Format

Send to

Choose Destination
Database (Oxford). 2011 Nov 26;2011:bar052. doi: 10.1093/database/bar052. Print 2011.

INOH: ontology-based highly structured database of signal transduction pathways.

Author information

1
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kashiwa, Japan.

Abstract

The Integrating Network Objects with Hierarchies (INOH) database is a highly structured, manually curated database of signal transduction pathways including Mammalia, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and canonical. Since most pathway knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. We use a hierarchical pathway representation model with a compound graph, and every pathway component in the INOH database is annotated by a set of uniquely developed ontologies. Finally, we developed the Similarity Search using the combination of a compound graph and hierarchical ontologies. The INOH database is to be a good resource for many users who want to analyze a large protein network. INOH ontologies and 73 signal transduction and 29 metabolic pathway diagrams (including over 6155 interactions and 3395 protein entities) are freely available in INOH XML and BioPAX formats. Database URL: http://www.inoh.org/.

PMID:
22120663
PMCID:
PMC3225078
DOI:
10.1093/database/bar052
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center