Additional information:

 

INO/HINO website:

http://www.ino-ontology.org/

 

INO in Ontobee: http://www.ontobee.org/browser/index.php?o=INO

HINO in Ontobee: http://www.ontobee.org/browser/index.php?o=HINO

 

Best,

Oliver

 

 

From: He, Yongqun
Sent: Tuesday, March 04, 2014 3:16 PM
To: obo-discuss@lists.sourceforge.net
Cc: He, Yongqun
Subject: Request namespaces for INO (Interaction Network Ontology) and HINO (Human INO)

 

Dear OBO-discuss:

 

Here I would like to request two related namespaces for inclusion in the OBO Foundry ontology library:

(1) INO: Interaction Network Ontology

(2) HINO: Human Interaction Network Ontology, which is an extension of INO.

 

INO is aligned with BFO. INO was initially developed to classify and represent different levels of interaction keywords used for literature mining of genetic interaction networks. The literature mining strategy and the INO name were described in our ontology-based literature mining paper in 2011:

         Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN- gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163.

         http://www.ncbi.nlm.nih.gov/pubmed/21624163

 

HINO is an extension of INO. HINO targets for ontologically representing human interactions and networks. The rationale for HINO development is as follows:

        Many resources, such as Reactome and KEGG, store manually curated interactions and pathways. However, there is no BFO-aligned interaction pathway ontology that specifies the information stored in Reactome and other databases. The curated data are commonly represented in BioPAX, an OWL-based biological pathway data exchange format. BioPAX represents these interactions and pathways as instances. BioPAX is successful in facilitating data exchange. However, individual entities, interactions, and pathways represented in BioPAX are all temporary instance IDs and cannot be exchanged among different resources. Given appropriate conditions, these interactions and pathways in Reactome and KEGG always occur. Therefore, they are more appropriately represented as ontology classes instead of instances. The HINO is aimed to provide non-redundant representations of human molecular interactions, pathways, and  networks. HINO was presented in ICBO-2013 as a poster:

http://ceur-ws.org/Vol-1060/icbo2013_submission_70.pdf

       More detail about HINO was recently published in a preprint in arXiv:

-          Abstract: http://arxiv.org/abs/1311.3355

-          PDF full text: http://arxiv.org/ftp/arxiv/papers/1311/1311.3355.pdf

 

Currently HINO only represents human molecular interactions and networks knowledge stored in Reactome. We are working to add more results from other interaction and pathway databases. Cross-references to the original database sources will be provided.

 

Suggestions, comments, and collaborations are welcome and appreciated.  

 

Thanks for your consideration,

 

Oliver

 

Yongqun "Oliver" He, DVM, PhD

Associate Professor

Unit for Laboratory Animal Medicine

Department of Microbiology and Immunology

Center for Computational Medicine and Bioinformatics

and Comprehensive Cancer Center

University of Michigan Medical School

Mail: 018 ARF, 1150 W. Medical Center Dr.

Ann Arbor, MI 48109

Email: yongqunh@med.umich.edu

Tel: 734-615-8231 (O)

http://www.hegroup.org/  

 

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