[Bioperl-l] parent <-> subject etc

[Hilmar Lapp]

I have to rush away, hence in short. Yes, you're pretty late. To be  
more precise, this terminology in the ontology modules has been there  
since October last year, and I've been asking people to check out the  
interfaces since 3 weeks. (!)

If there's a community vote to change it, I'm willing to change it.  
It's Ewan who decides whether this goes into 1.2.1 or will be another  
API change down the road.

	-hilmar

On Monday, March 24, 2003, at 08:27  AM, Lincoln Stein wrote:

> A little late for me to chime in here, I know, but I would avoid  
> "child" and
> "parent" terms because they imply a directionality that is appropriate  
> for
> some, but not all, relationships.  Same for target and source.
>
> (subject,predicate,object) is nicely neutral and accepted in the  
> ontology
> community.  For the uninitiated, (subject,relationship type,object) is  
> easier
> to understand.
>
> Lincoln
>
>
> On Wednesday 19 March 2003 04:04 pm, Chris Mungall wrote:
>> On Wed, 19 Mar 2003, Hilmar Lapp wrote:
>>> There are different names around for the triple (actually, a  
>>> quadruple
>>> with the namespace) making up the relationship between two vertices:
>>>
>>> 	(subject,predicate,object)
>>>
>>> or
>>>
>>> 	(child,relationship type,parent)
>>>
>>> or
>>>
>>> 	(target,relationship type,source)
>>>
>>> Some people have expressed in the past that some of these depictions
>>> are inferior to others for some reason or another, which quite  
>>> frankly
>>> I don't agree with (e.g., subject/predicate/object may make a lot of
>>> sense for ontology terms, but not really for feature graphs). To me
>>
>> for containment graphs or is-a inheritance graphs, the semantics of
>> 'parent' vs 'child' is obvious, but this is not the case for other  
>> kinds
>> of graph. using subject/object there is no potential for ambiguity.
>>
>>> it's mostly a matter of taste, consistency, and documentation to make
>>> sure the directionality doesn't get confused (feature graphs,
>>> bioentry-bioentry relationships, and term-term relationships are all
>>> directed).
>>>
>>> So, just to be sure I'm not confused already, if I define that the  
>>> last
>>> (3rd) element in the aforementioned tuples has the smaller distance  
>>> to
>>> the root along the 1st element's path to the root, then the order of
>>> elements above depicts the equivalent designations, right?
>>
>> if you're asking if they are all equivalent, yes. ie child=subject
>>
>> i think it's wrong to thing in terms of graphs that are always rooted  
>> -
>> what about cyclical graphs?
>>
>>> Once we all agree on this I'll document it in RelationshipI and the
>>> biosql schema.
>>>
>>> 	-hilmar
>>
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>
> --  
> ======================================================================= 
> =
> 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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