O/R mapping [was Re: [Bioperl-l] pipeline]

[Elia Stupka]

> mundane stuff. It's still not ideal but it's about the best way we have of
> working in the object-centic mode right now.

Ok, I see we agree...

...but I also agree with Ewan, we need some form of chemical to reach your
state of e-mailing :)

> I have a feeling it will be useful for managing data of a comparative
> nature. Excuses for introducing trees, graphs, fun things like that. Once
> we have some decent comparative data for drosophila - v soon - I may
> actually have to back up this statement.

Now this the interesting bit, I follow (believe it or not) how it is
helpful for GO and other hierarchical stuff, I don't really see where it
will aid in the comparative stuff (apart from trees I guess)

> constraints and transformations making your data rock solid. e.g. making
> sure every confirmed gene has a certain kind of evidence. The nearest UML
> has is OCL (Object Constraint Language) which I don't know much about but
> looks a bit crap.

Isn't it overkill to have all of this in place to "make sure data is rock
solid". From my experience making sure data is biologically rock solid has
very little to do with how you check for that (from some horrible perl
hash to your funky stuff), but more with whether you have really thought
of every possible annoying exception that can happen in a genome, what
weird data can come out from a supposedly clean database, and other (sorry
oh so mortal!) problems of the kind...

> That's ok, it's quite possibly all completely irrelevant anyway.

Not irrelevant, it just poses a few problems:

1)We need to clone a few Chris Mungalls
2)We need to make sure they have 2 weeks of pure free time
3)Put them in a room to code this up
4)Make sure they convince everybody else it is worth switching to this
system
5)Find another two weeks for them to teach the new system to everybody
else

:)

In 2004....

:)

Elia

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