BioPortal: A Web Repository for Biomedical Ontologies and Data Resources
Résumé
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval,
data annotation, naturalʼlanguage processing, and decision support. BioPortal
(http://bioportal.bioontology.org) is a Web based system that serves as a repository for biomedical
ontologies developed in OWL, OBO format, RRF, or Protégé frames. Features of BioPortal include
mappings between ontologies, visualization of terms and relations, and the ability to comment on individual
terms within an ontology or the entire ontology. In addition, users can add information on projects that use
ontologies and link these to ontologies in BioPortal as well as add reviews and ratings of ontologies. In this
way, BioPortal supports communityʼbased participation in the evaluation and evolution of ontology content.
In addition to Webʼbased access, BioPortal provides programmatic access to the ontology content via a
suite of REST web services.
BioPortal also serves as a gateway to search and integrate multiple biomedical resources such as PubMed
abstracts, ClinicalTrials.gov, the Gene Expression Omnibus (GEO), and ArrayExpress. The included
biomedical resources are first annotated with terms from ontologies in BioPortal and then the annotations
are expanded through the use of semantic expansion components, such as is_a transitive closure and
ontology mappings. The key functionality of the ontologyʼbased indexing is to enable users to locate
biomedical data resources related to particular ontology concepts. We have also made the ontologyʼterm
recognition functionality available as an automatic “annotator” web service for public use in collaborative
curation workflows or web applications.
In this way, BioPortal provides investigators, curators, and developers a “oneʼstop shop” where they can
learn what biomedical ontologies exist, what a particular ontology might be good for, how ontologies are
being used, how individual ontologies relate to one another, as well as to be able to access biomedical
ontologies programmatically for use in their own applications and data repositories. BioPortal is a product of
the National Center for Biomedical Ontology, one of seven National Centers for Biomedical Computing
created under the NIH Roadmap.