https://github.com/cthoyt/ohmi

OHMI: The Ontology of Host-Microbiome Interactions

https://github.com/cthoyt/ohmi

Repository

OHMI: The Ontology of Host-Microbiome Interactions

https://github.com/cthoyt/OHMI/blob/master/

# OHMI
OHMI: The Ontology of Host-Microbiome Interactions

A microbiome is an ecological community of commensal, symbiotic and pathogenic microorganisms found in and on all multicellular organisms (https://en.wikipedia.org/wiki/Microbiota). Microbiomes have been found in associated with both healthy and diseases humans and other animal organisms.  Extensive microbiome research has been conducted in the past decade. There are many micrbiome-focused initiatives such as the Human Microbiome Project (https://commonfund.nih.gov/hmp/index) and Host Microbiome Initiative (https://research.medicine.umich.edu/research-strengths/host-microbiome-initiative). With the large volume of microbiome related data generated, it has become critical to ontologically represent a variety of host microbiome and host-microbiome interaction data types and knowledge to support advanced data standardization, integration, sharing, and analysis.  

OHMI is aimed to ontologically represent various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.    

The development of the OHMI is a collaborative community effort, currently by ontology developers from the University of Michigan, the University of Pennsylvania, and the Medical University of South Carolina.  

# Developers 
- Yang Wang
- Jihad Obeid 
- Jie Zheng
- Anna Maria Masci
- Haihe Wang
- Hong Yu 
- Yongqun Oliver He

# Source code 
http://purl.obolibrary.org/obo/ohmi.owl
(License: http://creativecommons.org/licenses/by/4.0/)

# Visualization:
Ontobee: http://www.ontobee.org/ontology/OHMI 
BioPortal: https://bioportal.bioontology.org/ontologies/OHMI 

# OBO Foundry access: 
http://www.obofoundry.org/ontology/ohmi.html 

# Citation:

He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Liu K, Wu J, Curtis JL, Smith B, Alekseyenko AV, Obeid JS. OHMI: the ontology of host-microbiome interactions. J Biomed Semantics. 2019 Dec 30;10(1):25. PMID: 31888755. PMCID: PMC6937947.
URL: https://www.ncbi.nlm.nih.gov/pubmed/31888755 

# News:

He Y, Wang H, Zheng J, Beiting DP, Masci AM, Yu H, Liu K, Wu J, Curtis JL, Smith B, Alekseyenko AV, Obeid JS. OHMI: the ontology of host-microbiome interactions. J Biomed Semantics. 2019 Dec 30;10(1):25. PMID: 31888755. PMCID: PMC6937947.

Y. HE, H. Wang, H. Yu, J. Zheng, D. P. Beiting, A. M. Masci, T. Putman, B. Smith, A. V. Alekseyenko, J. S. Obeid. OHMI: the Community-Based Ontology of Host-Microbiome Interactions (Hmi) to Support Standardized Hmi Representation and Analysis. ASM Microbe 2018. June 7-11, Atlanta, GA, USA. Accepted. 

Jihad S. Obeid, Alexander V. Alekseyenko, Jie Zheng, Anna Maria Masci, Yongqun "Oliver" He. An Ontology for Host-Microbiome Interactions. 23rd International Scientific Symposium on Biometrics (BioStat 2017), Sibenik, Croatia, 7-10 June 2017. 

Jihad Obeid. An Ontology for Host-Microbiome Interactions. 2017 SCTR Scientific Retreat on the Human Microbiome. MUSC Bioengineering Auditorium, Room 110, Wednesday, May 3, 2017.  
Web: http://academicdepartments.musc.edu/sctr/programs/retreats/2017_Microbiome/microbiome 

See more details:  
https://github.com/OHMI-ontology/OHMI/wiki/News

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