[BioSQL-l] Re: [Bioperl-l] parent <-> subject etc

[Hilmar Lapp]

Good point. Hadn't thought about this yet.

So, do we then want this connotation for bioentry and seqfeature  
relationships or do we not? I tend to think we don't, especially not  
for bioentry relationships. Aaron seems to concur? Anyone else wants to  
weigh in?

	-hilmar

On Tuesday, March 25, 2003, at 06:27  AM, Lincoln Stein wrote:

> What I meant was that while parent/child and subject/object are both
> directional, the parent/child pair tends to connote the following
> relationships as well:
>
> 	larger/smaller
> 	earlier/later
> 	container/contents
> 	superclass/subclass
> 	nearer-the-root/nearer-the-leaf
>
> Parent/child also implies grandparents and grandchildren, that is, a  
> position
> in a tree structure.  Subject/object does not.
>
> Lincoln
>
> On Tuesday 25 March 2003 07:21 am, Aaron J Mackey wrote:
>> On Tue, 25 Mar 2003, Hilmar Lapp wrote:
>>> <digression to="biosql">
>>> Quite honestly though, I'm not sure why your arguments wouldn't also
>>> apply to bioentry and seqfeature relationships - shouldn't we rename
>>> parent/child there too?
>>> </digression>
>>
>> I think for seqfeatures, the parent/child stuff stems from the idea  
>> that
>> we were just going to store subseqfeatures; but as soon as you made  
>> that a
>> many-to-many sort of relationship, you invited the possibility of a  
>> graph,
>> not a strict hierarchical tree, and so now, yes, I agree with the  
>> above
>> "digression".  subject/object/predicate it is (with sub-seqfeatures
>> adhering to SO or some other ontology, perhaps the aforementioned  
>> internal
>> "biosql" ontology for API-supported stuff)
>>
>> One ignorant question: someone mentioned that while parent<->child  
>> has an
>> inherent directionality to it; I also believe that subject<->object  
>> has a
>> similar directionality.  This isn't a bad thing, per se, but it does  
>> imply
>> that our graph structures are always directed (i.e. if I want to model
>> synonyms, I need relationships in both directions).  One should note  
>> that
>> "commutativity" in grammar is written with a "pair" as the subject:  
>> "These
>> two things are the same".  But in our data models all we get to do is  
>> "A
>> is the same as B; B is the same as A".  Is there some ontology-savvy
>> solution to this small conundrum?
>>
>> Great discussion; I do wish we had it earlier.  There's now at least 4
>> ontology implementations floating about, all with strengths and
>> weaknesses.
>>
>> -Aaron
>
> --  
> ======================================================================= 
> =
> Lincoln D. Stein                           Cold Spring Harbor  
> Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ======================================================================= 
> =
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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