Implementation of linked data in the life sciences at BioHackathon 2011

Kiyoko F. Aoki-Kinoshita, Akira R. Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao, Shuichi Kawashima, Shinobu Okamoto, Toshiaki Katayama, Soichi Ogishima

Research output: Contribution to journalReview article

5 Citations (Scopus)

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.

Original languageEnglish
Article number3
JournalJournal of Biomedical Semantics
Volume6
Issue number1
DOIs
Publication statusPublished - Jan 7 2015
Externally publishedYes

Fingerprint

Biological Science Disciplines
Interoperability
Data description
Language
Query languages
Databases
Ontology
Information Storage and Retrieval
Semantics
Data visualization
Software
Research Personnel
Semantic Web
Technology
Costs and Cost Analysis
Personnel
Network protocols
Costs

Keywords

  • Alzheimer's disease
  • Data integration
  • DDBJ
  • Faceted search interface
  • Glycobiology
  • PDBj
  • Semantic Web

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Computer Networks and Communications
  • Health Informatics

Cite this

Aoki-Kinoshita, K. F., Kinjo, A. R., Morita, M., Igarashi, Y., Chen, Y. A., Shigemoto, Y., ... Ogishima, S. (2015). Implementation of linked data in the life sciences at BioHackathon 2011. Journal of Biomedical Semantics, 6(1), [3]. https://doi.org/10.1186/2041-1480-6-3

Implementation of linked data in the life sciences at BioHackathon 2011. / Aoki-Kinoshita, Kiyoko F.; Kinjo, Akira R.; Morita, Mizuki; Igarashi, Yoshinobu; Chen, Yi an; Shigemoto, Yasumasa; Fujisawa, Takatomo; Akune, Yukie; Katoda, Takeo; Kokubu, Anna; Mori, Takaaki; Nakao, Mitsuteru; Kawashima, Shuichi; Okamoto, Shinobu; Katayama, Toshiaki; Ogishima, Soichi.

In: Journal of Biomedical Semantics, Vol. 6, No. 1, 3, 07.01.2015.

Research output: Contribution to journalReview article

Aoki-Kinoshita, KF, Kinjo, AR, Morita, M, Igarashi, Y, Chen, YA, Shigemoto, Y, Fujisawa, T, Akune, Y, Katoda, T, Kokubu, A, Mori, T, Nakao, M, Kawashima, S, Okamoto, S, Katayama, T & Ogishima, S 2015, 'Implementation of linked data in the life sciences at BioHackathon 2011', Journal of Biomedical Semantics, vol. 6, no. 1, 3. https://doi.org/10.1186/2041-1480-6-3
Aoki-Kinoshita, Kiyoko F. ; Kinjo, Akira R. ; Morita, Mizuki ; Igarashi, Yoshinobu ; Chen, Yi an ; Shigemoto, Yasumasa ; Fujisawa, Takatomo ; Akune, Yukie ; Katoda, Takeo ; Kokubu, Anna ; Mori, Takaaki ; Nakao, Mitsuteru ; Kawashima, Shuichi ; Okamoto, Shinobu ; Katayama, Toshiaki ; Ogishima, Soichi. / Implementation of linked data in the life sciences at BioHackathon 2011. In: Journal of Biomedical Semantics. 2015 ; Vol. 6, No. 1.
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