OPMI: Ontology of Precision Medicine and Investigation

This GitHub website is the home page of OPMI.

OPMI is an application ontology to support precision medicine and related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. OPMI reuses, aligns, and integrates related terms from existing ontologies in the OBO ontology liborary.

OPMI was first developed by extracting general precision medicine related terms from the Ontology of Respiratory Disease Investigation (ORDI). Primarily developed by Drs. Hong Yu, Jie Zheng, and Oliver He, ORDI is an application ontology aimed to represent ontology terms related to respiratory diseases and related investigations. Dr. Hong Yu is a respiratory disease clinician and professor. ORDI was developed to represent the entities and relations related to clinical phenotypes, lab testing, and working environmental conditions, social economic situations, etc. The ORDI work with its use case study was presented in the Biocuration-2018 conference held at Shanghai, China.

OPMI is now supported by the new NIH/NIDDK-supported Kidney Precision Medicine Project (KPMP, http://kpmp.org). With >20 universities/institutes involved, KPMP aims to study a large number of human subjects with the acute kidney injury (AKI) and chronic kidney disease (CKD). As requested by the KPMP consortium, OPMI aims to represent and standardize the entities associated with precision medicine, including all the data/metadata types, investigation processes, and analysis in various aspects of clinical, pathological, and molecular studies to be conducted in KPMP. Example KPMP data types include clinical electronical health record types, pathological image data types, and various Omics data types.

OPMI has now been approved to be an OBO Foundry library ontology: http://obofoundry.org/ontology/opmi.html.

Collaborations are welcome. A very active collaboration OPMI has is the the collaboration with clinicaltrials.gov and many collaborators to develop clinical trial-specific terms with the aim to standardize and integrate clinical trial data. See more details in the meeting notes: https://docs.google.com/document/d/1VnmFhqFwfH3qcShiZUTO9ALF-3JKCs2oa3MQ2LotH6U/edit.

Use the following URI to download this ontology

• http://purl.obolibrary.org/obo/opmi.owl

Note that the source ontology is an OWL file.

• Default browsing in Ontobee: http://www.ontobee.org/ontology/OPMI
• Browsing in NCBO BioPortal: https://bioportal.bioontology.org/ontologies/OPMI

http://obofoundry.org/ontology/opmi.html.

• He Y, Ong E, Schaub J, Dowd F, O’Toole JF, Siapos A, Reich C, Seager S, Wan L, Yu H, Zheng J, Stoeckert C, Yang X, Yang S, Steck B, Park C, Barisoni L, Kretzler M, Himmelfarb J, Iyengar R, Mooney SD, for the Kidney Precision Medicine Project Consortium. OPMI: the Ontology of Precision Medicine and Investigation and its support for clinical data and metadata representation and analysis. The 10th International Conference on Biomedical Ontology (ICBO-2019), July 30 - August 2, 2019, Buffalo, NY, USA. 10-page full length article.