title: INOH: ontology-based highly structured database of signal transduction pathways.
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/
authors: Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kashiwa, Japan.
authors: Satoko
authors: S
authors: Yamamoto
authors: Noriko
authors: N
authors: Sakai
authors: Hiromi
authors: H
authors: Nakamura
authors: Hiroshi
authors: H
authors: Fukagawa
authors: Ken
authors: K
authors: Fukuda
authors: Toshihisa
authors: T
authors: Takagi
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D004331:Drosophila melanogaster; D008322:Mammals; D053858:Metabolic Networks and Pathways; D015398:Signal Transduction; D009626:Terminology as Topic; D014584:User-Computer Interface; D014982:Xenopus laevis