INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form.
The system contains a number of unique features to encode this type
of knowledge. Biological terms such as protein names typically
represent abstract, conceptual molecules that are used for unspecified
organisms. Biologists interpret the name as a specific instance of
protein using background knowledge. For example, the term "MAP-kinase"
indicates ERK1 of a human, JNK1 of a mouse, p38alpha of a rat, etc.
These abstract names are collected from the literature and are organized into an ontology to annotate abstract objects in pathways. In addition, each term has links to database such as SWISS-PROT and Gene Ontology (GO).
The system provides pathway information as a composite of biological events, since functional knowledge is usually described as a set of fragmented processes. Each event is annotated with entries of a event ontology, which also has links to GO.
- Fukuda, K. 2008. INOH pathway database: Curation, Annotation, Integration. InterOntology08, 1(1), pp.47-50 (2008).
- Fukuda, K., Yamamoto, S., Sakai, N., Nakanishi, Y., Nakamura, H., Takagi, T.: "Graphical Syntax and Query for Pathway Database", The 10th World Multi-Conference on Systemics, Cybernetics and Infrmatics, pp7-10 (2006).
- Tatsuya Kushida, Toshihisa Takagi, and Ken Ichiro Fukuda. 2006. Event Ontology: A Pathway-Centric Ontology for Biological Processes. Pacific Symposium on Biocomputing 11:152-163(2006).
- Kushida, T., Yamamoto, S., Yamagata, Y., Asanuma, T., Hattori, E., Takagi, T. and Fukuda, K. 2005. Research on biological pathways peculiar to woody perennial Plants using a pathway database : P-INOH. Proceedings of International Workshop on Knowledge Discovery and Data Management in Biomedical Science. 2005.5, pp.56-67
- Fukuda, K. 2005. Higher Order Knowledge Proceeding : Pathway Database and Ontologies. Genomics & Informatics, vol.3, No.2, ISSN 1598-866X, 2005.6, pp.47-51
- Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi and Ken Ichiro Fukuda. 2004. An Ontology for Annotation of Signal Transduction Pathway Molecules in the Scientific Literature: Molecule Role Ontology. Comparative and Functional Genomics, Volume 5, Issue 6-7, Pages 528-536 (2004).
- Ken Ichiro Fukuda, Toshihisa Takagi. 2004. A Pathway Editor for Literature-based Knowledge Curation. APBC 2004, pp.339-344. (pre print version here)
- Ken Ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi. 2004. Pathway Database: Higher Order Knowledge in Biology. Information Processing Society of Japan (IPSJ), Transactions on Databases, vol.45 No.SIG7(TOD 22) June 2004, pp.77-84
- Ken Ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi. 2003. FREX: a query interface for biological processes with a hierarchical and recursive structures. In Silico Biol. 4, 0007 (2003).
- Ken Ichiro Fukuda, Toshihisa Takagi. 2001. Knowledge Representation of Signal Transduction Pathways. Bioinformatics 2001. Vol.17, pp.829-837
- Satoko Sakai, Noriko Sakai, Hiromi Nakamura, Ken Fukuda, Toshihisa Takagi. 2009. INOH Pathway Database. MBSJ 2009 (The 32nd Annual Meeting of the Molecular Biology Society of Japan).
- Satoko Sakai, Noriko Sakai, Hiromi Nakamura, Ken Fukuda, Toshihisa Takagi. 2009. INOH Pathway Database. GIW 2009 (The 20th International Conference on Genome Informatics).
- Fukuda, K. 2008. The INOH Pathway Database. Workshop on Ontologies of Cellular Networks.
- Ken Fukuda. 2008. INOH pathway database: Curation, Annotation, Integration. Interdisciplinary Ontology Conference (InterOntology08).
- Ken Fukuda. 2008. INOH Pathway Event Ontology. PAG-XVI 2008 (the 16th International Plant and Animal Genome Conference).
- Fukuda, K., Yamamoto, S., Sakai, N., Nakamura, H., Takagi, T. 2007. INOH pathway database and BioPAX export. ISMB 2007 (15th Annual International Conference on Intelligent Systems for Molecular Biology).
- Emek Demir(Memorial Sloan-Kettering Cancer Center), Ken Fukuda, Toshihisa Takagi, Chris Sander(Memorial Sloan-Kettering Cancer Center). 2007. Paxtools: A software library for accessing and analyzing biological pathway information. ISMB 2007.
- Ken Fukuda. 2007. INOH curation. BioPAX Workshop 2007.
- Noriko Sakai, Satoko Yamamoto, Hiromi Nakamura, Toshihisa Takagi,Ken Fukuda. 2007. INOH Pathway Data and Ontologies. JSBi 2007 (The 2007 Annual Conference of Japanese Society for Bioinformatics).
- Satoko Sakai, Noriko Sakai, Hiromi Nakamura, Ken Fukuda, Toshihisa Takagi. 2007. MBSJ 2007 (The 30th Annual Meeting of the Molecular Biology Society of Japan).
- Fukuda, K., Yamamoto, S., Sakai, N., Nakamura, H., Takagi, T. 2006. INOH pathway data ontologies. ISMB 2006.
- Sakai, N., Yamamoto, S., Nakamura, H., Nakanishi, Y., Takagi, T., Fukuda, K. 2006. INOH Pathway Data Ontologies. GIW 2006 (The 17th International Conference on Genome Informatics).
- Fukuda, K. 2005. INOH database - pathway data and pathway Ontologies. The 1st International BioPAX Symposium.
- Noriko Sakai, Tatsuya Kushida, Satoko Yamamoto, Emi Hattori, Hiromi Nakamura, Yuki Yamagata, Yukiko Nakanishi, Toshihisa Takagi, Ken Ichiro Fukuda. 2005. INOH: Pathways and Ontologies. GIW 2005.
- Tatsuya Kushida, Satoko Yamamoto, Takao Asanuma, Emi Hattori, Yuki Yamagata, Toshihisa Takagi, Ken Ichiro Fukuda. 2005. Event Ontology: Biological ontology for annotating biological pathways and sub-pathways. ISMB 2005.
- Ken Ichiro Fukuda, Takao Asanuma, Satoko Yamamoto, Tatsuya Kushida, Emi Hattori, Yuki Yamagata, Toshihisa Takagi. 2005. INOH pathway database. ISMB 2005.
- Takao Asanuma, Tatsuya Kushida, Satoko Yamamoto, Yuki Yamagata, Azumi Sekiguchi, Toshihisa Takagi, Ken Ichiro Fukuda. 2004. INOH: A Pathway Database of Biological Events. GIW 2004.
- Ken Ichiro Fukuda, Naotaka Ono, Satoko Yamamoto, Tatsuya Kushida, Yuki Yamagata, Toshihisa Takagi. 2004. INOH: A pathway database of biological events. ISMB/ECCB 2004.
- Satoko Yamamoto, Toshihisa Takagi, Ken Ichiro Fukuda. 2004. Classifying Molecules by their Roles. The Seventh Annual Bio-ontologies Meeting 2004.(presentation slides)
- Satoko Yamamoto, Tatsuya Kushida, Naotaka Ono, Yuki Yamagata, Toshihisa Takagi, Ken Ichiro Fukuda. 2003. INOH: a textual knowledge based pathway databases. GIW 2003.
- Ken Ichiro Fukuda. 2003. Signal Transduction Pathway Database: Bio-processes, Sub-processes, and their mechanisms. BMES 2003 Annual Fall Meeting.
- Ken Ichiro Fukuda. 2003. A recursively decomposable pathway DB: Annotating processes and sub-processes. The 5th BioPathways meeting 2003.
- Ken Ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi. 2003. A Pathway DB: Annotating Signal Transduction Pathways with bio-processes using hierarchical multi-layered structures. ISMB 2003.
- Toshihisa Takagi (Principal Investigator)
- Ken Ichiro Fukuda (co-PI)
- Satoko Yamamoto
- Noriko Sakai
- Hiromi Nakamura
Comments would be appreciated!
All rights of all INOH Products ("INP"s) and INOH Services (the Service) belongs to Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology and the Graduate School of Frontier Sciences, The University of Tokyo (the INOH database project, "INDP").
2. The license granted hereunder shall become effective on the date the LICENSEE first accesses the INPs and remains in force until terminated as provided in this Term of Use.
3 INDP expressly disclaims any warranty that queries to the INPs and other information which the LICENSEE transmits over the World Wide Web will be protected from third party access. Any loss or damage caused to the LICENSEE out of or in connection with the access to and/or use of INPs will be borne exclusively by User, and Academic User agrees that neither INDP nor any of their respective directors, offices or employees shall have any liability for any such loss or damage.
4 INDP is not obligated to provide the LICENSEE with any support relating to the use of the INPs.
5 It is requested that in any subsequent use of this work, the INOH project be given appropriate acknowledgment.
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