INOH

2023/06/29

Web Site: (Closed) http://inoh.hgc.jp/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/inoh/

The database is a highly structured, manually curated database of signal transduction pathways.

README Content

Database Component
Data Description
License
Update History
Literature
Contact address

1. Database Component

README
MoleculeRole Ontology
Linkage image file of MoleculeRole Ontology
Event Ontology
Linkage image file of Event Ontology
Location Ontology
Linkage image file of Location Ontology
Signal Transduction Pathway Data
Metabolic Pathway Data

Return to Top

2. Data Description

2.1 README

Data name	README
Description of data contents	HTML file to describe "INOH" data.
File	README_e.html (English)

Return to Top

2.2 MoleculeRole Ontology

Data name	MoleculeRole Ontology
Description of data contents	MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.
File	inoh_moleculerole_ontology.zip (673KB)

Data items are the following:

Data item	Description
inoh_id	ID of the term
alt_id	Altanative ID of the term
name	Name of the term
synonym	Synonym of the term
def	Definition of the term
xref_analog	Cross-reference to other ontology term
comment	Comment of the term
linkage	Image file that represents "is_a" and "part_of" relations between terms.
inoh_client	Link to start the INOH Client application.
is_a	Definition of "is_a" relation.
relationship	Definition of "part_of" relation.
is_obsolete	The flag that indicates whether the term is obsolete or not. "true" indicates that the term is obsolete.

Return to Top

2.3 Linkage image file of MoleculeRole Ontology

Data name	Linkage image file of MoleculeRole Ontology
Description of data contents	Linkage image file of MoleculeRole Ontology. 9,217 PNG files are compressed into a ZIP file.
File	IMR.zip (17.9MB)

Return to Top

2.4 Event Ontology

Data name	Event Ontology
Description of data contents	Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
File	inoh_event_ontology.zip (188KB)

Data items are the following:

Data item	Description
inoh_id	ID of the term
alt_id	Altanative ID of the term
name	Name of the term
synonym	Synonym of the term
def	Definition of the term
xref_analog	Cross-reference to other ontology term
comment	Comment of the term
linkage	Image file that represents "is_a" and "part_of" relations between terms.
inoh_client	Link to start the INOH Client application.
is_a	Definition of "is_a" relation.
relationship	Definition of "part_of" relation.
is_obsolete	The flag that indicates whether the term is obsolete or not. "true" indicates that the term is obsolete.

Return to Top

2.5 Linkage image file of Event Ontology

Data name	Linkage image file of Event Ontology
Description of data contents	Linkage image file of Event Ontology. 3,829 PNG files are compressed into a ZIP file.
File	IEV.zip (15.6MB)

Return to Top

2.6 Location Ontology

Data name	Location Ontology
Description of data contents	Location Ontology is an ontology of cellular location.
File	inoh_location_ontology.zip (5.3KB)

Data items are the following:

Data item	Description
inoh_id	ID of the term
alt_id	Altanative ID of the term
name	Name of the term
synonym	Synonym of the term
def	Definition of the term
xref_analog	Cross-reference to other ontology term
comment	Comment of the term
linkage	Image file that represents "is_a" and "part_of" relations between terms.
inoh_client	Link to start the INOH Client application.
is_a	Definition of "is_a" relation.
relationship	Definition of "part_of" relation.
is_obsolete	The flag that indicates whether the term is obsolete or not. "true" indicates that the term is obsolete.

Return to Top

2.7 Linkage image file of Location Ontology

Data name	Linkage image file of Location Ontology
Description of data contents	Linkage image file of Location Ontology. 53 PNG files are compressed into a ZIP file.
File	ILC.zip (119KB)

Return to Top

2.8 Signal Transduction Pathway Data

Data name	Signal Transduction Pathway Data
Description of data contents	Signal transduction pathway data is well-annotated, machine-processable data collected from literature.
File	inoh_signal_transduction_pathway.zip (5.7KB)

Data items are the following:

Data item	Description
Pathway Name	Name of signal transduction pathway
INOH format	Link to INOH format file
BioPAX level2 format	Link to BioPAX level2 format file
BioPAX level3 format	Link to BioPAX level3 format file
PubMed ID	Link to PubMed

Return to Top

2.9 Metabolic Pathway Data

Data name	Metabolic Pathway Data
Description of data contents	Metabolic pathway data is well-annotated, machine-processable data collected from literature.
File	inoh_metabolic_pathway.zip (1KB)

Data items are the following:

Data item	Description
Pathway Name	Name of metabolic pathway
INOH format	Link to INOH format file
BioPAX level2 format	Link to BioPAX level2 format file
BioPAX level3 format	Link to BioPAX level3 format file

Return to Top

3. License

Last updated : 2023/06/29

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "INOH © the INOH database project (INDP) licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.

With regard to this database, you are licensed to:

freely access part or whole of this database, and acquire data;
freely redistribute part or whole of the data from this database; and
freely create and distribute database and other derivative works based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
You must distribute any derivative work based on part or whole of the data from this database under the license.
You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Contact the database creator:

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

Return to Top

4. Update History

Date	Update contents
2017/11/30	Archive version V3 Released. INOH English archive site is opened.
2006/02/01	INOH (http://www.inoh.org/) is opened.

Return to Top

5. Literature

Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T.
INOH: ontology-based highly structured database of signal transduction pathways.
Database (Oxford). 2011 Nov 26;2011:bar052. Print 2011.
PMID: 22120663

Fukuda K.
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).

Kushida T, Takagi T, Fukuda K.
Event ontology: a pathway-centric ontology for biological processes.
Pac Symp Biocomput. 2006:152-63.
PMID: 17094236

Kushida, T., Yamamoto, S., Yamagata, Y., Asanuma, T., Hattori, E., Takagi, T. and Fukuda, K.
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.
Higher Order Knowledge Proceeding : Pathway Database and Ontologies.
Genomics & Informatics, vol.3, No.2, ISSN 1598-866X, 2005.6, pp.47-51

Yamamoto S, Asanuma T, Takagi T, Fukuda K.
The Molecule Role Ontology: An Ontology for Annotation of Signal Transduction Pathway Molecules in the Scientific Literature.
Comp Funct Genomics. 2004;5(6-7):528-36.
PMID: 18629146

Ken-ichiro Fukuda, Toshihisa Takagi.
A Pathway Editor for Literature-based Knowledge Curation.
APBC 2004, pp.339-344.

Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi.
Pathway Database: Higher Order Knowledge in Biology.
nformation Processing Society of Japan (IPSJ), Transactions on Databases, vol.45 No.SIG7(TOD 22) June 2004, pp.77-84

Fukuda K, Yamagata Y, Takagi T.
FREX: a query interface for biological processes with hierarchical and recursive structures.
In Silico Biol. 2004;4(1):63-79. Epub 2004 Feb 22.
PMID: 15089754

Fukuda K, Takagi T.
Knowledge representation of signal transduction pathways.
Bioinformatics. 2001 Sep;17(9):829-37.
PMID: 11590099

Return to Top

6. Contact address

When you have any question about "INOH", contact the following:

https://form2.jst.go.jp/s/contact_nbdc

Return to Top