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This vignette describes all the columns of data (aka return fields) you can request from each UniProt database. This is relevant for uniprot_map() when mapping to UniParc/UniRef and for uniprot_search().

  • field = string to use in the fields argument
  • label = name of column that will be returned

uniref

section field label
Names & Taxonomy id Cluster ID
Names & Taxonomy name Cluster Name
Names & Taxonomy common_taxon Common taxon
Names & Taxonomy common_taxonid Common taxon ID
Names & Taxonomy organism_id Organism IDs
Names & Taxonomy organism Organisms
Sequences identity Identity
Sequences length Length
Sequences sequence Reference sequence
Miscellaneous types Types
Miscellaneous members Cluster members
Miscellaneous count Size
Date of created Date of creation

uniparc

section field label
Names & Taxonomy upi Entry
Names & Taxonomy gene Gene names
Names & Taxonomy organism_id Organism ID
Names & Taxonomy organism Organisms
Names & Taxonomy protein Protein names
Names & Taxonomy proteome Proteomes
Sequences checksum Checksum
Sequences length Length
Sequences sequence Sequence
Miscellaneous accession UniProtKB
Date of first_seen First seen
Date of last_seen Last seen
Family & Domains CDD CDD
Family & Domains Gene3D Gene3D
Family & Domains HAMAP HAMAP
Family & Domains PANTHER PANTHER
Family & Domains Pfam Pfam
Family & Domains PIRSF PIRSF
Family & Domains PRINTS PRINTS
Family & Domains PROSITE PROSITE
Family & Domains SFLD SFLD
Family & Domains SMART SMART
Family & Domains SUPFAM SUPFAM
Family & Domains TIGRFAMs TIGRFAMs

proteomes

section field label
Names & Taxonomy upid Proteome Id
Names & Taxonomy organism Organism
Names & Taxonomy organism_id Organism Id
Names & Taxonomy components Components
Names & Taxonomy mnemonic Taxon mnemonic
Names & Taxonomy lineage Taxonomic lineage
Names & Taxonomy busco BUSCO
Miscellaneous cpd CPD
Miscellaneous genome_assembly Genome assembly ID
Miscellaneous genome_representation Genome representation
Miscellaneous protein_count Protein count

taxonomy

section field label
Taxonomy id Taxon Id
Taxonomy mnemonic Mnemonic
Taxonomy scientific_name Scientific name
Taxonomy common_name Common name
Taxonomy synonyms Synonyms
Taxonomy other_names Other Names
Taxonomy rank Rank
Taxonomy reviewed Reviewed
Taxonomy lineage Lineage
Taxonomy strains Strains
Taxonomy parent Parent
Taxonomy hosts Virus hosts
Taxonomy links Links
Taxonomy statistics Statistics

keywords

section field label
Keywords id Keyword ID
Keywords name Name
Keywords definition Definition
Keywords category Category
Keywords synonyms Synonyms
Keywords gene_ontologies Gene Ontologies
Keywords links Links
Keywords children Children
Keywords parents Parents
Keywords statistics Statistics

citations

section field label
Literature id Citation Id
Literature doi Doi
Literature title Title
Literature authors Authors
Literature authoring_group Authoring Group
Literature journal Journal
Literature publication_date Publication date
Literature first_page First page
Literature last_page Last page
Literature volume Volume
Literature reference Reference
Literature lit_abstract Abstract/Summary
Literature statistics Statistics

diseases

section field label
Disease id DiseaseEntry ID
Disease name Name
Disease acronym Mnemonic
Disease definition Description
Disease alternative_names Alternative Names
Disease cross_references Cross Reference
Disease keywords Keywords
Disease statistics Statistics

locations

section field label
Subcellular location id Subcellular location ID
Subcellular location name Name
Subcellular location definition Description
Subcellular location category Category
Subcellular location keyword Keyword
Subcellular location synonyms Synonyms
Subcellular location content Content
Subcellular location gene_ontologies Gene Ontologies
Subcellular location note Note
Subcellular location references References
Subcellular location links Links
Subcellular location is_a Is a
Subcellular location part_of Is part of
Subcellular location statistics Statistics