General information of database
info Alternative name Integrating Network Objects with Hierarchies
info Creator
Creator Name:
Toshihisa Takagi*
Link to J-GLOBAL
Link to researchmap
Creator Affiliation:
School of Science, The University of Tokyo
Creator Name:
Ken-ichiro Fukuda
Link to J-GLOBAL
Link to researchmap
Creator Affiliation:
Information and Communication Infrastructure Division, National Institute of Advanced Industrial Science and Technology
Creator Name:
Satoko Yamamoto
Creator Affiliation:
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency
Creator Name:
Noriko Sakai
Creator Affiliation:
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency
Creator Name:
Hiromi Nakamura
Creator Affiliation:
Information and Mathematical Science and Bioinformatics Co., Ltd.
info Database classification Metabolic and Signaling Pathways - Metabolic pathways
Metabolic and Signaling Pathways - Protein-protein interactions
Metabolic and Signaling Pathways - Signalling pathways
info Database description INOH database is a highly structured, manually curated database of signal transduction pathways. The database focuses on curating and encoding textual knowledge in scientific articles into a machine-processable form.
info Features and manner of utilization of database INOH database provides signal transduction pathway data which is well-annotated by the INOH ontology terms.
INOH curators who have a biological background created pathways and annotated every pathway component by a set of uniquely developed ontologies.
The INOH Client tool, which is a pathway navigation/editor tool, is freely downloadable.
INOH pathway diagrams are freely available in INOH XML and BioPAX formats.
info Background and funding
Name:
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency
Link to J-GLOBAL
Link to Life science projects in Japan
info Reference(s)
Article title:
INOH: ontology-based highly structured database of signal transduction pathways.
Author name(s):
Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T.
Journal:
Database (Oxford). 2011 Nov 26;2011:bar052. Print 2011.
Article title:
INOH pathway database: Curation, Annotation, Integration.
Author name(s):
Fukuda K.
Journal:
InterOntology08, 1(1), pp.47-50 (2008).
Article title:
Graphical Syntax and Query for Pathway Database
Author name(s):
Fukuda, K., Yamamoto, S., Sakai, N., Nakanishi, Y., Nakamura, H., Takagi, T.
Journal:
The 10th World Multi-Conference on Systemics, Cybernetics and Infrmatics, pp7-10 (2006).
Article title:
Event ontology: a pathway-centric ontology for biological processes.
Author name(s):
Kushida T, Takagi T, Fukuda K.
Journal:
Pac Symp Biocomput. 2006:152-63.
Article title:
Research on biological pathways peculiar to woody perennial Plants using a pathway database : P-INOH.
Author name(s):
Kushida, T., Yamamoto, S., Yamagata, Y., Asanuma, T., Hattori, E., Takagi, T. and Fukuda, K.
Journal:
Proceedings of International Workshop on Knowledge Discovery and Data Management in Biomedical Science. 2005.5, pp.56-67
Article title:
Higher Order Knowledge Proceeding : Pathway Database and Ontologies.
Author name(s):
Fukuda, K.
Journal:
Genomics & Informatics, vol.3, No.2, ISSN 1598-866X, 2005.6, pp.47-51
Article title:
The Molecule Role Ontology: An Ontology for Annotation of Signal Transduction Pathway Molecules in the Scientific Literature.
Author name(s):
Yamamoto S, Asanuma T, Takagi T, Fukuda K.
Journal:
Comp Funct Genomics. 2004;5(6-7):528-36.
External Links:
Link to PubMed
Link to J-GLOBAL
Article title:
A Pathway Editor for Literature-based Knowledge Curation.
Author name(s):
Ken-ichiro Fukuda, Toshihisa Takagi.
Journal:
APBC 2004, pp.339-344.
Article title:
Pathway Database: Higher Order Knowledge in Biology.
Author name(s):
Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi.
Journal:
nformation Processing Society of Japan (IPSJ), Transactions on Databases, vol.45 No.SIG7(TOD 22) June 2004, pp.77-84
Article title:
FREX: a query interface for biological processes with hierarchical and recursive structures.
Author name(s):
Fukuda K, Yamagata Y, Takagi T.
Journal:
In Silico Biol. 2004;4(1):63-79. Epub 2004 Feb 22.
Article title:
Knowledge representation of signal transduction pathways.
Author name(s):
Fukuda K, Takagi T.
Journal:
Bioinformatics. 2001 Sep;17(9):829-37.
External Links:
Link to PubMed
Link to J-GLOBAL
Original website information
info Database maintenance site The Institute of Medical Science, The University of Tokyo
*The original website was terminated.
info URL of the original website (Closed) http://inoh.hgc.jp/
info Operation start date 2006年02月01日
info Last update date 2011年03月29日
info URL of the portal site -
info Whole data download (Closed) http://inoh.hgc.jp/download.html
info Referenced database -
info Entry list Available
info Query search Available
info Web services Available
info URL of Web services (Closed) http://inoh.hgc.jp/inoh_api_manual.html
info Need for user registration Not available