gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/uniprot-database/references/api_fields.md

UniProt API Fields Reference

Complete list of available fields for customizing UniProt API queries. Use these fields with the fields parameter to retrieve only the data you need.

Usage

Add fields parameter to your query:

https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length

Multiple fields are comma-separated. No spaces after commas.

Core Fields

Identification

• accession - Primary accession number (e.g., P12345)
• id - Entry name (e.g., INSR_HUMAN)
• uniprotkb_id - Same as id
• entryType - REVIEWED (Swiss-Prot) or UNREVIEWED (TrEMBL)

Protein Names

• protein_name - Recommended and alternative protein names
• gene_names - Gene name(s)
• gene_primary - Primary gene name
• gene_synonym - Gene synonyms
• gene_oln - Ordered locus names
• gene_orf - ORF names

Organism Information

• organism_name - Organism scientific name
• organism_id - NCBI taxonomy identifier
• lineage - Taxonomic lineage
• virus_hosts - Virus host organisms (for viral proteins)

Sequence Information

• sequence - Amino acid sequence
• length - Sequence length
• mass - Molecular mass (Daltons)
• fragment - Whether entry is a fragment
• checksum - Sequence CRC64 checksum

Annotation Fields

Function and Biology

• cc_function - Function description
• cc_catalytic_activity - Catalytic activity
• cc_activity_regulation - Activity regulation
• cc_pathway - Metabolic pathway information
• cc_cofactor - Cofactor information

Interaction and Localization

• cc_interaction - Protein-protein interactions
• cc_subunit - Subunit structure
• cc_subcellular_location - Subcellular location
• cc_tissue_specificity - Tissue specificity
• cc_developmental_stage - Developmental stage expression

Disease and Phenotype

• cc_disease - Disease associations
• cc_disruption_phenotype - Disruption phenotype
• cc_allergen - Allergen information
• cc_toxic_dose - Toxic dose information

Post-translational Modifications

• cc_ptm - Post-translational modifications
• cc_mass_spectrometry - Mass spectrometry data

Other Comments

• cc_alternative_products - Alternative products (isoforms)
• cc_polymorphism - Polymorphism information
• cc_rna_editing - RNA editing
• cc_caution - Caution notes
• cc_miscellaneous - Miscellaneous information
• cc_similarity - Sequence similarities
• cc_sequence_caution - Sequence caution
• cc_web_resource - Web resources

Feature Fields (ft_)

Molecular Processing

• ft_signal - Signal peptide
• ft_transit - Transit peptide
• ft_init_met - Initiator methionine
• ft_propep - Propeptide
• ft_chain - Chain (mature protein)
• ft_peptide - Peptide

Regions and Sites

• ft_domain - Domain
• ft_repeat - Repeat
• ft_ca_bind - Calcium binding
• ft_zn_fing - Zinc finger
• ft_dna_bind - DNA binding
• ft_np_bind - Nucleotide binding
• ft_region - Region of interest
• ft_coiled - Coiled coil
• ft_motif - Short sequence motif
• ft_compbias - Compositional bias

Sites and Modifications

• ft_act_site - Active site
• ft_metal - Metal binding
• ft_binding - Binding site
• ft_site - Site
• ft_mod_res - Modified residue
• ft_lipid - Lipidation
• ft_carbohyd - Glycosylation
• ft_disulfid - Disulfide bond
• ft_crosslnk - Cross-link

Structural Features

• ft_helix - Helix
• ft_strand - Beta strand
• ft_turn - Turn
• ft_transmem - Transmembrane region
• ft_intramem - Intramembrane region
• ft_topo_dom - Topological domain

Variation and Conflict

• ft_variant - Natural variant
• ft_var_seq - Alternative sequence
• ft_mutagen - Mutagenesis
• ft_unsure - Unsure residue
• ft_conflict - Sequence conflict
• ft_non_cons - Non-consecutive residues
• ft_non_ter - Non-terminal residue
• ft_non_std - Non-standard residue

Gene Ontology (GO)

• go - All GO terms
• go_p - Biological process
• go_c - Cellular component
• go_f - Molecular function
• go_id - GO term identifiers

Cross-References (xref_)

Sequence Databases

• xref_embl - EMBL/GenBank/DDBJ
• xref_refseq - RefSeq
• xref_ccds - CCDS
• xref_pir - PIR

3D Structure Databases

• xref_pdb - Protein Data Bank
• xref_pcddb - PCD database
• xref_alphafolddb - AlphaFold database
• xref_smr - SWISS-MODEL Repository

Protein Family/Domain Databases

• xref_interpro - InterPro
• xref_pfam - Pfam
• xref_prosite - PROSITE
• xref_smart - SMART

Genome Databases

• xref_ensembl - Ensembl
• xref_ensemblgenomes - Ensembl Genomes
• xref_geneid - Entrez Gene
• xref_kegg - KEGG

Organism-Specific Databases

• xref_mgi - MGI (mouse)
• xref_rgd - RGD (rat)
• xref_flybase - FlyBase (fly)
• xref_wormbase - WormBase (worm)
• xref_xenbase - Xenbase (frog)
• xref_zfin - ZFIN (zebrafish)

Pathway Databases

• xref_reactome - Reactome
• xref_signor - SIGNOR
• xref_signalink - SignaLink

Disease Databases

• xref_disgenet - DisGeNET
• xref_malacards - MalaCards
• xref_omim - OMIM
• xref_orphanet - Orphanet

Drug Databases

• xref_chembl - ChEMBL
• xref_drugbank - DrugBank
• xref_guidetopharmacology - Guide to Pharmacology

Expression Databases

• xref_bgee - Bgee
• xref_expressionetatlas - Expression Atlas
• xref_genevisible - Genevisible

Metadata Fields

Dates

• date_created - Entry creation date
• date_modified - Last modification date
• date_sequence_modified - Last sequence modification date

Evidence and Quality

• annotation_score - Annotation score (1-5)
• protein_existence - Protein existence level
• reviewed - Whether entry is reviewed (Swiss-Prot)

Literature

• lit_pubmed_id - PubMed identifiers
• lit_doi - DOI identifiers

Proteomics

• proteome - Proteome identifier
• tools - Tools used for annotation

Retrieving Available Fields Programmatically

Use the configuration endpoint to get all available fields:

curl https://rest.uniprot.org/configure/uniprotkb/result-fields

Or in Python:

import requests
response = requests.get("https://rest.uniprot.org/configure/uniprotkb/result-fields")
fields = response.json()

Common Field Combinations

Basic protein information

fields=accession,id,protein_name,gene_names,organism_name,length

Sequence and structure

fields=accession,sequence,length,mass,xref_pdb,xref_alphafolddb

Functional annotation

fields=accession,protein_name,cc_function,cc_catalytic_activity,cc_pathway,go

Disease information

fields=accession,protein_name,gene_names,cc_disease,xref_omim,xref_malacards

Expression patterns

fields=accession,gene_names,cc_tissue_specificity,cc_developmental_stage,xref_bgee

Complete annotation

fields=accession,id,protein_name,gene_names,organism_name,sequence,length,cc_*,ft_*,go,xref_pdb

Notes

1. Wildcards: Some fields support wildcards (e.g., cc_* for all comment fields, ft_* for all features)

2. Performance: Requesting fewer fields improves response time and reduces bandwidth

3. Format dependency: Some fields may be formatted differently depending on output format (JSON vs TSV)

4. Null values: Fields without data may be omitted from response (JSON) or empty (TSV)

5. Arrays vs strings: In JSON format, many fields return arrays of objects rather than simple strings

Resources

• Interactive field explorer: https://www.uniprot.org/api-documentation
• API fields endpoint: https://rest.uniprot.org/configure/uniprotkb/result-fields
• Return fields documentation: https://www.uniprot.org/help/return_fields