main

About INOH

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.

Papers

Posters and Oral presentations

Staff

Graduate School of Frontier Science, The University of Tokyo

Computational Biology Research Center (CBRC)

Japan Science and Technology Agency (JST)

Information and Mathematical Science Laboratory, Inc.

Contact us

Comments would be appreciated!

EmailAddress

Terms of Use

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").

By accessing and/or obtaining any INPs, you agree that you have read, understood, and will comply with all terms and conditions set in this Terms of Use, whereupon, these terms of use shall constitute a legally binding agreement between you (the LICENSEE) and INDP. Please refrain from accessing or using any INPs if you do not wish to be bound by these terms of use.

1. Subject to the terms and conditions of these terms of use, INDP grants LICENSEE a non-exclusive, non-transferable and non-sublicenseable license to access and use INPs.

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.

6 INPs may provide links to other World Wide Web sites or resources. INDP does not endorse or is responsible for any data, software or other content available from such sites or resources or their privacy policies. The LICENSEE acknowledges and agrees that INDP shall not be liable, directly or indirectly, for any damage or loss (direct or indirect) relating to User's use of or reliance on such data, software or other content. The LICENSEE shall be solely responsible for obtaining any necessary licenses and/or for compliance with applicable terms of use, as may be required to use data, software or other content from such sites or resources.

7 THE LICENSEE ACKNOWLEDGES THAT THE INPS, INCLUDING WITHOUT LIMITATION, THE DATABASE OF INFORMATION CONTAINED THEREIN, IS EXPERIMENTAL AND ACADEMIC IN NATURE, AND IS NOT LICENSED BY THE U.S. FOOD AND DRUG ADMINISTRATION OR ANY OTHER REGULATORY BODY.

8 THE INPS ARE PROVIDED ON AN 'AS IS' AND 'AS AVAILABLE' BASIS WITH ALL FAULTS. INDP MAKES NO WARRANTY OR REPRESENTATION OF ANY KIND, EXPRESS OR IMPLIED, WITH RESPECT TO THE SERVICE OR THE WEBSITE, INCLUDING, WITHOUT LIMITATION, ANY WARRANTY OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT OF THIRD PARTY RIGHTS. WITHOUT DEROGATING FROM THE GENERALITY OF THE FOREGOING, INDP DOES NOT WARRANT THAT THE INPS WILL MEET USER'S REQUIREMENTS OR THAT USE OF INPS WILL BE FREE OF INFECTION OR VIRUSES, ERROR-FREE, UNINTERRUPTED, SECURE OR WILL PRODUCE ACCURATE RESULTS. THE LICENSEE SHALL BEAR TOTAL AND EXCLUSIVE RESPONSIBILITY AND RISK FOR THE USE OF INPS. THE LICENSEE SHALL BE SOLELY RESPONSIBLE FOR ANY RESULTING DAMAGE TO USER'S COMPUTER SYSTEMS OR LOSS OF DATA.

9 ACADEMIC USER AGREES THAT INDP AND THEIR RESPECTIVE DIRECTORS, OFFICERS AND EMPLOYEES (COLLECTIVELY, THE "INDEMNITEES") SHALL NOT BE LIABLE FOR ANY CLAIMS, DEMANDS, LIABILITIES, COSTS, LOSSES, DAMAGES OR EXPENSES (INCLUDING LEGAL COSTS AND ATTORNEYS' FEES) CAUSED TO OR SUFFERED BY ANY PERSON OR ENTITY (INCLUDING WITHOUT LIMITATION, USER), THAT DIRECTLY OR INDIRECTLY ARISE OUT OF OR RESULT FROM USE OF THE SERVICE BY USER, BREACH OF THESE TERMS OF USE BY LICENSEE OR VIOLATION OF ANY RIGHTS OF ANY THIRD PARTY (ALL OF THE FOREGOING, COLLECTIVELY, "CLAIMS"). WITHOUT DEROGATING FROM THE GENERALITY OF THE FOREGOING, THE INDEMNITEES SHALL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, CONSEQUENTIAL OR PUNITIVE DAMAGES, INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOST DATA OR LOST PROFITS WHETHER ARISING FROM OR RELATING TO TORT (INCLUDING NEGLIGENCE), CONTRACT OR OTHERWISE.

10 The LICENSEE agrees not to reverse engineer, recompile, disassemble, copy or otherwise attempt to discern the source code of any component of INPs. INDP reserves the right to terminate any CPU intensive processes. Academic User may not mount an attack against the Service, attempt to gain root access, or conduct any other activity intended to disrupt the Service.

11 Changes and amendments to this Term of Use shall be published under http://www.inoh.org (the Website) and become effective upon the date of publication. The LICENSEE will not receive a personal notice of such changes and amendments. The LICENSEE agrees to monitor the Website regularly for notices of such changes. By continuing to access and/or use the Service after such changes and amendments become effective, The LICENSEE shall be deemed to have accepted the modified Term of Use.

12 INDP's failure to exercise or enforce any right or provision of the Term of Use shall not constitute a waiver of such right or provision.