The BridgeDb DataSource Ontology

Version 2.1.0

This page describes the BridgeDb ontology http://vocabularies.bridgedb.org/ops# - make sure to visit our homepage too!

OWL ontology and SKOS vocabulary:

RDFa Turtle JSON-LD N-Triples RDF/XML

License:

Apache License, version 2.0

Namespaces

@prefix bdb: <http://vocabularies.bridgedb.org/ops#> .

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd:< http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .

Classes

Data Source

bdb:DataSource

A resource that defines identifiers for some biological entity, like a gene, protein, or metabolite.

Organism

bdb:Organism

An organism.

Linkset

void:Linkset

Class from the VoID Ontology.

Concept

skos:Concept

Class from the SKOS Ontology.

Code Mapper

bdb:CodeMapper

Identifiers.org Info Pattern

bdb:IdentifiersOrgInfoPattern

Identifiers.org Pattern

bdb:IdentifiersOrgPattern

Subclass of URI Pattern.

Lens

bdb:Lens

URI Pattern

bdb:UriPattern

Transitive

bdb:Transitive

Object Properties

About Organism

bdb:aboutOrganism

Organism for all entities with identifiers from this datasource. This property has DataSource as domain and Organism as range.

Assertion Method

bdb:assertionMethod

The method by which the links in the Linkset have been asserted. This property has Linkset as domain.

Fulfills Lens

bdb:fulfillsLens

This property has Linkset as domain.

Has Data Type

bdb:hasDataType

This property has DataSource as domain and SKOS Concept as range.

Has Data Source

bdb:hasDataSource

Primary URI Pattern

bdb:hasPrimaryUriPattern

The primary URI pattern for identifiers from this data source. There can be only one. This property has DataSource as domain and is subproperty of has URI Pattern.

Identifiers.org URL

bdb:hasIdentifiersOrgPattern

Identifiers.org URL for identifiers from this data source. This property has DataSource as domain and is subproperty of has URI Pattern.

Has URI Pattern

bdb:hasUriPattern

A URI pattern for identifiers from this data source. Can be more than one. This property has DataSource as domain and is subproperty of has URI Pattern.

Is Transitive Via

bdb:isTransitiveVia

This property has DataSource as domain and DataSource as range.

Is URI Pattern Of

bdb:isUriPatternOf

This property is the inverse of has URI Pattern.

Linkset Justification

bdb:linksetJustification

The reason why the Linkset claims these concepts are equivalent. This property has VoID Linkset as domain and SKOS Concept as range.

Object's Datatype

bdb:objectsDatatype

The type of concept the objects of the triples in the Linkset represent. This property has VoID Linkset as domain and SKOS Concept as range.

Object's Species

bdb:objectsSpecies

The species of concept the objects of the triples in the Linkset represent. This property has VoID Linkset as domain and SKOS Concept as range.

Subject's Datatype

bdb:subjectsDatatype

The type of concept the subjects of the triples in the Linkset represent. This property has VoID Linkset as domain and SKOS Concept as range.

Subject's Species

bdb:subjectsSpecies

The species of concept the subjects of the triples in the Linkset represent. This property has VoID Linkset as domain and SKOS Concept as range.

Data Properties

Full Name

bdb:fullName

The full name of the data source. This property has DataSource as domain.

System Code

bdb:systemCode

Short code unique for a data source. Often consisting of two or three characters. This property has DataSource as domain.

Main URL

bdb:mainUrl

Main URL of the website of the data source. This property has DataSource as domain.

Example Identifier

bdb:idExample

An example identifier for this data source. This property has DataSource as domain.

Is primary

bdb:primary

This predicates can be used to indicate of this data source is a primary data source. This property has DataSource as domain and XSD boolean as range.

Entity Type

bdb:type

Type of entity that are identified by identifiers from this data source. Example types include probe, gene, metabolite, and interaction. This property has DataSource as domain.

Has Regular Expression

bdb:hasRegexPattern

The regular expression of the format of the identifiers of this data source. This property has DataSource as domain.

Has URI Regular Expression

bdb:hasRegexUriPattern

This property has DataSource as domain.

Organism Code

bdb:code

Short code for an organism. Normally is one or two characters long. This property has Organism as domain.

Short Name

bdb:shortName

Short or common name of the organism. This property has Organism as domain.

Latin Name

bdb:latinName

Latin name of the organism. This property has Organism as domain.

Has Postfix

bdb:hasPostfix

This property has URI Pattern as domain.

Has Prefix

bdb:hasPrefix

This property has URI Pattern as domain.

Is Deprecated By

bdb:isDeprecatedBy

Is Symmmetric

bdb:isSymmetric

This property has XSD boolean as range.

URN Base

bdb:urnBase

This property has Data Source as domain.

Various

bdb:various

Xref Prefix

bdb:xrefPrefix

This property has Code Mapper as domain.

Technical notes

The conversion of ops#foo to index.html#foo is done with .htaccess and a RewriteRule. The source code is available from the bridgedb/vocabulary repository at GitHub, see also the recent changes.

This OWL ontology can be extracted as the RDF formats Turtle, JSON-LD, N-Triples or RDF/XML, provided by the RDF.rb Distiller.

The Open PHACTS specification on Dataset Descriptions uses some of these terms.