The RIKEN integrated database of mammals

Masuya, Hiroshi; Makita, Yuko; Kobayashi, Norio; Nishikata, Koro; Yoshida, Yuko; Mochizuki, Yoshiki; Doi, Koji; Takatsuki, Terue; Waki, Kazunori; Tanaka, Nobuhiko; Ishii, Manabu; Matsushima, Akihiro; Takahashi, Satoshi; Hijikata, Atsushi; Kozaki, Kouji; Furuichi, Teiichi; Kawaji, Hideya; Wakana, Shigeharu; Nakamura, Yukio; Yoshiki, Atsushi; Murata, Takehide; Fukami-Kobayashi, Kaoru; Mohan, S. Sujatha; Ohara, Osamu; Hayashizaki, Yoshihide; Mizoguchi, Riichiro; Obata, Yuichi; Toyoda, Tetsuro

doi:10.1093/nar/gkq1078

Cited by 22 publications

(18 citation statements)

References 46 publications

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“…In [14], Masuya et al describe the development of the RIKEN integrated database of mammals. This database integrates heterogeneous mammal-related data stored in multiple individual databases of related research projects.…”

Section: Fig 1 the Searching And Selection Processesmentioning

confidence: 99%

“…Another indirect approach is presented in [14]. Masuya et al use YAMATO-GXO Lite, which aims to provide an explicit specification of the field of experimental genetics.…”

Section: Rq1 How Have Foundational Ontologies Been Used As Part Of Ementioning

confidence: 99%

“…Masuya et al [14] examined, at development time, the schemas of the databases to be integrated and, then classified their contents and semantics under YAMATO-GXO Lite, in a job that they consider to be comparable to database annotation. YAMATO-GXO Lite is implemented in RDF and OWL, and the database annotations are made in these languages to support queries at run time.…”

Section: Rq2 Do the Studies Use Ontologies At Development Time At Rmentioning

confidence: 99%

See 2 more Smart Citations

Foundational Ontologies for Semantic Integration in EAI: A Systematic Literature Review

Nardi

Falbo

Almeida

2013

IFIP Advances in Information and Communication Technology

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Despite (i) the recognized benefits of using ontologies in semantic EAI initiatives, (ii) the benefits of using foundational ontologies for promoting meaning negotiation and common understanding, and (iii) the importance of the semantic integration issue in EAI area, foundational ontologies have not yet become widely adopted in EAI initiatives for dealing with semantic conflicts. This has led us to investigate, through a systematic review of the literature, the adoption of foundational ontologies in EAI initiatives, with the purpose of understanding the current role of these ontologies in EAI and identifying gaps for future research, in which the potential benefits of such ontologies could be explored. We consider: (i) the role of foundational ontologies as part of the integration approach; (ii) the use of ontologies at development time and/or at run time; and (iii) the adoption of systematic approaches for semantic EAI.

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Section: Fig 1 the Searching And Selection Processesmentioning

confidence: 99%

“…Another indirect approach is presented in [14]. Masuya et al use YAMATO-GXO Lite, which aims to provide an explicit specification of the field of experimental genetics.…”

Section: Rq1 How Have Foundational Ontologies Been Used As Part Of Ementioning

confidence: 99%

Section: Rq2 Do the Studies Use Ontologies At Development Time At Rmentioning

confidence: 99%

See 1 more Smart Citation

Foundational Ontologies for Semantic Integration in EAI: A Systematic Literature Review

Nardi

Falbo

Almeida

2013

IFIP Advances in Information and Communication Technology

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“…Referring to this annotation, the system can intelligently process heterogeneous data sets. In other words, a simple accumulation of databases can be used as a single integrated database [21]. In addition, this reorganized public data is openly available for downloading from the web site of the Biological Linked Open Data (BioLOD) [1] in various data formats.…”

Section: Linked Open Data For Knowledge Discoverymentioning

confidence: 99%

Roles and Applications of Biomedical Ontologies in Experimental Animal Science

Masuya

2012

Exp. Anim.

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Abstract:A huge amount of experimental data from past studies has played a vital role in the development of new knowledge and technologies in biomedical science. The importance of computational technologies for the reuse of data, data integration, and knowledge discoveries has also increased, providing means of processing large amounts of data. In recent years, information technologies related to "ontologies" have played more significant roles in the standardization, integration, and knowledge representation of biomedical information. This review paper outlines the history of data integration in biomedical science and its recent trends in relation to the field of experimental animal science.

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“…To effectively use both well-formed RDF datasets and a vast number of biomedical documents, the extension of current query languages should support not only Boolean relationships but also statistically evaluated relationships. In this chapter, we will discuss the development of a web-based tool named Positional Medline (PosMed) that can immediately suggest genes related to a certain phenotype by accessing a Semantic Web based databases over omics entities named the Scientists' Networking System (SciNetS; Masuya et al, 2010) and document databases (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%