bridgedbjs

Class: EntityReference

BridgeDb. EntityReference

protectednew BridgeDb.EntityReference(instance)

entity-reference.js, line 20

Used internally to create a new EntityReference instance

Name Type Description
instance Object

Methods

innercreateEnrichmentStream(options){Stream}

entity-reference.js, line 148

Create a Node.js/Highland stream through which entity references can be piped to enrich each one with data from BridgeDb.

Name Type Description
options Object optional
Name Type Default Description
organism Boolean true optional

Enrich with organism name.
context Boolean true optional

Enrich with JSON-LD @context.
dataset Boolean true optional

Enrich from data-sources.txt (metadata about biological datasets).
xref Boolean true optional

Enrich with IRI (URL) for BridgeDb webservices to enable getting xrefs for this entity reference.

innerenrich(input, options){Stream.<EntityReference>}

entity-reference.js, line 202

Enrich entity reference. Default is to enrich as much as possible with data from BridgeDb, with the exception of not dereferencing any xref IRIs, but this enrichment can be controlled by setting the relevant option(s) to false.

Name Type Description
input Object | String | Stream

Entity reference(s). Each one must have an identifier (e.g. ENSG00000160791) and means for identifying the dataset.

Acceptable entityReference input arguments:

 1. BridgeDb xref IRI (URL) or identifiers.org IRI as string
   BridgeDb xref IRI @example:
   'http://webservice.bridgedb.org/Human/xrefs/L/1234'
   identifiers.org IRI @example:
   'http://identifiers.org/ncbigene/1234'
 2. Object with at least one of these properties:
   a. { 'id': identifiers.org IRI }
   b. { bridgeDbXrefsIri: BridgeDb xref IRI }
   c. { xref: [
          BridgeDb xref IRI
          ...
        ]
      }
 3. Object with both of these properties:
   {
     db: official, standardized database name
     identifier: entity reference identifier, such as ChEBI:1234
   }
 4. Object with both of these properties:
   {
     bridgeDbDataSourceName: database name as used in BridgeDb
     identifier: entity reference identifier, such as ChEBI:1234
   }
options Object optional
Name Type Default Description
organism Boolean true optional

Enrich with organism name.
context Boolean true optional

Enrich with JSON-LD @context.
dataset Boolean true optional

Enrich from data-sources.txt (metadata about biological datasets).
xref Boolean true optional

Enrich with IRI (URL) for BridgeDb webservices to enable getting xrefs for this entity reference.
Returns:
EntityReference with as many properties as possible added, unless otherwise specified by options.

innerexists(systemCode, identifier, organism){Stream.<Boolean>}

entity-reference.js, line 431

Check whether an entity reference with the specified identifier is known by the specified dataset.

Name Type Description
systemCode String
identifier String
organism String | Organism

Organism or name in English or Latin or taxonomy IRI like http://identifiers.org/taxonomy/9606.
Returns:
Whether specified entity reference exists.

innerfreeSearch(args, organism){Stream.<EntityReference>}

entity-reference.js, line 547

Get potential matches for a desired entity reference by free text search for matching symbols or identifiers. See also Java documentation.

Name Type Description
args Object
Name Type Description
attribute String

Attribute value to be used as search term
organism String | Organism

Organism or name in English or Latin or taxonomy IRI like http://identifiers.org/taxonomy/9606.
args.type JsonldType optional

Entity reference type, such as ProteinReference, DnaReference, SmallMoleculeReference, etc. Not currently being used, but we might use it in the future to help narrow down the search results.
args.db String optional

Desired dataset name, such as Ensembl or Uniprot
Returns:
EntityReference, enriched from data-sources.txt and BridgeDb organism data.
Example
myBridgeDbInstance.entityReference.freeSearch({
  attribute: 'Nfkb1',
  organism: 'Mouse'
}).each(function(searchResult) {
  console.log('Result for Nfkb1');
  console.log(searchResult);
});

innermap(args){Stream.<EntityReference>}

entity-reference.js, line 690
Name Type Description
args Object
Name Type Description
targetPreferredPrefix String

The Miriam namespace / identifiers.org preferredPrefix.
sourceEntityReference String | Object

@see bridgeDb.entityReference.enrich() method for what constitutes a usable entityReference
Returns:
One or more entity references with the target preferredPrefix.

innernormalize(entityReference){Stream.<EntityReference>}

entity-reference.js, line 709

Normalize object properties

Name Type Description
entityReference String | Object
Returns:
EntityReference
comments powered by Disqus