Re: [Obo-phenotype] disposition in PATO vs. disposition in BFO

[Chris M. <cj...@fr...>]

Just a bit of background for those not familiar with the BFO upper  
ontology we are using to help organize ontologies.

BFO makes a distinction between dispositions and qualities - see the  
definitions Bill provides below. You can think of a disposition as  
something that can be realized, whereas something does or does not  
have a quality at any given time. A glass may have a disposition to  
shatter (when dropped on the ground, say), whereas at this particular  
time it may have the quality of being solid, in a certain shape etc.

Does this distinction matter? It might do, for integrating data from  
different sources, assays etc.  It's always good to be absolutely  
clear about what a term means. A disposition to shed foliage is  
different from not having foliage:

PATO has a very minimal disposition branch at the moment:

+/ PATO:0000001 quality
++is_a PATO:0001241 quality of continuant
+++is_a PATO:0001238 relational quality of continuant
++++is_a PATO:0001727 disposition
+++++is_a PATO:0001728 multi-cellular organismal disposition
++++++is_a PATO:0001729 disposition to shed
+++++++is_a PATO:0001730 deciduous (generic)
+++++++is_a PATO:0001731 deciduous (plant)
+++++++is_a PATO:0001732 non-deciduous (any body part)
+++++++is_a PATO:0001733 evergreen (plant)
+++++++is_a PATO:0001734 semi-deciduous(plant)

Now this is causing a problem for folks like Bill who are pulling  
together ontologies from multiple sources. One ontology says quality  
and disposition are disjoint, but PATO violates that.

Bill's problem would be solved by shifting disposition up to be a  
root node alongside disposition (they share the same parent in the  
bridging ontology; we could add that to PATO to give a shared root if  
we wanted, it's not so important). Note that we would want to keep  
this in PATO as to move it out would be too confusing. For most use  
cases, quality terms and disposition terms would be used in the same  
contexts.

Now this does create a potential confusion for users - wherever we  
have previously been talking of qualities we are not talking of  
qualities-or-dispositions (or dependents).

This isn't coming out of nowhere: it's been languishing in the  
tracker the last 9 months:
http://sourceforge.net/tracker/index.php? 
func=detail&aid=1675411&group_id=76834&atid=595654

Thanks for bringing it up Bill.

My feeling is that we need a stronger sense of what the requirements  
are for dispositions from users. I know a lot of people are currently  
interested in behaviour phenotypes, and many of these would seem  
intimately connected to dispositions. We also want to avoid creating  
new sources of confusion (example: is a disposition to blink in  
bright light the same as sensitivity to light?). It may be the case  
that users would prefer to see dispositions in a new ontology,  
distinct from PATO.

For now I suggest Bill carries on treating the root node of PATO as a  
BFO:quality, as the BFO bridge states. We can have a brief moratorium  
on placing new child terms of PATO:0001727 until we have collected a  
mass of terms, and then decide what to do (which may involve  
obsoleting PATO:0001727 and creating a repaced_by node, in a new  
ontology or new root).

On Jan 21, 2008, at 1:48 AM, Bill Bug wrote:

> Dear PATO folk,
>
> I just noticed PATO includes a class "pato:disposition" as a sub- 
> type of "pato:relational quality of continuant".
>
> Can someone provide info on how this relates to "bfo:disposition"  
> in BFO, which there is a sub-type of "bfo:realizable_entity" and  
> thus a "nephew (or is it niece)" class to "bfo:quality".  I realize  
> the debate amongst BFO users & developers as how to interpret the  
> distinctions between realizable entities - specifically  
> "bfo:function" and "bfo:disposition" is still somewhat up in the  
> air, but I hadn't thought this included clouding the distinction  
> between "bfo:quality" and "bfo:realizable entity".
>
> Even if this distinction between "bfo:realizable entity" and  
> "bfo:quality" is somewhat in doubt, given the bfo-to-pato bridge  
> defines "bfo:quality" the parent of "pato:quality", it's difficult  
> to understand how to relate the potential sibling (or equivalence)  
> relation between "bfo:quality" and "bfo:disposition" to the  
> position of "pato:disposition" as being classes deeper in the  
> hierarchy from "bfo:quality" - i.e.:
> 	"pato:disposition" -> "pato:relational quality of continuant" -->  
> "pato:quality of continuant" --> "pato:quality" --> "bfo:quality"
>
> I'd like to think I'm just being confused by a pair of disparate  
> classes that happen to have the same name, but I don't think that  
> is the case, as the PATO definition of "disposition" - despite the  
> enormous difficulty in defining a useful definition for  
> bfo:disposition (i.e., one that is consistent, cogent, and  
> complete) - appears to be trying to specify the same sort of  
> entities as bfo:disposition is trying to representation - i.e.:
>
> pato:disposition:
> 	A prevailing tendency, mood, or inclination. (from Merriam- 
> Webster's dictionary apparently)
>
> bfo:disposition:
> 	Definition: A realizable entity that essentially causes a specific  
> process or transformation in the object in which it inheres, under  
> specific circumstances and in conjunction with the laws of nature.  
> A general formula for dispositions is: X (object) has the  
> disposition D to (transform, initiate a process) R under conditions C.
>
> I would also note that "pato:disposition" inherits useful links to  
> PATO relations - i.e.:
> 	inheres_in:
> 		domain: "pato:quality of continuant"
> 		range: "snap:continuant"
> 	towards:
> 		domain: "pato:relational quality of continuant"
> 		range: "bfo:entity"
>
> These properties are in fact required to make effective use of  
> "bfo:disposition" as well (but are not currently being asserted for  
> "bfo:dispisition" - nor can they be, since bfo.owl doesn't make  
> reference to OBO-RO or PATO), so it would be useful to somehow  
> reconcile what appears right now to be a pair of parallel classes  
> that ultimately seek to provide the same representational capability.
>
> Many thanks for any specifics you can offer regarding this relation  
> between "pato:disposition" and "bfo:disposition".
>
> Cheers,
> Bill
>
> P.S.: I'm including Holger Stenzhorn (curator of the BFO OWL file)  
> on this post to make sure he is in the loop on this discussion. I  
> thought that might be more expeditious to actually resolving the  
> issue than to simply double post this to both the PATO and BFO lists.
>
>
> William Bug, M.S., M.Phil.                                          
> 		email: wb...@nc...
> Ontological Engineer (Programmer Analyst III)		work: (610) 457-0443
> Biomedical Informatics Research Network (BIRN)
> and
> National Center for Microscopy & Imaging Research (NCMIR)
> Dept. of Neuroscience, School of Medicine
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla, CA 92093
>
> Please note my email has recently changed
>
>
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