RDF in BioPortal
You can access RDF graphs for all BioPortal ontologies at our prototype SPARQL endpoint.
Goals for generating RDF for BioPortal content
We had the following goals in generating RDF for BioPortal:
- Provide RDF for each class in BioPortal so that we can have a URL to a concept that resolves to a set of RDF triples that provide essential information about the term.
- Provide an RDF dump of each ontology in BioPortal to put them in a tripelstore to enable SPARQL access to the ontologies
Our goal was not to provide an RDF graph that covers the complete content of each ontology. Rather, we wanted to provide uniform RDF format for all the terms from the ontologies that were originally developed in different formats.
In order to have an RDF graph for each term, we must have an http URI for the term. We used the following approach to determine the URIs for the terms for ontologies in different formats:
- OWL and RDF ontologies: these ontologies already have http URIs for each resource that they define. We used the URIs provided by ontology authors.
- OBO ontologies: terms in the ontologies in the OBO format do not have http URIs. We used the same URIs that the OBO library uses for these terms
- RRF and Protege ontologies: terms in these ontologies do not have http URIs. We generate the URIs in the following form for these terms:
Accessing RDF content
There are two ways to access the RDF content that we generate for BioPortal ontologies and their terms:
- Use the NCBO prototype SPARQL endpoint
- Use the RDF Term Service to get an RDF snippet for a single term or several terms and the
RDF Download Service to download the whole ontology in RDF. Note that the second service will provide only some basic information about each term, not all the relations that are defined in the ontology.
Content of the RDF graph
For each term in BioPortal, we provide the following information in the RDF graph:
- id (including the original id, using skos:notation)
- preferred name
- superclasses (for OWL, Protege, and OBO)
- skos:broader and skos:narrower for terms from RRF ontologies
- all annotation properties for terms in OWL ontologies
- part-of relations for OBO terms