Class: BridgeDb

new BridgeDb(options)

main.js, line 76

Creates a new BridgeDb instance. There is no need to use the "new" keyword.

Name Type Description

options

object

optional

Overwrite any or all of the defaults in config.js

Name	Type	Default	Description
`baseIri`	string	'http://pointer.ucsf.edu/d3/r/data-sources/bridgedb.php/'	optional Base IRI (URL) for your BridgeDb webservice instance. TODO Enable CORS at bridgedb.org, because the default should be 'http://webservice.bridgedb.org/', but we are forced to use pointer as a proxy for now for CORS so that web browsers can access the data.

[options.datasetsMetadataIri=
   'https://cdn.rawgit.com/bridgedb/BridgeDb/master/org.bridgedb.bio/
       resources/org/bridgedb/bio/datasources.txt']

string

Location (URL) of the datasources.txt file that contains metadata for selected biological datasets. This metadata includes information such as name (e.g., Entrez Gene), Miriam identifier (e.g., urn:miriam:ncbigene) and BridgeDb system code (e.g., L).

options.organism

string

optional

Full name in Latin, e.g., Homo sapiens. Each bridgedbjs instance has one organism associated with it. Specifying it here will result in faster response times, because bridgedbjs will not have to infer it from the other provided data.

Example

BridgeDb = require('bridgedb'); // Only needed if using Node.js.
var myBridgeDbInstance = new BridgeDb({
  baseIri: 'http://webservice.bridgedb.org/', // Optional
  datasetsMetadataIri:
   'http://pointer.ucsf.edu/d3/r/data-sources/bridgedb-datasources.php'  // Optional
});

Classes

Dataset
EntityReference
Organism
Xref