Abstract
The broad dissemination of information is a key issue in improving access to existing bioresources. We attempted to develop Linked Open Data (LOD) for bioresources available at the RIKEN BioResource Center. The LOD consists of standardized, structured data available openly on the World Wide Web, including published bioresource information for 5,000 mouse strains and 3,600 cell lines. The LOD includes links to publically available information, such as genes, alleles, and ontologies, providing phenotypic information through the BioLOD website. As a result, information on mouse strains and cell lines have been connected to various data items in public databases and other project-oriented databases. Thus, through the use of LOD, dispersed efforts to produce different databases can be easily combined. Through these efforts, we expect to contribute to the global improvement of access to bioresources.
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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, 85–96 (2009)
Nakamura, Y.: Bio-resource of human and animal-derived cell materials. Exp. Anim. 59, 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, 115–124 (2010)
The International Mouse Phenotyping Consortium, http://www.mousephenotype.org
Cell Line Ontology, http://bioportal.bioontology.org/ontologies/1314
RIKEN adopts Semantic Web as the data-release standard of its database-construction infrastructure. RIKEN Press Release, http://www.riken.jp/engn/r-world/info/release/press/2009/090331_2/
RIKEN BRC Mouse Web Catalog, http://www2.brc.riken.jp/lab/animal/search.php
RKIEN BRC Cell Line Web Catalog, http://www2.brc.riken.jp/lab/cell/search.php
Masuya, H., Makita, Y., Kobayashi, N., Nishikata, K., Yoshida, Y., Mochizuki, Y., Doi, K., Takatsuki, T., Waki, K., Tanaka, N., Ishii, M., Matsushima, A., Takahashi, S., Hijikata, A., Kozaki, K., Furuichi, T., Kawaji, H., Wakana, S., Nakamura, Y., Yoshiki, A., Murata, T., Fukami-Kobayashi, K., Mohan, S., Ohara, O., Hayashizaki, Y., Mizoguchi, R., Obata, Y., Toyoda, T.: The RIKEN integrated database of mammals. Nucleic Acids Res. 39(Database issue), D861–D870 (2011)
BioLOD, http://biolod.org
BioSPARQL
BioLOD for BRC mouse strain, http://biolod.org/class/cria315s1i/BRC_Mouse_Strain
BioLOD for BRC cell line, http://biolod.org/class/cria322s1i/BRC_Cell_Line
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J., OBI Consortium, Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.A., Scheuermann, R.H., Shah, N., Whetzel, P.L., Lewis, S.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255 (2007)
Mizoguchi, R.: Tutorial on ontological engineering - Part 2: Ontology development, tools and languages. New Generation Computing 22, 61–96 (2004)
Mizoguchi, R.: Tutorial on ontological engineering - Part 3: Advanced course of ontological engineering. New Generation Computing 22, 198–220 (2004)
Kozaki, K., Sunagawa, E., Kitamura, Y., Mizoguchi, R.: Role Representation Model Using OWL and SWRL. In: Proc. of 2nd Workshop on Roles and Relationships in Object Oriented Programming, Multiagent Systems, and Ontologies, pp. 39–46 (2007)
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Masuya, H. et al. (2013). Development of Linked Open Data for Bioresources. In: Takeda, H., Qu, Y., Mizoguchi, R., Kitamura, Y. (eds) Semantic Technology. JIST 2012. Lecture Notes in Computer Science, vol 7774. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37996-3_28
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DOI: https://doi.org/10.1007/978-3-642-37996-3_28
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