Ontology-Based Querying with Bio2RDF’s Linked Open Data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-04

AUTHORS

Alison Callahan, José Cruz-Toledo, Michel Dumontier

ABSTRACT

BACKGROUND: A key activity for life scientists in this post "-omics" age involves searching for and integrating biological data from a multitude of independent databases. However, our ability to find relevant data is hampered by non-standard web and database interfaces backed by an enormous variety of data formats. This heterogeneity presents an overwhelming barrier to the discovery and reuse of resources which have been developed at great public expense.To address this issue, the open-source Bio2RDF project promotes a simple convention to integrate diverse biological data using Semantic Web technologies. However, querying Bio2RDF remains difficult due to the lack of uniformity in the representation of Bio2RDF datasets. RESULTS: We describe an update to Bio2RDF that includes tighter integration across 19 new and updated RDF datasets. All available open-source scripts were first consolidated to a single GitHub repository and then redeveloped using a common API that generates normalized IRIs using a centralized dataset registry. We then mapped dataset specific types and relations to the Semanticscience Integrated Ontology (SIO) and demonstrate simplified federated queries across multiple Bio2RDF endpoints. CONCLUSIONS: This coordinated release marks an important milestone for the Bio2RDF open source linked data framework. Principally, it improves the quality of linked data in the Bio2RDF network and makes it easier to access or recreate the linked data locally. We hope to continue improving the Bio2RDF network of linked data by identifying priority databases and increasing the vocabulary coverage to additional dataset vocabularies beyond SIO. More... »

PAGES

s1

References to SciGraph publications

  • 2012-12. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2011-12. Integrating systems biology models and biomedical ontologies in BMC SYSTEMS BIOLOGY
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  • 2011-12. Linked open drug data for pharmaceutical research and development in JOURNAL OF CHEMINFORMATICS
  • 2011-12. Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics in BMC BIOINFORMATICS
  • 2006-12. cPath: open source software for collecting, storing, and querying biological pathways in BMC BIOINFORMATICS
  • 2010-06. Modeling biomedical experimental processes with OBI in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2011-12. Semantic Web integration of Cheminformatics resources with the SADI framework in JOURNAL OF CHEMINFORMATICS
  • 2008-10. Automatic medical encoding with SNOMED categories in BMC MEDICAL INFORMATICS AND DECISION MAKING
  • 2005-05. Relations in biomedical ontologies in GENOME BIOLOGY
  • 2008-12. iRefIndex: A consolidated protein interaction database with provenance in BMC BIOINFORMATICS
  • 2010-12. Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data in BMC BIOINFORMATICS
  • 2012-02. Toward interoperable bioscience data in NATURE GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/2041-1480-4-s1-s1

    DOI

    http://dx.doi.org/10.1186/2041-1480-4-s1-s1

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23735196


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