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

[Hilmar Lapp]

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'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
-------------------------------------------------------------