[Bioperl-l] parent <-> subject etc

[Hilmar Lapp]

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.

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.

Thank you.

	-hilmar

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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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