On 6 Dec 2006, at 19:47, Arek Kasprzyk wrote:
On 6 Dec 2006, at 18:48, Brian Osborne wrote:
Arek,
Hi Brian,
I took a quick look at the documentation at biomart.org and what I
found
seems to suggest that the combination of Biomart and Chado is still a
bit
"experimental". Or am I mistaken? Is Biomart .5 and some recent Chado
schema
a perfectly stable and usable combination?
no, it is not at present. We have done some promising preliminary work
on automatic Chado to BioMart conversion a while back but nobody has
been working
on it ever since. However, as we are now going to work intensively on
MartBuilder to train it with variety of schemas, it is likely that
chado
will be tried again, this time providing some stable conversion
a small correction :)
actually, there is a gff->biomart tool available on GMOD site. So it is
possible
at present to dump chado to gff and then convert it to BioMart. This
will of course
not convert chado as a whole but if you are looking for something like
that, that's available
already.
As I said above we are now trying to train MBuilder 'properly' and our
first 'victim' will
be Ensembl and some other schemas but chado will be definitely included
there at some stage
a.
a.
Thanks again,
Brian O.
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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