Abstract
The amount and heterogeneity of life-science datasets published on the Web have considerably increased recently. However, biomedical scientists face numerous serious difficulties in finding, using and publishing useful databases. In order to solve these issues, we developed a Resource Description Framework-based database platform, called RIKEN MetaDatabase, which allows biologists to easily develop, publish and integrate databases. The platform manages metadata of both research data and individual data described with standardised vocabularies and ontologies, and has a simple browser-based graphical user interface for viewing data including tabular and graphical views. The platform was released in April 2015, and 110 databases including mammalian, plant, bioresource and image databases with 21 ontologies have been published through this platform as of July 2016. This paper describes the technical knowledge obtained through the development and operation of RIKEN MetaDatabase as a challenge for accelerating life-science data distribution promotion.
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References
Vasilevsky, N., Johnson, T., Corday, K., Torniai, C., Brush, M., Segerdell, E., Wilson, M., Shaffer, C., Robinson, D., Haendel, M.: Research resources: curating the new eagle-i discovery system. Database (Oxford), 20:2012 (2012)
Belleau, F., Nolin, M.A., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed. Inform. 41(5), 706–716 (2008)
Whetzel, P.L., Noy, N.F., Shah, N.H., Alexander, P.R., Nyulas, C., Tudorache, T., Musen, M.A.: BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 39(Web Server issue): W541–W545 (2011)
Wolstencroft, K., Owen, S., Horridge, M., Krebs, O., Mueller, W., Snoep, J.L., du Preez, F., Goble, C.: RightField: embedding ontology annotation in spreadsheets. Bioinformatics 27(14), 2021–2012 (2011)
The FANTOM Consortium and the RIKEN PMI and CLST (DGT): A promoter-level mammalian expression atlas. Nature 507, 462–470 (2014)
Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., Fujita, M., Motohashi, R., Nagata, N., Takagi, T., Shinozaki, K., Matsui, M.: The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J. 45, 974–985 (2006)
Sugahara, M., Asada, Y., Shimada, H., Taka, H., Kunishima, N.: HATODAS II: heavy-atom database system with potentiality scoring. J. Appl. Crystallogr. 42, 540–544 (2009)
Yoshiki, A., Ike, F., Mekada, K., Kitaura, Y., Nakata, H., Hiraiwa, N., Mochida, K., Ijuin, M., Kadota, M., Murakami, A., Ogura, A., Abe, K., Moriwaki, K., Obata, Y.: The mouse resources at the RIKEN BioResource center. Exp. Anim. 58(2), 85–96 (2009)
Nakamura, Y.: Bio-resource of human and animal-derived cell materials. Exp. Anim. 59(1), 1–7 (2010)
Yokoyama, K.K., Murata, T., Pan, J., Nakade, K., Kishikawa, S., Ugai, H., Kimura, M., Kujime, Y., Hirose, M., Masuzaki, S., Yamasaki, T., Kurihara, C., Okubo, M., Nakano, Y., Kusa, Y., Yoshikawa, A., Inabe, K., Ueno, K., Obata, Y.: Genetic materials at the gene engineering division. RIKEN BioResource Center. Exp. Anim. 59(2), 115–124 (2010)
Yamaguchi, A., Kozaki, K., Lenz, K., Wu, H., Yamamoto, Y., Kobayashi, N.: Efficiently finding paths between classes to build a SPARQL query for life-science databases. In: Qi, G., Kozaki, K., Pan, J.Z., Yu, S. (eds.) JIST 2015. LNCS, vol. 9544, pp. 321–330. Springer, Heidelberg (2016). doi:10.1007/978-3-319-31676-5_24
Hoehndorf, R., Schofield, P.N., Gkoutos, G.V.: PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res. 39(18), 119 (2011)
Robinson, P.N., Khler, S., Oellrich, A.: Sanger Mouse Genetics Project, Wang, K., Mungall, C.J., Lewis, S.E., Washington, N., Bauer, S., Seelow, D., Krawitz, P., Gilissen, C., Haendel, M., Smedley, D.: Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 24(2), 340–348 (2014)
Dickinson, M.E., Flenniken, A.M., Ji, X., Teboul, L., Wong, M.D., White, J.K., Meehan, T.F., Weninger, W.J., Westerberg, H., Adissu, H., et al.: High-throughput discovery of novel developmental phenotypes. Nature 537(7621), 508–514 (2016)
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Kobayashi, N., Lenz, K., Masuya, H. (2016). RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences. In: Li, YF., et al. Semantic Technology. JIST 2016. Lecture Notes in Computer Science(), vol 10055. Springer, Cham. https://doi.org/10.1007/978-3-319-50112-3_8
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DOI: https://doi.org/10.1007/978-3-319-50112-3_8
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