#acl All:read DanieleMerico:write,delete,revert
#format wiki
#language en

= Background for a Clinical Phenotype Ontology =

These notes are preparatory for the [http://www.bioontology.org/wiki/index.php/DallasWorkshop Dallas Workshop]:
"Signs, Symptoms and Findings: First Steps Toward an Ontology of Clinical Phenotypes" [[BR]]
I will also attempt at adopting, at the same time, a more realist or more epistemological perspective.

== Diagnostic Evidences, Physiological Phenomena, Pathological Patient Classes ==
The meta-model of the NEUROWEB Reference Ontology can be generalized. It relies on this analytical deconstruction of the general workflow in medical diagnosis:
 1. collect '''diagnostic evidences''', which are stored in the medical record in the form of clinical indicators [[BR]]
 ~- Note: the term ''diagnostic evidence'' puts the accent on the inference of a certain phenomenon from certain observations, and according to a varying mix of general theory and expert, thus is more related to the context (diagnostic process); the term ''clinical indicator'' puts the accent on a storable item of information -~
 1. infer the occurrence of '''(Patho)Physiological Phenomena''', referring to the standing Anatomic-Physiological model of the human organism [[BR]]
 ~- Note: how the inference is formulated is pretty much of a hard matter; eraly AI approaches attempted at replacing the physician in this task, but substantially failed; here the accent is mostly on the ''content theory'', rather than the ''inference mechanism'' -~
 1. assign the patient to a formal '''Pathological Class''', useful for standardized treatment decision, clinical trials, genetic or other kind of association studies, etc...

~- Example: simplified diagnosis of a stroke:  -~
~-  1. identify symptoms of cognitive and motory impairment,  -~
~-  1. perform brain imaging and identify a darker area possibly corresponding to a brain lesion,  -~
~-  1. infer that a brain lesion occurred because of the formation of an obstructing body (different possible causes), which eventually obstructed a brain artery, -~
~-  1. finalize the diagnosis and assign the patient to a class -~ 

Different areas of medicine are expected to have different taxonomies of Pathological Classes, but most of the content theory concerning (Patho)Physiological Phenomena is expected to be shared, to a certain degree (although there are probably problems of granularity, and different perspective). [[BR]]
~- Test case: how shared is the notion of ''Stenosis''? -~