nvaldivi / ogms

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Status of 'bodily process' #74

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
What is the status of 'bodily process'?

From the 2009 paper: (a primitive) "Bodily processes are processes unfolding in 
or on the body in which physical components serve as participant."

From Werner and Barry's 2010 paper on mental disease: (defined, L1 occurrent) 
"Process in which at least one Bodily Component of an Organism participates".

The 2010 paper defines it, whereas the 2009 stipulates it as primitive, along 
with 'physical component', 'bodily quality', 'physical basis', 'clinically 
abnormal' and 'homeostasis', only to be elucidated. In the current version of 
OGMS it's a child of bfo:process, but has no definition. I couldn't find any 
relevant mention of it in the issue tracker, or the current reference document. 

If it is to remain primitive, then shouldn't it be placed with 'realization', 
'physical basis', 'clinically abnormal' under 'undefined primitive term'? If 
not, then a discussion as to whether keep it and provide a definition or to 
drop it should be started.

Original issue reported on code.google.com by mpjens@gmail.com on 20 Apr 2012 at 7:38

GoogleCodeExporter commented 8 years ago
Currently 'bodily process' is a placeholder genus term whose only function is 
to ensure that its child terms can be expressed using an Aristotelian 
definition in line with the 2009 paper.  

The 2010 paper definition of 'bodily process' has yet to be considered. I 
personally think it is too expansive. It would permit things like catching a 
butterfly to be 'bodily processes' just because arms participate in them (or 
even "larger" processes such as "philosophical debates"). What we really want 
for OGMS are those processes considered by systems biologists (immune system 
processes, respiratory system processes, etc..)  

A better approach that would capture what we need for OGMS would not just talk 
about which entities participate, but where the process occurs (roughly we want 
the process to occur in regions overlapping the extended organism...allowing 
that things happening on the skin might be bodily processes in this sense).  So 
we need a mix of 'participates_in' and 'unfolds_in' for a formal definition. 

My attempt: 

bodily process =def a processual entity that has a part of an extended organism 
as a participant and unfolds in a region that overlaps the extended organism.

bodily process = 'processual entity' AND has_participant SOME (part_of SOME 
'extended organism') AND unfolds_in SOME (overlaps SOME 'extended organism

Using the def of 'unfolds in' from RO proposed:
"P unfolds_in C : the execution of P is spatially contained by C. forall pP,  
forall c' partipates_in p, c' located_in C at t, for some t in P"

Original comment by albertgo...@gmail.com on 25 Apr 2012 at 1:59

GoogleCodeExporter commented 8 years ago
Don't use RO proposed. It has been superseded by

* http://purl.obolibrary.org/obo/bfo.owl
* http://purl.obolibrary.org/obo/ro.owl

Use occurs in:

http://purl.obolibrary.org/obo/BFO_0000066

Also - just use GO biological process, no need for bodily process

Original comment by cmung...@gmail.com on 25 Apr 2012 at 6:46