[Bioperl-l] parent <-> subject etc

[Hilmar Lapp]

On Monday, March 24, 2003, at 11:31  PM, Chris Mungall wrote:

>
> Sorry for the tetchy tone of that last email

That's alright, I asked for it. I vented, you vented. Time to go back 
to normal :)

I guess we're taking a different approach here, namely a purely applied 
one. We built those modules bottom-up (hence the "engine" first), 
trying to have something functional quickly, and the overall design as 
simple as possible. I deliberately hoped that others (e.g. you) would 
sanity check and weigh in to prevent it from becoming simpler than 
necessary. So, I didn't actually want to be the only driver, which I 
ended up as though.

I still think the current status is not that bad. What I wanted to 
achieve with the overhaul that I started is not only to make it biosql 
compatible, but also to get an API out into 1.2.1 that can be further 
built upon instead of having to obsolete it in half a year. I'd 
appreciate your review/comment on this question, but I understand if 
you can't afford the time. Maybe since it's simply so young the 
necessity to scrap the API down the road is inevitable anyway as we 
learn more lessons.

As for the terminology, you're clearly right. Unless someone wants to 
keep the existing parent/child naming, I'll change that to 
subj/pred/obj, with undocumented aliases parent/child. Ewan, I'm afraid 
this better goes into 1.2.1. ETA tomorrow or Wednesday.

<digression to="biosql">
Quite honestly though, I'm not sure why your arguments wouldn't also 
apply to bioentry and seqfeature relationships - shouldn't we rename 
parent/child there too?
</digression>

Thanks for the pointers, I appreciate that. I was trying to get away 
with being ignorant, but probably that's not going to work.

> - 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?

I'd be glad to. You raise some good points about how frame or DL based 
ontologies would fit into the current model, and frankly I don't know.

	-hilmar

>
> 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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>>
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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