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QuickGO Web Services

QuickGO can supply GO term information and GO annotation data via REST web services. The details of each service can be found below; a WADL description of the services can be found here.

Term information

Use this URI template to access this data as a service:

GTerm?id=termID&format=format

FormatDescription
miniMini HTML, suitable for dynamically embedding in popup boxes
oboOBO format snippet
oboxmlOBO XML format snippet

Notes

  • Example clients are available in:

Annotation

Use this URI template to access this data as a service:

GAnnotation?format=download-format&limit=max-number-of-rows{&gz}{&field=value{,value}}

Notes

  • Any number of fields can be specified; they will be AND'ed together.
  • Any number of values can be specified for each field; they will be OR'ed together.
  • Values should be URI encoded.
  • The file will be truncated if more than the specified number of annotations are found. The file is roughly 170 bytes/annotation (not gzipped).
  • The file will be gzipped if the gz parameter is supplied.
  • Example clients are available in:

Description of Fields and Values

Field name Value Examples
format Download file format gaf, gpa, gene2go, proteinList, fasta, tsv
limit Download limit (number of lines). Note that the default limit is 10,000 rows, which may not be sufficient for the data set that you are downloading. To bypass this default, and return the entire data set, specify a limit of -1.
gz gzips the downloaded file
goid GO identifiers either directly or indirectly (descendant GO identifiers) applied in annotations GO:0002080
aspect Use this to limit the annotations returned to a specific ontology or ontologies (Molecular Function, Biological Process or Cellular Component) F, P, C
relType By default, QuickGO will display annotations to GO terms that are related to that specified in the goid parameter by is_a, part_of and occurs_in relations; this parameter allows you to override that behaviour. IPO=
See here for the list of available relations.
termUse If you set this parameter to slim, then QuickGO will use the supplied set of GO identifiers as a slim and will map the annotations up to these terms. See here for more details.
The default behaviour (termUse=ancestor) is to not perform this mapping.
ancestor (default) or slim
evidence Annotation evidence code (Ev) category IDA, IC, ISS, IEA
source Annotation provider UniProtKB, HGNC
ref PubMed or GO reference supporting annotation. Can refer to a specific reference identifier or category (for category level, use * after ref type) PUBMED:*, GO_REF:0000002, 16262699
with Additional supporting information supplied in IEA, ISS, IPI, IC evidenced annotations; see: GO documentation. Can refer to a specific identifier or category (for category level, use * after with type) EC:2.5.1.30, IPR000092, HAMAP:*
tax NCBI taxonomic identifer of annotated protein 9606
protein Specifies one or more sequence identifiers or accessions from available database(s) (see DB filter column) Mm.363225, P99999
qualifier Tags that modify the interpretation of an annotation NOT, colocalizes_with, contributes_to
db Protein database (identifier type) UniProtKB, UniGene, Ensembl
q Advanced query. Used to customize GO annotation sets using Boolean operators See Advanced Query section below
col This parameter, which is currently only applicable to the tsv download format, allows you to specify a comma-separated list of columns that you want to be included in the returned data set.
The list below shows the available column names; clicking on the name of a column will take you to the description of the column in the QuickGO help file. The default set of columns is shown in bold text.
proteinDB,proteinID,goID,goName,aspect

Advanced Query

Advanced query syntax and valid fields are listed in Advanced search. Only one advanced query may be specified, and it will be AND'ed with any other query criteria.
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Please send comments, suggestions or bug reports to goa@ebi.ac.uk. Click here for details of how to cite UniProt-GOA and QuickGO.
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