BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse

Patricia Whetzel,Nicholas Griffith,Nigam Shah,Barry Smith,Clement Jonquet,Benjamin Dai,Daniel Rubin,Chris Callendar,Christopher Chute,Margaret-Anne Storey,Cherie Youn,Natalya Noy,Michael Dorf,Mark Musen,Adrien Coulet

doi:10.1038/npre.2009.3868.1

Patricia Whetzel, Nicholas Griffith + Show 13 more

Open Access

https://doi.org/10.1038/npre.2009.3868.1

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Journal: Nature Precedings	Publication Date: Oct 16, 2009
Citations: 5	License type: CC BY 3.0

Affiliation: Stanford University

Abstract

AbstractBioPortal ("http://bioportal.bioontology.org":http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Protégé frames, and RDF. Features include browsing, searching, and visualization of ontologies. Searching of integrated data resources is also possible through ontology-based indexing of biomedical resources with BioPortal ontologies.

Highlights

As the number of biomedical ontologies increases, so does the number of repositories that index and organize ontologies
The Open Biomedical Resources (OBR) component automatically indexes the metadata for important biomedical data sets available online, and links the underlying data sets to the terms in the ontologies in BioPortal and UMLS
Open Biomedical Repository (OBR) allows biomedical investigators to use the terms in the BioPortal ontologies to enhance their ability to search for relevant online data in a manner that is not possible with conventional keyword search strategies

Summary

Introduction

As the number of biomedical ontologies increases, so does the number of repositories that index and organize ontologies. To create OBR, we have indexed biomedical data sets available online (e.g. entries in GEO, ClinicalTrials.gov) with ontologies in BioPortal. We plan to include the ability to access the mapping data via the BioPortal Web services.

Results

Conclusion