[Bioperl-l] Bio::Ontology::Ontology

Hilmar Lapp hlapp at gmx.net
Fri Feb 10 21:39:39 UTC 2006


please allow me to copy the list in my response. There's many good and 
insightful people on the list who may have something to add or 
different ideas.

I've come across that problem myself, for instance with InterPro. What 
I've done so far simply is to stick it unstructured into the definition 
slot, which is not helpful if your purpose goes further than just 
displaying it in an unstructured fashion.

I'm not sure you would want to create another class for this (like 
AnnotatedOntology). One could make Bio::Ontology::Ontology (i.e., the 
implementation, probably not the interface) annotatable (i.e., 
implement Bio::Annotatable), which supposedly would be simple to do 
(AnnotationCollection is already implemented, you'd just return an 
instance of it).

Even though tag/value pairs sound like quick&fast way to go I'm leaning 
against it; in essence we're moving away from that elsewhere 
(SeqFeatureI) and hence I don't think we should restart it here.

I'm not giving a definitive answer here, just my (initial) thoughts. 
Hope that helps nonetheless. Can you fancy yourself trying the 
Annotatable approach and let us know how it goes?


On Feb 10, 2006, at 8:39 AM, Sohel Merchant wrote:

> Hi Hilmar,
>   How are you doing? I am Sohel Merchant, a programmer at dictyBase, 
> Northwestern University. I am working on a parser for an ontology 
> file. I really like the ontology object model which you have 
> contributed to Bioperl. I think its just Awesome!! One of things which 
> I thought would be great to capture is the ontology headers. Right now 
> one can specify only the name, authority information. I was wondering 
> if there is any way, I could also capture other ontology file headers 
> like version of the file, date when that ontology file was made. I was 
> thinking of making a header class or alternatively it could go as Hash 
> of values in the Bio::Ontology::Ontology class itself. I wanted to 
> know whets your thoughts about on this.
> Thanks,
> Sohel Merchant
> dictyBase
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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