[moby] Re: [MOBY-dev] how to handle errors in a biomoby service?

[Mark Wilkinson]

Hi all,

Thanks for writing this up so clearly!  I agree 100% that the current
error-reporting system in BioMOBY is insufficient (it was never part of
the initial proposal, and even that initial proposal was cut by 80%,
so...)

I am a bit wary of two aspects of the solution you propose, though I
need more time to think about exactly why they make me nervous:

1)  Mixing metadata (errors) into the data seems... well... wrong
somehow.  I would prefer a solution that somehow used the serviceNotes
block as the place to put error messages, and added an attribute to teh
mobyData, Collection, or Simple tags that Xref'ed a node in the
serviceNotes block.  I wasn't in Malaga for the discussion, so perhaps
there is a strong argument for putting it there that I am unaware of?

2)  overloading the articleName attribute in the Simple/Collection tag
(and especially in the case where Simples are part of a Collection)
would then give **three** different "meanings" to the articleName
attribute!!  It's bad enough that we already have two different uses for
that attribute... I'm reluctant to add one more to the fray! :-)  Let's
create a new attribute instead of adding a new meaning to an existing
one.


I hope others will participate in this discussion - it's been pretty
quiet out there!  I have not thought deeply about error reporting, and I
would prefer to leave the final decision to people who *have* thought
deeply about it.  I am perfectly happy to simply sign-off on whatever
the expert group decides - I really do not want to be the arbiter of the
final decision in this matter because I just don't have the full scope
of the problem in my head!  I am happy, however, to participate in the
overall debate leading up to that decision.

M



-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274