BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
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Published:2019-09-23
Issue:
Volume:8
Page:1677
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ISSN:2046-1402
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Container-title:F1000Research
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language:en
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Short-container-title:F1000Res
Author:
Katayama ToshiakiORCID, Kawashima Shuichi, Micklem GosORCID, Kawano ShinORCID, Kim Jin-Dong, Kocbek Simon, Okamoto Shinobu, Wang Yue, Wu Hongyan, Yamaguchi AtsukoORCID, Yamamoto Yasunori, Antezana ErickORCID, Aoki-Kinoshita Kiyoko F., Arakawa Kazuharu, Banno Masaki, Baran Joachim, Bolleman Jerven T.ORCID, Bonnal Raoul J. P., Bono HidemasaORCID, Fernández-Breis Jesualdo T., Buels Robert, Campbell Matthew P., Chiba Hirokazu, Cock Peter J. A., Cohen Kevin B., Dumontier Michel, Fujisawa Takatomo, Fujiwara Toyofumi, Garcia LeylaORCID, Gaudet Pascale, Hattori Emi, Hoehndorf Robert, Itaya Kotone, Ito Maori, Jamieson Daniel, Jupp Simon, Juty Nick, Kalderimis Alex, Kato FumihiroORCID, Kawaji Hideya, Kawashima Takeshi, Kinjo Akira R., Komiyama Yusuke, Kotera Masaaki, Kushida TatsuyaORCID, Malone James, Matsubara MasaakiORCID, Mizuno Satoshi, Mizutani SayakaORCID, Mori Hiroshi, Moriya Yuki, Murakami Katsuhiko, Nakazato Takeru, Nishide Hiroyo, Nishimura YosukeORCID, Ogishima Soichi, Ohta Tazro, Okuda Shujiro, Ono Hiromasa, Perez-Riverol YassetORCID, Shinmachi Daisuke, Splendiani Andrea, Strozzi Francesco, Suzuki ShinyaORCID, Takehara Junichi, Thompson Mark, Tokimatsu Toshiaki, Uchiyama IkuoORCID, Verspoor KarinORCID, Wilkinson Mark D.ORCID, Wimalaratne Sarala, Yamada IssakuORCID, Yamamoto Nozomi, Yarimizu Masayuki, Kawamoto Shoko, Takagi Toshihisa
Abstract
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.
Funder
National Bioscience Database Center
Publisher
F1000 Research Ltd
Subject
General Pharmacology, Toxicology and Pharmaceutics,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine
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