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

Norio Kobayashi, Norio Kobayashi, Manabu Ishii, Yuko Yoshida, Yuko Makita, Akihiro Matsushima, Yoshiki Mochizuki, Tetsuro Toyoda
2010 Nature Precedings  
Integration of various omics databases is a fundamental approach Ontological inference search at SciNetS for comprehensive understanding of life phenomena Scientists' g for comprehensive understanding of life phenomena. Scientists Networking System (SciNetS) is a Semantic Web-based data Networking System (SciNetS) is a Semantic Web based data repository that realises database integration by collecting metadata repository that realises database integration by collecting metadata of databases
more » ... ribed as a set of triples consisting of two bio-of databases described as a set of triples consisting of two bioitems such as gene and ontology terms and a semantically defined items such as gene and ontology terms and a semantically defined relationship between these bio items These triples are curated relationship between these bio-items. These triples are curated from various life-sciences databases including gene-publication from various life-sciences databases including gene-publication relationships manually curated from MEDLINE and gene-relationships manually curated from MEDLINE and gene phenotype relationships extracted from published databases by phenotype relationships extracted from published databases by computer programs SciNetS internally forms a metadata network computer programs. SciNetS internally forms a metadata network by maximally concatenating triples. by maximally concatenating triples. SciNetS Search realizes a cross search over the integrated SciNetS Search realizes a cross-search over the integrated databases by traversing the metadata network managed by databases by traversing the metadata network managed by S S S S S SciNetS. SciNetS Search allows a user to discover bio-items Sc etS Sc etS Sea c a o s a use to d sco e b o te s included in the ontological category specified by the user The included in the ontological category specified by the user. The results include bio-items not only having a user's keyword but also results include bio-items not only having a user s keyword but also i ll i f d f h bi i i d semantically inferred from these bio-items using metadata Related se a ca y e ed o ese b o e s us g e ada a relationships and are ranked using statistical scores computed on databases relationships, and are ranked using statistical scores computed on the basis of the metadata network SciNetS Search is available via the basis of the metadata network. SciNetS Search is available via ' b b d id h i i 30 Ontologicallya user's web browser and provides search service against over 30 categorised p g million bio items of 100 thousand categories and 100 million databases million bio-items of 100 thousand categories and 100 million relationships curated from over 100 public omics databases of relationships curated from over 100 public omics databases of i i i l di h i d A bid i The cross-search is various species including human, mouse, rice and Arabidopsis. The cross-search is completed in a few seconds p g , , p List of sub-completed in a few seconds. categories 1 Database integration with Virtual Laboratories Fi 3 Inference search results using ontological concept of hierarchy 1. Database integration with Virtual Laboratories S i ( S) Fig. 3 Inference search results using ontological concept of hierarchy l ti hi (L ft) A k d h th RIKEN as a Service (LaaS) relationships. (Left) A keyword cross-search over the RIKEN as a Service (LaaS) integrated database of mammals categorised on the bases of integrated database of mammals categorised on the bases of ontology (Right) A
doi:10.1038/npre.2010.5083 fatcat:h3a7p7y675a4xgnwdrncnbjpjq