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
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
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
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
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
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
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
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
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 |