On 24 Sep 2007, at 11:03, Matthias Haimel wrote:
Hi Arek,
thanks for your fast respond. This would work - I tried to this on the
BioMart but I weren't able to find the last link yet. May you could
give me a hint where I can add the missing annotation?
Dataset 1:
1) ENSEMBL Homology
2) RAT
3) MOUSE
4) Orthologues
Dataset 2:
1) select mouse
2) Attributes -> External -> IPI ID
Till now it looks like:
? - Rat - mouse - IPI
ok, I was actually thinking about datasets from ensembl (not ensembl
homology)
for this you need to
Dataset1 mouse (ensembl 46)
Fitler IPI
Dataset2 rat (ensembl 46)
Attributes: (Gene/external) IPI
it works the other way round too.
Once you set up your query , If you need perl API script or web service
to the the same thing for you click on a 'Perl' button to get
a script or XML button to get a web service query respectively
a.
Thanks,
Matthias
Arek Kasprzyk wrote:
On 24 Sep 2007, at 10:33, Matthias Haimel wrote:
Hi Arek,
How can I map External identifier across species using BioMart? The
reason is that I have an IPI user request who wants to map IPI
identifier between mouse and rat.
Hi Matthias,
You can certainly map IPI ids for mouse in mouse dataset and then
pull out all the rat
homologue genes corresponding to the mouse ones with all the
relevant annotation including rat IPIs.
(or vice versa). Would this work for you?
a.
Thanks for your help,
Matthias
-- Matthias Haimel
EMBL-European Bioinformatics Institute Tel: +44-(0)1223-494 436
Wellcome Trust Genome Campus, Hinxton Fax: +44-(0)1223-494 468
Cambridge CB10 1SD, UK email: [EMAIL PROTECTED]
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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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---------
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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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