[Bioperl-l] Bio::Annotation::SimpleValue, keywords()

[Ewan Birney]

On Mon, 23 Sep 2002, Hilmar Lapp wrote:

> Two ideas/proposals in one:
> 
> 1) RichSeqI::keywords is currently implemented as keeping the string 
> as one, no splitting into individual keywords. In a database (yeah, 
> here's biosql) however, one would rather want to store them 
> separately I think. In a sense, keywords are an ontology. Also they 
> are annotation. I propose to stick keywords onto a sequence's 
> AnnotationCollection, using e.g. tag 'keyword' and class SimpleValue 
> (but see below).
> 
> 2) Bio::Annotation::SimpleValue actually resembles an ontology term, 
> doesn't it? Well, not always probably (thinking descriptions and 
> alike). If SimpleValue is not an ontology term itself, then what 
> about adding Bio::Annotation::OntologyTerm, which would just adapt 
> Bio::AnnotationI to Bio::Ontology::TermI?
> 

I like this idea - I would vape SimpleValue and claim that it should be an 
ontology term. Or perhaps it *could be* an ontology term. Hmmm. (values 
being numbers?)

> 
> I'm thinking about how to best store gene names in biosql ... they 
> presently come as Bio::Annotation::SimpleValue, and I think we want 
> them end up in an ontology.
> 
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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