Access EBI QuickGO REST API with promises and streams
npm install bionode-quickgoAcess EBI QuickGO REST API with promises and streams.
Access EBI QuickGO REST API with promises and streams.
* bionode-quickgo
* _static_
* .GAnnotationAsync(fields) ⇒ Promise
* .GAnnotation(fields) ⇒ Stream
* .GTerm(fields) ⇒ Stream
* .GTermAsync(fields) ⇒ Promise
* _inner_
* ~format : String
* ~limit : String
* ~gz : String
* ~goid : String
* ~aspect : String
* ~relType : String
* ~termUse : String
* ~evidence : String
* ~source : String
* ~ref : String
* ~with : String
* ~tax : String
* ~protein : String
* ~qualifier : String
* ~db : String
* ~q : String
* ~col : String
* ~id : String
* ~format : String
* ~annotationRequest(fields) ⇒ Object
* ~termRequest(fields) ⇒ Object
Kind: static method of bionode-quickgo
| Param | Type | Description |
| --- | --- | --- |
| fields | Object | valid query fields |
Kind: static method of bionode-quickgo
| Param | Type | Description |
| --- | --- | --- |
| fields | Object | valid query fields |
Kind: static method of bionode-quickgo
| Param | Type | Description |
| --- | --- | --- |
| fields | Object | valid query fields, id required |
Kind: static method of bionode-quickgo
| Param | Type | Description |
| --- | --- | --- |
| fields | Object | valid query fields, id required |
Kind: inner property of bionode-quickgo
Default: gaf
Example
``js`
gaf, gpa, gene2go, proteinList, fasta, tsv$3
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.
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
9001, -1$3
gzips the downloaded file
Kind: inner property of bionode-quickgo
Default: false
Example
`js`
false, true$3
GO identifiers either directly or indirectly (descendant GO
identifiers) applied in annotations
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
GO:0002080$3
Use this to limit the annotations returned to a specific ontology or
ontologies (Molecular Function, Biological Process or Cellular Component)
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
F, P, C$3
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.
See Ontology Relations.
Kind: inner property of bionode-quickgo
Default: IPO=
Example
`js`
? (ancestor)
= (indentity)
I (is_a)
P (part_of)
O (occurs_in)
R (regulates)
+ (positively_regulates)
- (negatively_regulates)$3
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.
Kind: inner property of bionode-quickgo
Default: ancestor
Example
`js`
ancestor, slim$3
Annotation evidence code (Ev) category
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
IDA, IC, ISS, IEA$3
Annotation provider
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
UniProtKB, HGNC$3
PubMed or GO reference supporting annotation. Can refer to a specific
reference identifier or category (for category level, use * after ref type)
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
PUBMED:*, GO_REF:0000002, 16262699$3
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)
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
EC:2.5.1.30, IPR000092, HAMAP:*$3
NCBI taxonomic identifer of annotated protein
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
9606$3
Specifies one or more sequence identifiers or accessions from
available database(s) (see DB filter column)
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
Mm.363225, P99999$3
Tags that modify the interpretation of an annotation
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
NOT, colocalizes_with, contributes_to$3
Protein database (identifier type)
Kind: inner property of bionode-quickgo
Default: ''
Example
`js`
UniProtKB, UniGene, Ensembl$3
Advanced query. Used to customize GO annotation sets using Boolean
operators. See Advanced Annotation Search
Kind: inner property of bionode-quickgo
Default: ''
Kind: inner property of bionode-quickgo
Default: 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice'
Example
`js`
'proteinDB,proteinID,goID,goName,aspect'$3
GO identifier
Kind: inner property of bionode-quickgo
Default: none
Example
`js``
GO:0003824
Kind: inner property of bionode-quickgo
Default: obo
Kind: inner method of bionode-quickgo
Returns: Object - {{method, uri, form} object for request}
| Param | Type | Description |
| --- | --- | --- |
| fields | Object | valid query fields |
Kind: inner method of bionode-quickgo
Returns: Object - {{method, uri, form} object for request}
| Param | Type | Description |
| --- | --- | --- |
| fields | Object | valid query fields |