[Bioperl-l] Bio::Ontology::Term needs Bio::Annotation::Reference

[Hilmar Lapp]

On Wednesday, December 10, 2003, at 03:26  AM, Juguang Xiao wrote:

> The term presenting InterPro record has the lists of attribute such as 
> examples in the member database, which acts as 
> Bio::Annotation::DBLink, and the related publications, which should be 
> presented by Bio::Annotation::Reference, but the current Term does not 
> contain that. So I will append the following pretty simple methods if 
> no objections from the list.
>
> add_reference (accept an array of arguments)
> get_references
> remove_references
>

Do you want to add this to Term or to InterProTerm only? Could make 
sense to add it to Term already (Bio::Ontology::Term, from which 
InterProTerm inherits). If you do that, don't forget to add it to 
Bio::Ontology::TermI as well.

> Accordingly, the biosql schema should have term_ref table, similar to 
> term_dbxref. (I leave this to Hilmar)
>

Hm. What bothers me about this is that slowly but steadily terms become 
redundant in their properties to bioentries. Also, when retrieving 
terms, the language binding code needs to look up all possible 
relationships for every term, as it doesn't know in advance that e.g. 
for GO terms there aren't going to be any references. (Uhm, maybe this 
isn't really true anymore anyway?)

OK so maybe that's what needs to be done then ...

	-hilmar

-- 
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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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