:2.7.11.1) -- enzyme classification
(go:0006915) -- Gene Ontology term ID
(xref:pdb-4HHB) -- cross-reference
(length:[100 TO 300]) -- sequence length range
(cc_disease:cancer) -- disease involvement
(ft_domain:SH2) -- domain annotation
(cc_subcellular_location:nucleus) -- subcellular location
(date_modified:[2024-01-01 TO *]) -- modification date

Combine with AND, OR, NOT:

(gene:BRCA1) AND (organism_id:9606) AND (reviewed:true)

Rate Limits

No hard published rate limit, but excessive requests will be throttled.
Use pagination (size + cursor) to batch results.
Batch ID mapping jobs instead of one-at-a-time lookups.
For large downloads, use the streaming endpoints or FTP site.
Respect Retry-After headers if you receive HTTP 429.

Error Format

{
  "url": "https://rest.uniprot.org/...",
  "messages": ["Error message here"]
}

HTTP 400 for bad queries, 404 for not found, 429 for rate limiting, 500 for server errors.

Mapping namespaces are directional: check https://rest.uniprot.org/configure/idmapping/fields for allowed from/to values. Preserve unmapped IDs and one-to-many mappings.

医学公开数据库查询与登记

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