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

chris mungall cjm at fruitfly.org
Tue Feb 21 01:48:57 UTC 2006

I like the idea of using an ontology to describe the ontology.

Note that the proposed structure:
OntologyI HAS_A Annotation::OntologyTerm IS_A TermI HAS_A OntologyI

will lead to cycles in the object graph when the metadata ontology 
describes itself.

actually, I think the ontology module already has object reference 
cycles. TermI->OntologyI->TermI

When I brought this up originally people didn't seem to care much - so 
long as you're only parsing GO then it's not a big issue, people have 
enough memory they won't notice a big chunk of memory that refuses to 
be garbage collected way after it's used. Of course, if you want to use 
bioperl to cycle though all of OBO + SnoMed + UMLS then it's a 
different story.

I think it's best of Sohel concentrates on getting obo.pm working, then 
we can start thinking as a group about the best way to capture ontology 
metadata. This includes metadata on the whole ontology, and metadata on 
the terms (eg synonyms).

To what extent are the current modules already in use? I think the 
object cycle is a serious flaw, will it be possible to fix this without 
a major overhaul?

On Feb 11, 2006, at 9:10 PM, Hilmar Lapp wrote:

> Sohel, please do keep the discussion on the list, in your own interest
> as there's a multitude of people who can respond to you.
> SimpleValue would probably be what I'd use too. As Heikki hinted you
> might even create an ontology for annotating ontologies, which would
> allow you to use Annotation::OntologyTerm for annotation, but then
> there's no qualifier value ...
> Bioperl 1.5.1 has been released last year, please check the website.
> 	-hilmar
> On Feb 10, 2006, at 3:32 PM, Sohel Merchant wrote:
>> Hi Hilmar,
>>   I really like your suggestion of implementing the Bio::AnnotatableI
>> interface in the Bio::Ontology::Ontology class. I am going to 
>> implement
>> this and play around a little with it. I am planning to use
>> Bio::Annotation::SimpleValue for annotating the header as it provides 
>> a
>> good way of specifying the Tag/value pair. What are your thoughts on
>> using this?
>>   Also, I was wondering if you have any idea about the scheduled date
>> for the Bioperl 1.51 release. I would like to contribute some stuff in
>> the next release.
>> Thanks,
>> Sohel.
>> -----Original Message-----
>> From: Hilmar Lapp [mailto:hlapp at gmx.net]
>> Sent: Friday, February 10, 2006 3:40 PM
>> To: Sohel Merchant
>> Cc: Bioperl
>> Subject: Re: Bio::Ontology::Ontology
>> Sohel,
>> 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?
>> 	-hilmar
>> 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
>> -------------------------------------------------------------
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
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