JSAI Technical Report, Type 2 SIG
Online ISSN : 2436-5556
BioLOD.org links open data of biological databases and supports visualization by existing applications
Koro NISHIKATAManabu ISHIIYuko YOSHIDANorio KOBAYASHISatoshi TAKAHASHIYoshiki MOCHIZUKIAkihiro MATSUSHIMAYoshiyuki TANAKADavid GIFFORDKoji DOIErimi HARADAYuko MAKITATetsuro TOYODA
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RESEARCH REPORT / TECHNICAL REPORT FREE ACCESS

2011 Volume 2011 Issue SWO-026 Pages 03-

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Abstract

The vast amount of various life sciences data at RIKEN and other institutes including ge-nome, transcriptome, proteome, metabolome, and phenome data are ontologically integrated into a com-mon system. The challenge is to facilitate data retrieval, integration and collaboration. BioLOD.org - the Biological Linked Open Data database (http://biolod.org) - provides over 6,800 downloadable OWL/RDF graph files of mutually linked public biological data organized as a semantic web using standardized for-mats of the World Wide Web Consortium Linking Open Data (W3C LOD) project. BioLOD.org mines numerous semantic links from original databases and re-classifies them into graph files based on ontology classifications. Relationships between the files are mutually and clearly referenced so it is easy to find other files associated by semantic links included in detailed data instances. BioLOD.org intensively sur-veyed both forward and reverse semantic link relationships from 36 databases for humans and mice, 33 databases for plants and 16 databases related to protein experiments and structures. BioLOD summarizes this information as archive files available for download in various useful formats. The BioLOD.org data-base uniquely provides Linked Open Data annotated contextually with biological vocabulary and supports visualization services to browse LOD data through SciNetS.org, repository services to deposit users' LOD through LinkData.org and SPARQL endpoint service for BioLOD data is through BioSPARQL.org.

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