BioPortal

BioPortal is a software tool that offers a centralized repository of biomedical ontologies. The tool provides access to ontologies in various formats like OWL, RDF, OBO format, and Protege frames through web services and web browsers. Researchers, clinicians, and developers can use the tool to programmatically access biomedical ontologies.

One of the key features of BioPortal is its ability to browse, search and visualize ontologies. This functionality allows users to easily find the information that they need, making it a valuable tool for data integration, information retrieval, data annotation, natural-language processing, and decision support.

Another important feature of BioPortal is its community-based participation. The tool allows users to add notes to ontology terms, mappings between terms, and ontology reviews based on usability, domain coverage, quality of content, documentation, and support. This facilitates the evaluation and evolution of ontology content, ensuring the quality and relevance of the information available on the platform.

BioPortal also enables the integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), [ClinicalTrials.gov](http://clinicaltrials.gov/), and ArrayExpress. This is done through the annotation and indexing of these resources with ontologies in BioPortal. This feature provides support to integrate data from a variety of biomedical resources, making it a one-stop shop for investigators, clinicians, and developers.

Topic

Ontology and terminology;Mapping;Medicine;Data integration and warehousing;Database management

Detail

  • Operation: Data retrieval;Ontology visualisation;ID mapping

  • Software interface: Web user interface

  • Language: Ruby

  • License: Other

  • Cost: Free

  • Version name: 6.10.2

  • Credit: National Center for Biomedical Ontology, under roadmap-initiative from the National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: https://bioportal.bioontology.org/feedback

  • Collection: -

  • Maturity: Mature

Publications

  • BioPortal: ontologies and integrated data resources at the click of a mouse.
  • Noy NF, et al. BioPortal: ontologies and integrated data resources at the click of a mouse. BioPortal: ontologies and integrated data resources at the click of a mouse. 2009; 37:W170-3. doi: 10.1093/nar/gkp440
  • https://doi.org/10.1093/nar/gkp440
  • PMID: 19483092
  • PMC: PMC2703982
  • BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.
  • Whetzel PL, et al. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. 2011; 39:W541-5. doi: 10.1093/nar/gkr469
  • https://doi.org/10.1093/nar/gkr469
  • PMID: 21672956
  • PMC: PMC3125807

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