Global

Type Definitions

DatasetObject

See void:Dataset

Properties:

Name	Type	Description
@context	JsonldContext	JSON-LD context.
id	Iri	Preferred IRI for identifying a dataset.
owl:sameAs	Array.<String>	Alternate IRI for identifying a dataset. See owl:sameAs.
name	String	Official, standardized name for the data set. See schema:name.
webPage	String	See Java documentation and xsd:anyURI.
uriRegexPattern	String	See void:uriRegexPattern.
exampleResource	Iri	See void:exampleResource.
exampleIdentifier	String	See idot:exampleIdentifier.
organism	String	Provided only if the dataset is for a single organism. See biopax:organism.
_bridgeDbType	String	Biological type, as used at BridgeDb. See Java documentation.
type	JsonldType	void:Dataset
subject	String | Array.<String>	Subject of the database, such as the biological type of its contained entity references. Biological type as used in GPML at WikiPathways and in PathVisio-Java: gpml:Type. Biological type as used in Biopax: see the domain for biopax:entityReference.
_isPrimary	Boolean	See Java documentation for "isPrimary" and for "primary" method.
identifierPattern	String	Regular expression for the identifiers from this dataset. See idot:identifierPattern.
preferredPrefix	String	Abbreviation as used by identifiers.org to identify a dataset. See idot:preferredPrefix.
alternatePrefix	Array.<String>	Abbreviation as used elsewhere to identify a dataset, such as at BridgeDb (bridgeDbSystemCode located both here and on its own). See idot:alternatePrefix.
bridgeDbSystemCode	String	See Java documentation.
bridgeDbDataSourceName	String	Name for the data set as used in the BridgeDb project.

DatasetArgsObject

At least one of the following properties must be provided.

Properties:

Name	Type	Argument	Description
id	Iri	<optional>
preferredPrefix	String	<optional>
bridgeDbSystemCode	String | Array.<String>	<optional>
name	String | Array.<String>	<optional>
identifier	String	<optional>	The identifier of the entity reference. This property will only be used if no other properties return results, because many different datasets have overlapping identifierPatterns.

EntityReferenceObject

See biopax:EntityReference

Properties:

Name	Type	Description
@context	JsonldContext	JSON-LD context.
id	Iri	JSON-LD IRI.
displayName	String	See biopax:displayName
db	String	See biopax:db
isDataItemIn	Dataset	The dataset (database) for the identifier. See SIO:001278
xref	Array.<String>	List of IRIs (URLs) for getting Xrefs, such as from the BridgeDb webservices or from mygene.info.
identifier	String	See biopax:id @example: "1234".
type	JsonldType	Biological type. See JSON-LD documentation

IriString

The keyword id indicates a unique identifier for a concept or thing. In JSON-LD terms, this unique identifier is called an IRI, which is usually a persistent (stable) URL. You can safely ignore this if you don't care about JSON-LD.

Example

http://identifiers.org/ncbigene/1234

JsonldContextString Object Array.<String> Array.<Object>

The keyword @context indicates an object with information for identifying or defining terms used in the data. The data is just regular JSON, so you can safely ignore the context. If you choose to use the context, you can work with JSON-LD tools to view the JSON as Linked Open Data.

JsonldTypeString Array.<String>

The keyword type sets data types in JSON-LD. You can safely ignore this if you don't care about JSON-LD.

OrganismObject

See snomedct:Organism

Properties:

Name	Type	Description
@context	JsonldContext	JSON-LD context.
id	Iri	Preferred IRI for identifying an organism, using Taxonomy ontology
nameLanguageMap	Object	Properties Name Type Description en String English name, when available. la String Full Latin name.

Stream

Node.js stream. This library additionally uses highland for easier stream handling, so you can use the highland methods on all streams returned.