/uniprot-database

UniProt ID Mapping Databases

Complete list of databases supported by the UniProt ID Mapping service. Use these database names when calling the ID mapping API.

Retrieving Database List Programmatically

import requests
response = requests.get("https://rest.uniprot.org/configure/idmapping/fields")
databases = response.json()

UniProt Databases

UniProtKB

• UniProtKB_AC-ID - UniProt accession and ID
• UniProtKB - UniProt Knowledgebase
• UniProtKB-Swiss-Prot - Reviewed (Swiss-Prot)
• UniProtKB-TrEMBL - Unreviewed (TrEMBL)
• UniParc - UniProt Archive
• UniRef50 - UniRef 50% identity clusters
• UniRef90 - UniRef 90% identity clusters
• UniRef100 - UniRef 100% identity clusters

Sequence Databases

Nucleotide Sequence

• EMBL - EMBL/GenBank/DDBJ
• EMBL-CDS - EMBL coding sequences
• RefSeq_Nucleotide - RefSeq nucleotide sequences
• CCDS - Consensus CDS

Protein Sequence

• RefSeq_Protein - RefSeq protein sequences
• PIR - Protein Information Resource

Gene Databases

• GeneID - Entrez Gene
• Gene_Name - Gene name
• Gene_Synonym - Gene synonym
• Gene_OrderedLocusName - Ordered locus name
• Gene_ORFName - ORF name

Genome Databases

General

• Ensembl - Ensembl
• EnsemblGenomes - Ensembl Genomes
• EnsemblGenomes_PRO - Ensembl Genomes protein
• EnsemblGenomes_TRS - Ensembl Genomes transcript
• Ensembl_PRO - Ensembl protein
• Ensembl_TRS - Ensembl transcript

Organism-Specific

• KEGG - KEGG Genes
• PATRIC - PATRIC
• UCSC - UCSC Genome Browser
• VectorBase - VectorBase
• WBParaSite - WormBase ParaSite

Structure Databases

• PDB - Protein Data Bank
• AlphaFoldDB - AlphaFold Database
• BMRB - Biological Magnetic Resonance Data Bank
• PDBsum - PDB summary
• SASBDB - Small Angle Scattering Biological Data Bank
• SMR - SWISS-MODEL Repository

Protein Family and Domain Databases

• InterPro - InterPro
• Pfam - Pfam protein families
• PROSITE - PROSITE
• SMART - SMART domains
• CDD - Conserved Domain Database
• HAMAP - HAMAP
• PANTHER - PANTHER
• PRINTS - PRINTS
• ProDom - ProDom
• SFLD - Structure-Function Linkage Database
• SUPFAM - SUPERFAMILY
• TIGRFAMs - TIGRFAMs

Organism-Specific Databases

Model Organisms

• MGI - Mouse Genome Informatics
• RGD - Rat Genome Database
• FlyBase - FlyBase (Drosophila)
• WormBase - WormBase (C. elegans)
• Xenbase - Xenbase (Xenopus)
• ZFIN - Zebrafish Information Network
• dictyBase - dictyBase (Dictyostelium)
• EcoGene - EcoGene (E. coli)
• SGD - Saccharomyces Genome Database (yeast)
• PomBase - PomBase (S. pombe)
• TAIR - The Arabidopsis Information Resource

Human-Specific

• HGNC - HUGO Gene Nomenclature Committee
• CCDS - Consensus Coding Sequence Database

Pathway Databases

• Reactome - Reactome
• BioCyc - BioCyc
• PlantReactome - Plant Reactome
• SIGNOR - SIGNOR
• SignaLink - SignaLink

Enzyme and Metabolism

• EC - Enzyme Commission number
• BRENDA - BRENDA enzyme database
• SABIO-RK - SABIO-RK (biochemical reactions)
• MetaCyc - MetaCyc

Disease and Phenotype Databases

• OMIM - Online Mendelian Inheritance in Man
• MIM - MIM (same as OMIM)
• OrphaNet - Orphanet (rare diseases)
• DisGeNET - DisGeNET
• MalaCards - MalaCards
• CTD - Comparative Toxicogenomics Database
• OpenTargets - Open Targets

Drug and Chemical Databases

• ChEMBL - ChEMBL
• DrugBank - DrugBank
• DrugCentral - DrugCentral
• GuidetoPHARMACOLOGY - Guide to Pharmacology
• SwissLipids - SwissLipids

Gene Expression Databases

• Bgee - Bgee gene expression
• ExpressionAtlas - Expression Atlas
• Genevisible - Genevisible
• CleanEx - CleanEx

Proteomics Databases

• PRIDE - PRIDE proteomics
• PeptideAtlas - PeptideAtlas
• ProteomicsDB - ProteomicsDB
• CPTAC - CPTAC
• jPOST - jPOST
• MassIVE - MassIVE
• MaxQB - MaxQB
• PaxDb - PaxDb
• TopDownProteomics - Top Down Proteomics

Protein-Protein Interaction

• STRING - STRING
• BioGRID - BioGRID
• IntAct - IntAct
• MINT - MINT
• DIP - Database of Interacting Proteins
• ComplexPortal - Complex Portal

Ontologies

• GO - Gene Ontology
• GeneTree - Ensembl GeneTree
• HOGENOM - HOGENOM
• HOVERGEN - HOVERGEN
• KO - KEGG Orthology
• OMA - OMA orthology
• OrthoDB - OrthoDB
• TreeFam - TreeFam

Other Specialized Databases

Glycosylation

• GlyConnect - GlyConnect
• GlyGen - GlyGen

Protein Modifications

• PhosphoSitePlus - PhosphoSitePlus
• iPTMnet - iPTMnet

Antibodies

• Antibodypedia - Antibodypedia
• DNASU - DNASU

Protein Localization

• COMPARTMENTS - COMPARTMENTS
• NeXtProt - NeXtProt (human proteins)

Evolution and Phylogeny

• eggNOG - eggNOG
• GeneTree - Ensembl GeneTree
• InParanoid - InParanoid

Technical Resources

• PRO - Protein Ontology
• GenomeRNAi - GenomeRNAi
• PubMed - PubMed literature references

Common Mapping Scenarios

Example 1: UniProt to PDB

from_db = "UniProtKB_AC-ID"
to_db = "PDB"
ids = ["P01308", "P04637"]

Example 2: Gene Name to UniProt

from_db = "Gene_Name"
to_db = "UniProtKB"
ids = ["BRCA1", "TP53", "INSR"]

Example 3: UniProt to Ensembl

from_db = "UniProtKB_AC-ID"
to_db = "Ensembl"
ids = ["P12345"]

Example 4: RefSeq to UniProt

from_db = "RefSeq_Protein"
to_db = "UniProtKB"
ids = ["NP_000207.1"]

Example 5: UniProt to GO Terms

from_db = "UniProtKB_AC-ID"
to_db = "GO"
ids = ["P01308"]

Usage Notes

1. Database names are case-sensitive: Use exact names as listed

2. Many-to-many mappings: One ID may map to multiple target IDs

3. Failed mappings: Some IDs may not have mappings; check the failedIds field in results

4. Batch size limit: Maximum 100,000 IDs per job

5. Result expiration: Results are stored for 7 days

6. Bidirectional mapping: Most databases support mapping in both directions

API Endpoints

Get available databases

GET https://rest.uniprot.org/configure/idmapping/fields

Submit mapping job

POST https://rest.uniprot.org/idmapping/run
Content-Type: application/x-www-form-urlencoded

from={from_db}&to={to_db}&ids={comma_separated_ids}

Check job status

GET https://rest.uniprot.org/idmapping/status/{jobId}

Get results

GET https://rest.uniprot.org/idmapping/results/{jobId}

Resources

• ID Mapping tool: https://www.uniprot.org/id-mapping
• API documentation: https://www.uniprot.org/help/id_mapping
• Programmatic access: https://www.uniprot.org/help/api_idmapping