Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Jul;37(Web Server issue):W170-3.
doi: 10.1093/nar/gkp440. Epub 2009 May 29.

BioPortal: ontologies and integrated data resources at the click of a mouse

Natalya F Noy  1 , Nigam H Shah, Patricia L Whetzel, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Daniel L Rubin, Margaret-Anne Storey, Christopher G Chute, Mark A Musen
Affiliations

BioPortal: ontologies and integrated data resources at the click of a mouse

Natalya F Noy et al. Nucleic Acids Res. 2009 Jul.

Abstract

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
BioPortal resources tab displaying the ontology-indexed resources for the term Hepatocellular Carcinoma.
Figure 2.
Figure 2.
BioPortal architecture.
See this image and copyright information in PMC

References

    1. Cote RG, Jones P, Martens L, Apweiler R, Hermjakob H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res. 2008;36:W372–W376. - PMC - PubMed
    1. Cote RG, Jones P, Apweiler R, Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics. 2006;7:97. - PMC - PubMed
    1. Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009;10(Suppl. 2):S1. - PMC - PubMed
    1. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007;25:1251–1255. - PMC - PubMed
    1. Fink JL, Kushch S, Williams PR, Bourne PE. BioLit: integrating biological literature with databases. Nucleic Acids Res. 2008;36:W385–W389. - PMC - PubMed

Publication types