bionode-quickgo v0.1.0

bionode-quickgo

Acess EBI QuickGO REST API with promises and streams.

API Documentation

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

bionode-quickgo.GAnnotationAsync(fields) ⇒ Promise

QuickGO Annotation service

Kind: static method of bionode-quickgo

bionode-quickgo.GAnnotation(fields) ⇒ Stream

QuickGO Annotation service

Kind: static method of bionode-quickgo

bionode-quickgo.GTerm(fields) ⇒ Stream

GO term information

Kind: static method of bionode-quickgo

bionode-quickgo.GTermAsync(fields) ⇒ Promise

GO term information

Kind: static method of bionode-quickgo

bionode-quickgo~format : String

Download file format

Kind: inner property of bionode-quickgo
Default: gaf
Example

gaf, gpa, gene2go, proteinList, fasta, tsv

bionode-quickgo~limit : String

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

bionode-quickgo~gz : String

gzips the downloaded file

Kind: inner property of bionode-quickgo
Default: false
Example

false, true

bionode-quickgo~goid : String

GO identifiers either directly or indirectly (descendant GO identifiers) applied in annotations

Kind: inner property of bionode-quickgo
Default: ''
Example

GO:0002080

bionode-quickgo~aspect : String

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

bionode-quickgo~relType : String

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)

bionode-quickgo~termUse : String

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

bionode-quickgo~evidence : String

Annotation evidence code (Ev) category

Kind: inner property of bionode-quickgo
Default: ''
Example

IDA, IC, ISS, IEA

bionode-quickgo~source : String

Annotation provider

Kind: inner property of bionode-quickgo
Default: ''
Example

UniProtKB, HGNC

bionode-quickgo~ref : String

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

bionode-quickgo~with : String

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:*

bionode-quickgo~tax : String

NCBI taxonomic identifer of annotated protein

Kind: inner property of bionode-quickgo
Default: ''
Example

9606

bionode-quickgo~protein : String

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

bionode-quickgo~qualifier : String

Tags that modify the interpretation of an annotation

Kind: inner property of bionode-quickgo
Default: ''
Example

NOT, colocalizes_with, contributes_to

bionode-quickgo~db : String

Protein database (identifier type)

Kind: inner property of bionode-quickgo
Default: ''
Example

UniProtKB, UniGene, Ensembl

bionode-quickgo~q : String

Advanced query. Used to customize GO annotation sets using Boolean operators. See Advanced Annotation Search

Kind: inner property of bionode-quickgo
Default: ''

bionode-quickgo~col : String

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'

bionode-quickgo~id : String

GO identifier

Kind: inner property of bionode-quickgo
Default: none
Example

GO:0003824

bionode-quickgo~format : String

Kind: inner property of bionode-quickgo
Default: obo

bionode-quickgo~annotationRequest(fields) ⇒ Object

generate an annotation request object

Kind: inner method of bionode-quickgo
Returns: Object - {{method, uri, form} object for request}

bionode-quickgo~termRequest(fields) ⇒ Object

generate an term request object

Kind: inner method of bionode-quickgo
Returns: Object - {{method, uri, form} object for request}

License

MIT http://jmazz.mit-license.org