NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation View Full Text


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Article Info

DATE

2017-12

AUTHORS

Marcos Martínez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos, Mark A. Musen

ABSTRACT

BACKGROUND: Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. METHODS: We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. RESULTS: Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. CONCLUSIONS: Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available (both via the user interface at http://bioportal.bioontology.org/recommender , and via a Web service API). More... »

PAGES

21

References to SciGraph publications

  • 2006. Ontology Selection for the Real Semantic Web: How to Cover the Queen’s Birthday Dinner? in MANAGING KNOWLEDGE IN A WORLD OF NETWORKS
  • 2000-05. Gene Ontology: tool for the unification of biology in NATURE GENETICS
  • 2015-12. Aber-OWL: a framework for ontology-based data access in biology in BMC BIOINFORMATICS
  • 2007-11. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration in NATURE BIOTECHNOLOGY
  • 2006-12. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries in BMC BIOINFORMATICS
  • 2000-08. Automatic recognition of multi-word terms:. the C-value/NC-value method in INTERNATIONAL JOURNAL ON DIGITAL LIBRARIES
  • 2010-06. Building a biomedical ontology recommender web service in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2009-05-22. Ontology Repositories in HANDBOOK ON ONTOLOGIES
  • 2004-06. Bio-ontologies—fast and furious in NATURE BIOTECHNOLOGY
  • 2012. A Multi-criteria Approach for Automatic Ontology Recommendation Using Collective Knowledge in RECOMMENDER SYSTEMS FOR THE SOCIAL WEB
  • 2009. Cupboard – A Place to Expose Your Ontologies to Applications and the Community in THE SEMANTIC WEB: RESEARCH AND APPLICATIONS
  • 2005. OntoSearch: An Ontology Search Engine in RESEARCH AND DEVELOPMENT IN INTELLIGENT SYSTEMS XXI
  • 2006. Ranking Ontologies with AKTiveRank in THE SEMANTIC WEB - ISWC 2006
  • 2013. Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking in ADVANCED INFORMATION SYSTEMS ENGINEERING
  • 2009-10-16. BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse in NATURE PRECEDINGS
  • 2001-05. The Semantic Web in SCIENTIFIC AMERICAN
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13326-017-0128-y

    DOI

    http://dx.doi.org/10.1186/s13326-017-0128-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1085913245

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28592275


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    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13326-017-0128-y'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13326-017-0128-y'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13326-017-0128-y'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13326-017-0128-y'


     

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