[BioSQL-l] Re: Ontology.category

[Hilmar Lapp]

OK so I'm going to do this (only in the HEAD revision).

	-hilmar

On Monday, September 23, 2002, at 10:35 AM, Chris Mungall wrote:

>
>
> On Sun, 22 Sep 2002, Hilmar Lapp wrote:
>
>> On bioperl we're currently thrashing out the best interface for
>> Bio::Ontology::Term. ChrisM proposes a link from Term to the
>> 'ontology category', i.e. a virtual root term or something. I think
>> having this is very useful; Dave Block has just hit this problem.
>>
>> Of course it can be solved in the db by a materialized view that
>> multiplies all relationships, and then you check for that parent
>> that doesn't have parents. Somewhat tedious though. Also, foregoes
>> the chance to have a UK on name within an ontology. Since I strongly
>> believe that there should be a UK on name, within an ontology or
>> globally (in fact, I've put one there), this means that with the
>
> not globally - in GO, there are two distinct terms 'glycine-gated 
> chloride
> channel', one pertaining to function the other to cellular component
>
>> present design terms can (often will) live in (have a path to) more
>> than one ontology. The problem with this is that the definition of a
>> term might not be exactly the same between different ontologies,
>> i.e., the semantics of a particular term may differ depending on
>> what the context-ontology is. You cannot capture this in the present
>> design.
>>
>> The alternative is to add a FK category_id on Ontology_Term to
>> itself that shall point to the term specifying the name of the
>> ontology. Subsequently, one can put a UK on (term_name,category_id).
>
> perfect
>
>> Thoughts/comments/preferences/votes?
>>
>> 	-hilmar
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>
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--
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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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