Return Fields - Other Databases

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