[Bioperl-l] parent <-> subject etc

[Chris Mungall]

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
>
>