Re: [Obo-format] property_value

[Alan R. <ala...@gm...>]

How does this interact with the RO ontology time-indexed instance- 
level properties of continuants:  *part_of, located_in,  
has_participant, etc. Even instance_of is time indexed.

I guess this is more a question of what is the intended semantics of  
OBO 1.3? Is it supposed to be consistent with the RO, or not yet.
If it is, how is one to interpret the use of the relations in RO  
without a way to specify the times? If the time is unspecified, do we  
understand it to be unknown?

BTW, in RO, I notice in the definition of preceded_by: "p'  
instantiates P' at time t", but that the instance_of relationship is  
defined to hold independent of time for processes.

Regarding the specific representation proposals, I suppose I am  
taking a step back and asking what the intended meaning and general  
strategy is - perhaps I am being premature in worrying about an OWL  
embedding. But to quickly comment, rdf:type is obviously incompatible  
in its naive form with a time indexed instance_of. Or is the idea  
that you would use holdsDuring on the instance_of tag and in rdf  
reify the rdf:type statement as for other properties. Note, however,  
that there isn't any semantic link between a reified triple and the  
actual triple.

For best practices, there seems to be some work that started, but  
hasn't finished at http://www.isi.edu/~pan/OWL-Time.html

BTW, where's the discussion of OBO 1.3 happen? Is there a draft  
document?

Best,
Alan

On Sep 25, 2006, at 7:00 PM, chris mungall wrote:

>
>> From: Alan Ruttenberg <alanruttenberg@gm...>
>> property_value
>> 2006-09-22 13:54
>>
>>   From the OBO file format:
>>  Tags in an [Instance] Stanza
>>
>>  property_value
>>  This tag binds a property to a value in this instance. The value of
>>  this tag is a relationship type id, a space, and a value specifier.
>>  The value specifier may have one of two forms; in the first form, it
>>  is just the id of some other instance, relationship type or term. In
>>  the second form, the value is given by a quoted string, a space, and
>>  datatype identifier. See Legal IDs and special identifiers for more
>>  information on legal datatype identifiers.
>>
>>  This doesn't make room for time for the instance level time  
>> dependent
>>  relations like part_of between continuants. Is an amendment in the
>>  works?
>
> This certainly isn't allowed in obof1.2, but may be allowed in future
> versions
>
> We've considered adding trailing qualifiers e.g.
>
> [Instance]
> id: foo:patient123
> property_value: OBO_REL:has_part foo:tumor9876
> {holdsDuring=foo:interval4567}
>
> Another option would be to use the obof way of doing reification (to
> be finalised in 1.3) and just treat holdsDuring as a relation on a
> reified statement. This would be consistent with N3, but not
> necessarily OWL. AFAIK there are no W3 best practices on instance-
> level time-indexed relations. The n-ary relations best practices
> document isn't much help here.
>
>>  -Alan
>
>