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. 2011 Jul;39(Web Server issue):W541-5.
doi: 10.1093/nar/gkr469. Epub 2011 Jun 14.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Patricia L Whetzel  1 , Natalya F Noy, Nigam H Shah, Paul R Alexander, Csongor Nyulas, Tania Tudorache, Mark A Musen
Affiliations

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Patricia L Whetzel et al. Nucleic Acids Res. 2011 Jul.

Abstract

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

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Figures

Figure 1.
Figure 1.
Screenshot of New Term proposal BioPortal Note Type.
Figure 2.
Figure 2.
BioPortal Widgets. Widgets are available for all ontologies in BioPortal. To view a demo of the Widget and get the code to use in your web site, click on the ‘Ontology Widgets’ tab.
See this image and copyright information in PMC

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References

    1. Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, et al. Big data: the future of biocuration. Nature. 2008;455:47–50. - PMC - PubMed
    1. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009;37:W170–173. - PMC - PubMed
    1. Ghazvinian A, Noy NF, Musen MA. Creating mappings for ontologies in biomedicine: simple methods work. AMIA Annu. Symp. proc. 2009;2009:198–202. - PMC - PubMed
    1. Jonquet C, Shah NH, Musen MA. The open biomedical annotator, San Francisco. Summit Trans Bioinformatics. 2009;2009:56–60. - 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

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