title: Implementation of linked data in the life sciences at BioHackathon 2011.
abstract: BACKGROUND
  Linked Data has gained some attention recently in the life sciences as an effective way to provide and share data. As a part of the Semantic Web, data are linked so that a person or machine can explore the web of data. Resource Description Framework (RDF) is the standard means of implementing Linked Data. In the process of generating RDF data, not only are data simply linked to one another, the links themselves are characterized by ontologies, thereby allowing the types of links to be distinguished. Although there is a high labor cost to define an ontology for data providers, the merit lies in the higher level of interoperability with data analysis and visualization software. This increase in interoperability facilitates the multi-faceted retrieval of data, and the appropriate data can be quickly extracted and visualized. Such retrieval is usually performed using the SPARQL (SPARQL Protocol and RDF Query Language) query language, which is used to query RDF data stores. For the database provider, such interoperability will surely lead to an increase in the number of users.
  
  
  RESULTS
  This manuscript describes the experiences and discussions shared among participants of the week-long BioHackathon 2011 who went through the development of RDF representations of their own data and developed specific RDF and SPARQL use cases. Advice regarding considerations to take when developing RDF representations of their data are provided for bioinformaticians considering making data available and interoperable.
  
  
  CONCLUSIONS
  Participants of the BioHackathon 2011 were able to produce RDF representations of their data and gain a better understanding of the requirements for producing such data in a period of just five days. We summarize the work accomplished with the hope that it will be useful for researchers involved in developing laboratory databases or data analysis, and those who are considering such technologies as RDF and Linked Data.
authors.affiliation: Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577 Japan.
authors.forename: Kiyoko F
authors.initials: KF
authors.lastname: Aoki-Kinoshita
authors.affiliation: Laboratory of Protein Informatics, Laboratory of Protein Databases, and Protein Data Bank Japan, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871 Japan.
authors.forename: Akira R
authors.initials: AR
authors.lastname: Kinjo
authors.affiliation: Center for Knowledge Structuring, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Mizuki
authors.initials: M
authors.lastname: Morita
authors.affiliation: National Institute of Biomedical Innovation, 7-6-8 Asagi Saito, Ibaraki-City, Osaka, 567-0085 Japan.
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Igarashi
authors.affiliation: National Institute of Biomedical Innovation, 7-6-8 Asagi Saito, Ibaraki-City, Osaka, 567-0085 Japan.
authors.forename: Yi-An
authors.initials: YA
authors.lastname: Chen
authors.affiliation: DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan.
authors.forename: Yasumasa
authors.initials: Y
authors.lastname: Shigemoto
authors.affiliation: DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan.
authors.forename: Takatomo
authors.initials: T
authors.lastname: Fujisawa
authors.affiliation: Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577 Japan.
authors.forename: Yukie
authors.initials: Y
authors.lastname: Akune
authors.affiliation: Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577 Japan.
authors.forename: Takeo
authors.initials: T
authors.lastname: Katoda
authors.affiliation: Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577 Japan.
authors.forename: Anna
authors.initials: A
authors.lastname: Kokubu
authors.affiliation: Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577 Japan.
authors.forename: Takaaki
authors.initials: T
authors.lastname: Mori
authors.affiliation: Next Generation Systems Core Function Unit, Eisai Product Creation Systems, Eisai Co., Ltd, Tsukuba, Ibaraki, Japan.
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.affiliation: Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa-shi, Chiba, 277-0871 Japan.
authors.forename: Shuichi
authors.initials: S
authors.lastname: Kawashima
authors.affiliation: Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa-shi, Chiba, 277-0871 Japan.
authors.forename: Shinobu
authors.initials: S
authors.lastname: Okamoto
authors.affiliation: Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa-shi, Chiba, 277-0871 Japan.
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Katayama
authors.affiliation: Department of Bioclinical informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi, 980-8575 Japan.
authors.forename: Soichi
authors.initials: S
authors.lastname: Ogishima
keywords: Alzheimer’s disease; DDBJ; Data integration; Faceted search interface; Glycobiology; PDBj; Semantic Web