SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web | Zendy

Tetsuro Toyoda | Zendy; Norio Kobayashi | Zendy; Manabu Ishii | Zendy; Yuko Yoshida | Zendy; Yuko Makita | Zendy; Akihiro Matsushima | Zendy; Yoshiki Mochizuki | Zendy

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SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web

Author(s) -

Tetsuro Toyoda,

Norio Kobayashi,

Manabu Ishii,

Yuko Yoshida,

Yuko Makita,

Akihiro Matsushima,

Yoshiki Mochizuki

Publication year - 2010

Publication title -

nature precedings

Language(s) - English

Resource type - Journals

ISSN - 1756-0357

DOI - 10.1038/npre.2010.5083.1

Subject(s) - metadata , computer science , information retrieval , ontology , world wide web , semantic search , database catalog , set (abstract data type) , semantic web , database , metadata repository , philosophy , epistemology , programming language

Integration of various omics databases is a fundamental approach for comprehensive understanding of life phenomena. Scientists’ Networking System (SciNetS) is a Semantic Web-based data repository that realises database integration by collecting metadata of databases described as a set of triples consisting of two bio-items such as gene and ontology terms and a semantically defined relationship between these bio-items. These triples are curated from various life-sciences databases including gene-publication relationships manually curated from MEDLINE and gene-phenotype relationships extracted from published databases by computer programs. SciNetS internally forms a metadata network by maximally concatenating triples. SciNetS Search realizes a cross-search over the integrated databases by traversing the metadata network managed by SciNetS. SciNetS Search allows a user to discover bio-items included in the ontological category specified by the user. The results include bio-items not only having a user’s keyword but also semantically inferred from these bio-items using metadata relationships, and are ranked using statistical scores computed on the basis of the metadata network. SciNetS Search is available via a user’s web browser and provides search service against over 30 million bio-items of 100 thousand categories and 100 million relationships curated from over 100 public omics databases of various species including human, mouse, rice and _Arabidopsis_

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