Awesome

The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the <a href="http://www.ifomis.org/bfo/">Basic Formal Ontology (BFO)</a> as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and <a href="http://obofoundry.org/ro/">OBO Relation Ontology</a> relations and is available in <a href="http://www.w3.org/TR/owl-features/">OWL</a> and <a href="http://www.geneontology.org/GO.format.obo-1_2.shtml">OBO</a> formats.

OGMS is based on the papers <a href="http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf">Toward an Ontological Treatment of Disease and Diagnosis</a> and <a href="http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf">On Carcinomas and Other Pathological Entities</a>. The ontology attempts to address some of the issues raised at the <a href="http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases">Workshop on Ontology of Diseases</a> (Dallas, TX) and the <a href="http://bimib.disco.unimib.it/index.php/SSFW09">Signs, Symptoms, and Findings Workshop</a>(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the <a href="http://www.ifomis.org/bfo">Basic Formal Ontology</a>.

NEWS: The OGMS-based Cardiovascular Disease Ontology was the winner of this year's Ontology Competition at the FOIS (Formal Ontology in Information Systems) conference in Rio de Janeiro. http://fois2014.inf.ufes.br/p/paper-and-competition-awards.html

We are always interested in application-specific use cases for OGMS, such as those described <a href="http://www.buffalo.edu/~ag33/OGMSApplied.ppt">here</a>. Existing and planned extensions of OGMS include:

• <a href="http://datahub.io/dataset/bioportal-sdo">Sleep Domain Ontology</a> (SDO)
• <a href="http://infectiousdiseaseontology.org/Home.html">Infectious Disease Ontology</a> (IDO) and its suite of <a href="http://infectiousdiseaseontology.org/page/Extensions">extensions</a>.
• <a href="http://code.google.com/p/omrse/">Ontology of Medically Relevant Social Entities</a> (OMRSE)
• <a href="http://code.google.com/p/vital-sign-ontology/">Vital Sign Ontology</a> (VSO)
• <a href="http://ontology.buffalo.edu/psychiatry/JBSCeustersSmith2010.pdf">Mental Diseases</a>
• <a href="http://ontology.buffalo.edu/smith/ppt/OGMS/OGMS_Applied.ppt">Examples of OGMS applied to specific diseases.</a>
• <a href="http://code.google.com/p/ohd-ontology">Oral Health and Disease ontology</a>
• <a href="http://code.google.com/p/cvdo/">Cardiovascular Disease Ontology</a>
• <a href="http://code.google.com/p/mental-functioning-ontology/">Mental Functioning Ontology</a>
• <a href="http://code.google.com/p/onstr/">Ontology for Newborn Screening Follow-up and Translational Research</a>
• <a href="http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/research/icbo2013_submission_40.pdf">Drug Ontology</a>
• <a href="http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_56.pdf">Model for Clinical Information</a> (MCI)
• <a href="http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/posters/icbo2013_submission_67.pdf">Ocular Disease Ontology</a> (ODO)

If you are interested in participating in the development of OGMS, please send email to rscheuermann@jcvi.org. Be sure to include a github-account username with your request.

OGMS development meeting notes and associated files are located: https://drive.google.com/drive/folders/1pSAYgVJHUxIZ0ZlxYbA4gGql8JKvETh4

Development Notes and agendas located at https://docs.google.com/document/d/1_gNPXjC2-pr5wvrmO1iVd2Cp9rzqf0qQG2L4UUJwBIs/edit

License

This project is licensed under the MIT License - see the https://opensource.org/licenses/MIT for details