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

Hilmar Lapp hlapp at gmx.net
Tue Feb 21 19:31:31 UTC 2006 

Send it to me. I'll review and check it in if appropriate. You should
also write a test (and include it in what you send to me; see t/*.t
for examples for how to write a test). (and obviously the test should
succeed)

Chris, I suppose this is the time to object - I would conceptually
like the ontology-based annotation too but now we are up against a
(hopefully) working implementation which can only be beaten by another
working implementation, and frankly I don't have time to attempt one
now.

   -hilmar

On 2/21/06, Sohel Merchant <s-merchant at northwestern.edu> wrote:
> Hi Hilmar and Chris,
>   I have played around a bit using Bio::Annotation::Collection to
> capture the headers of an ontology file. It behaves pretty well and
> avoids the cycle issue which might arise by suing ontology to describe
> the ontology. I have an initial version of a working parser for obo flat
> file format.
>
> Chris, I was able to model any kind of relationship by using some of the
> functionality in the Bio::Ontology::SimpleGoEngine which, I had
> initially overlooked.
>
> I would like to commit this code to the Bioperl CVS, but I don't have
> write access to it I believe. Can I send the stuff to either of you
> guys?
>
> Hilmar, I would like your feedback on the code base and would be happy
> to make any changes required before we commit it to the CVS.
>
> Thanks,
> Sohel Merchant.
> dictyBase
>
> -----Original Message-----
> From: drycafe at gmail.com [mailto:drycafe at gmail.com] On Behalf Of Hilmar
> Lapp
> Sent: Monday, February 20, 2006 8:53 PM
> To: chris mungall
> Cc: Bioperl; Sohel Merchant
> Subject: Re: [Bioperl-l] Bio::Ontology::Ontology
>
> On 2/20/06, chris mungall <cjm at fruitfly.org> wrote:
> >
> > 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.
>
> Yes I know, that's why I didn't want to be too vocal about it ...
>
> >
> > 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.
>
> There is a method that destroys the cycle: $ontology->close()
> (this is also an interface method)
>
> Essentially, the cycle is not in OntologyI itself but in OntologyI
> HAS-A OntologyEngineI; i.e., the latter holds (may hold) references to
> terms which (may) hold a reference to an OntologyI which holds a
> reference to the OntologyEngineI.
>
> I say 'may' in parentheses because an implementation may use tricks
> like late instantiation, stringified references (handles), and weak
> references. It's possible to avoid the cycle altogether using such
> tricks but it remains questionable how much this then affects
> performance, and how ugly and incomprehensible the code would become.
> Since there is the close() method I haven't bothered yet trying a
> fully de-cycled implementation.
>
> > Of course, if you want to use
> > bioperl to cycle though all of OBO + SnoMed + UMLS then it's a
> > different story.
>
> Well if you want to keep all three in memory for some kind of
> cross-reasoning then yes you are in trouble. But if you do one
> ontology after another, you'd just have make sure to call close() on
> an ontology once you're done with it.
>
> >
> > 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 don't know about others but I use them often.
>
> > I think the object cycle is a serious flaw, will it be possible to fix
> this without
> > a major overhaul?
>
> If I recall correctly the way go-perl circumvents this is by having
> the ontology of a term as a flat attribute. This also means that when
> having a term alone, you cannot ask for its connected terms. It's been
> a while, so Chris set me straight where this is not true.
>
> It should be possible to come up with an implementation of OntologyI
> that for all intents and purposes behaves like a flat scalar giving
> the name until you call one of its graph traversal methods. At that
> point it would instantiate the engine from persistent storage (file,
> or a database connection), or retrieve one from a 'store'. The latter
> is I believe what Allen started with the OntologyStore, but again I
> would need to check the details.
>
>     -hilmar
>
> >
> >
> > 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
> > > -------------------------------------------------------------
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>
> --
> ----------------------------------------------------------
> : Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
> ----------------------------------------------------------
>
>
>


--
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: Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
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