BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

T. Katayama, M.D. Wilkinson, K.F. Aoki-Kinoshita, J.C.P. Prins

Research output: Contribution to journalArticleAcademicpeer-review

30 Citations (Scopus)

Abstract

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
Original languageEnglish
Article number5
JournalJournal of Biomedical Semantics
Volume5
DOIs
Publication statusPublished - 2014

Keywords

  • genome analysis environment
  • metabolic pathways
  • web services
  • gene
  • sequences
  • software
  • biology
  • normalization
  • collection
  • glycomics

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