Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Biocuration 2010

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

Abstract

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.

Author information

Affiliations

Authors

Rights and permissions

Creative Commons Attribution 3.0 License.

Reprints and Permissions

About this article

Cite this article

Toyoda, T., Kobayashi, N., Ishii, M. et al. SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web. Nat Prec (2010). https://doi.org/10.1038/npre.2010.5083.1

Download citation

Keywords

  • Semantic Web
  • Cloud Computing
  • Data integration

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing