[Hackathon] Re: [Bioperl-l] proposed change to Bio::SeqFeature::Gene::*

Mark Wilkinson markw at illuminae.com
Wed Jun 18 17:47:24 EDT 2003

On Wed, 2003-06-18 at 10:30, David Block wrote:

> If I could just jump in here, :-)
> We didn't have the SO at the time.  I think it's clear from both
> Mark's work and mine (Hilmar can vouch for me) that the Genquire
> people were not opposed to ontologies in principle - rather, we were
> ahead of the tools. 

Well... the problem was bigger than that.  For example, as I recall,
when Bioperl parses e.g. GFF, it takes the third column ('featurename')
and assigns that to the primary_tag.  There are no rules about what is
allowed in that field in GFF, so if Bioperl is going to assume that this
tag has some implicit additional meaning (other than just an arbitrary
string representing the name) then you should not be using that column
as the primary tag.  The fact that it does strongly implies that the
primary_tag value *should not* be interpreted.  Thus, since we couldn't
safely put any meaning into primary_tag, we needed to put that meaning
into the object's @ISA.

If primary_tag is now going to be linked to an ontology I will be
thrilled, but then it does change the "meaning" of that tag... and in
fact, it might be nicer for primary_tag to then return an ontology Node
object of some sort, rather than just a string...

> Please break everything - Mark is paying a summer student to fix
> Genquire anyway :-)

Two, in fact!!  :-)

I'm actually quite shocked at how well Genquire has survived the changes
in Bio::SeqI, which now implements all sorts of new interfaces that
didn't exist when we originally wrote Genquire.  One of the students is
now implementing those interfaces in the Genquire::Seq objects and then
we should be able to import any datatype that BioPerl supports, do
many/most Bioperl Seq and Seqfeature manipulations using the Genqurie
GUI, and write-out in any datatype that BioPerl supports (or write out
to the db).  I am hoping that we can resurrect interest in Genquire once
this is done.

> And thanks, Chris, for your GenbankWhateverUnFlattener code.  Someone
> had to try, and Mark and I kept thinking about it.  We're happy to let
> you guys do it.

yeah... I thought about it for a while, and my hair went white...  I'm
really happy that it is done!  thanks!!


Mark Wilkinson <markw at illuminae.com>

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