Acess 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
- .GAnnotationAsync(fields) ⇒
- 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
- ~format :
- static
QuickGO Annotation service
Kind: static method of bionode-quickgo
Param | Type | Description |
---|---|---|
fields | Object |
valid query fields |
QuickGO Annotation service
Kind: static method of bionode-quickgo
Param | Type | Description |
---|---|---|
fields | Object |
valid query fields |
GO term information
Kind: static method of bionode-quickgo
Param | Type | Description |
---|---|---|
fields | Object |
valid query fields, id required |
GO term information
Kind: static method of bionode-quickgo
Param | Type | Description |
---|---|---|
fields | Object |
valid query fields, id required |
Download file format
Kind: inner property of bionode-quickgo
Default: gaf
Example
gaf, gpa, gene2go, proteinList, fasta, tsv
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
9001, -1
gzips the downloaded file
Kind: inner property of bionode-quickgo
Default: false
Example
false, true
GO identifiers either directly or indirectly (descendant GO identifiers) applied in annotations
Kind: inner property of bionode-quickgo
Default: ''
Example
GO:0002080
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
F, P, C
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
? (ancestor)
= (indentity)
I (is_a)
P (part_of)
O (occurs_in)
R (regulates)
+ (positively_regulates)
- (negatively_regulates)
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
ancestor, slim
Annotation evidence code (Ev) category
Kind: inner property of bionode-quickgo
Default: ''
Example
IDA, IC, ISS, IEA
Annotation provider
Kind: inner property of bionode-quickgo
Default: ''
Example
UniProtKB, HGNC
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
PUBMED:*, GO_REF:0000002, 16262699
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
EC:2.5.1.30, IPR000092, HAMAP:*
NCBI taxonomic identifer of annotated protein
Kind: inner property of bionode-quickgo
Default: ''
Example
9606
Specifies one or more sequence identifiers or accessions from available database(s) (see DB filter column)
Kind: inner property of bionode-quickgo
Default: ''
Example
Mm.363225, P99999
Tags that modify the interpretation of an annotation
Kind: inner property of bionode-quickgo
Default: ''
Example
NOT, colocalizes_with, contributes_to
Protein database (identifier type)
Kind: inner property of bionode-quickgo
Default: ''
Example
UniProtKB, UniGene, Ensembl
Advanced query. Used to customize GO annotation sets using Boolean operators. See Advanced Annotation Search
Kind: inner property of bionode-quickgo
Default: ''
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
- proteinSymbol
- qualifier
- goID
- goName
- aspect
- evidence
- ref
- with
- proteinTaxon
- date
- from
- splice
- proteinName
- proteinSynonym
- proteinType
- proteinTaxonName
- orginalTermID
- originalGOName
Kind: inner property of bionode-quickgo
Default: 'proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice'
Example
'proteinDB,proteinID,goID,goName,aspect'
GO identifier
Kind: inner property of bionode-quickgo
Default: none
Example
GO:0003824
Format | Description |
---|---|
mini | Mini Mini HTML, suitable for dynamically embedding in popup boxes |
obo | OBO format snippet |
oboxml | OBO XML format snippet |
Kind: inner property of bionode-quickgo
Default: obo
generate an annotation request object
Kind: inner method of bionode-quickgo
Returns: Object
- {{method, uri, form} object for request}
Param | Type | Description |
---|---|---|
fields | Object |
valid query fields |
generate an term request object
Kind: inner method of bionode-quickgo
Returns: Object
- {{method, uri, form} object for request}
Param | Type | Description |
---|---|---|
fields | Object |
valid query fields |