[Bioperl-l] parent <-> subject etc

[Chris Mungall]

Sorry for the tetchy tone of that last email - I don't mean to sound
unappreciative of all the great stuff you & the rest of GNF have done.

I'd be interested in discussing some extensions to the ontology modules
for dealing with some of the things I mentioned at the end. Given that my
email response rate is rather poor and we're both on the west coast not a
million miles from each other, what about meeting up to discuss future
plans for the ontology modules?

On Mon, 24 Mar 2003, Chris Mungall wrote:

>
>
> On Mon, 24 Mar 2003, Hilmar Lapp wrote:
>
> > On Monday, March 24, 2003, at 12:55  PM, Chris Mungall wrote:
> >
> > > surely the onus is on you to
> > > justify divergence from both the entire ontology community & bioSQL?
> >
> > So let me vent some frustration here.
> >
> > 1) We (GNF) have been driving forward the ontology support in bioperl
> > since September last year. This was the first time ever we ventured
> > into ontologies, and we were well aware that an "entire ontology
> > community" had long existed before, but apparently the motivation to
> > drive ontology support in bioperl was minor to not existent in that
> > community. I have repeatedly bugged the "ontology community" to please
> > weigh in and weigh in early, help, discuss, debate. Search the mailing
> > list archives for the result.
>
> I don't think the general ontology community hang out on bioperl much -
> just the subset who are also into biology and perl.
>
> > 2) The currently "divergent" terminology used in bioperl was the one
> > that after hours of discussion came out as most understandable to us,
> > us being at that time entirely new to ontologies. subj/pred/obj was
> > just incomprehensible, like it or not. When I overhauled the ontology
> > modules, and, Chris, when we were in Singapore, there were plenty of
> > pledges I made and plenty of opportunities to chime in and provide
> > insight from the "entire ontology community". No-one of that community
> > apparently even bothered to help ensure that the bioperl ontology
> > terminologies are sensible on the background of the domain knowledge
> > too.
> >
> > 3) As for biosql, term relationships to me are no different to feature
> > and bioentry relationships. For feature and bioentry relationships we
> > use parent/child, and everyone seems to be alright with this.
> >
> > Bottom line is, I said before that I'm willing to change it according
> > to community input, but the onus if there is any is clearly on the
> > "entire ontology community" to provide their insight and help, and to
> > provide that before the last minute, and to continue providing it.
> > Letting the lay people march ahead and then asking them for
> > justification why they marched into that evidently stupid direction is
> > not a very productive way to get things done and get them done right.
>
> I appreciate all the work GNF has done here. I'm sorry if I can't always
> get my comments in on time to suit your schedule.
>
> Bear in mind that back in september I had a large body of functioning code
> for dealing with ontologies - interfaces, classes, parsers, tests - all
> ready to check in, see:
> http://bioperl.org/pipermail/bioperl-l/2002-September/009414.html
>
> You jumped in the drivers seat, checked in your own code, and I was fine
> with that. There were certainly plenty of flaws in my design. However, now
> that you're in the drivers seat it behooves you to get some kind of
> roadmap or at least an idea of the lay of the land. There is no shortage
> of introductory documentation out there on ontologies, particularly W3C
> ontology languages such as OWL and its predecessor DAML+OIL. Perhaps it is
> the case that these are not relevant to the particular problems we face in
> bioinformatics (personally I do not believe this to be the case).
> Nevertheless, one thing I believe is constant from the latest description
> logics to the earliest semantic networks is the concept of binary
> predicates consisting of a subject and an object. I'm sorry this was
> incomprehensible to you at first (a bit of cursory research in the field
> would have sorted that out) - I guarantee it will be nowhere near as
> incomprehensible as when we eventually have ontologies with this:
>
> parent=X
> child=Y
> relationship= synthesises
>
> does X synthesise Y or does Y synthesise X? Show me a document that I can
> refer to in order to find the correct interpretation. Presumably this
> would have to be some within-bioperl standard, buried deep in pod docs
> somewhere. Is this good? (And the mind boggles if the relationship we're
> focused on is 'is_parent_of')
>
> subject=X
> object=Y
> relationship= synthesises
>
> is completely unambiguous - you can refer to either any document on
> semantic webs written in the last thirty years, the W3C RDF standard or
> failing that, basic grammatical rules. X is the subject of the sentence
> (ie it is the thing synthesising), and Y is the object (the thing being
> synthesised). I would prefer the more standard 'predicate' instead of
> 'relationship'.
>
> I'm sorry I didn't chime in with this sooner (I thought I had done).
> (Anyway, can't we just make parent a synonym method of object as a
> compromise?). To be honest I don't have the energy to keep up to date with
> everything in bioperl, I can't multitask that well, usually I save it all
> up for a few bioperl days where I try and take it in at once. It's harder
> when a lot of my ontology-related headspace is occupied with the go-dev
> codebase and getting around a lot of the mistakes I made with the object
> model there that I don't want to see replicated in bioperl.
>
> I'm still not sure who the 'entire ontology community' is you are
> petitioning for insight and help. I'm giving what help I can, but I don't
> consider myself part of that community, I'm just a dilettante (paying
> attention to what Robert Stevens' group is doing helps me a lot - though I
> take full responsibility for any rubbish i may come out with). I'd urge
> you to also search further afield for that insight and help. I would also
> urge you - as I'm sure I have before - to start thinking about ontologies
> that have relationships other than is_a and part_of, cyclical
> relationships, and also about how property-based ontologies (frame-style
> systems and full blown description logics) fit into your model.
>
> > Thank you.
> >
> > 	-hilmar
> >
> >
>
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