OGMS Monthly Call 21OCT2015

Agenda 1.Implementation- Definition and placement of ‘injury’ (Sagar) 1.Propositions + Discussion – Cleanup of ‘process’ hierarchy and related terms (Sagar + Group feedback) 2.Action items from previous call

Implementation of Injury

Implementation- Protégé

Implementation- Changes committed to GitHub

Process hierarchy terms to review Definitions + Placement

Google doc of terms

Adjustment to ‘Inflammation process’ def Current def: A process which is a response by an organism's tissues that is generally identified by swelling or localized pain Change def proposed: Include the inputs of the occurent, change term: Inflammatory process Reasoning: 1. Given: - inputs: response of immune system to protect against harmful or foreign substances - outputs: underabundance of leukocytes to protect body tissues  damaged tissue, possible infection overabundance of leukocytes  accumulation of leukocytes in tissue region, blocks function Problem: A. The definition of inflammation should not be limited to its outputs/symptoms, but also include the inputs/triggers of the occurent Proposal: A bodily process caused by some disorder that results in the recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling.

Inflammatory Process bodily process vs pathological bodily process by cause: accumulation of immune response (passing a threshold), a pathologic bodily process

Adjustment to ‘Prophylaxis’ def Current def: A planned process that has the objective to reduce the risk of acquiring one or more disorders. Change proposed: Change term to ‘Disease prophylaxis’ Reasoning: 1. Given: - If condom is a prophylactic - Condom has_role to prevent conception - Conception is not a disorder, but a condition. Problem: Prophylaxis is not limited to preventing a disorder, but also includes preventing a condition or collection of symptoms Proposed change: **Change the term to ‘Disease prophylaxis’- to fit scope of OGMS

Action items- previous call

Tracker item for ‘dysfunction’ Compare with scope of ‘clinically abnormal’ Clinically abnormal is currently not defined in OGMS or any other ontology Submitted tracker item in OGMS #97

‘Bodily process’ def Current proposed def: A normal biological process which occurs in the body of an organism Biological Process (GO): A biological process term describes a series of events accomplished by one or more organized assemblies of molecular functions.  Examples of broad biological process terms are "cellular physiological process" or "signal transduction". Examples of more specific terms are "pyrimidine metabolic process" or "alpha-glucoside transport". The general rule to assist in distinguishing between a biological process and a molecular function is that a process must have more than one distinct steps.  A biological process is not equivalent to a pathway. At present, the GO does not try to represent the dynamics or dependencies that would be required to fully describe a pathway.

Term examples of human, animal, plant scope Jie

OGMS/OBI Alignment discussion Jie