[biomart-users] IPI ID Conversion

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[biomart-users] IPI ID Conversion

Seth Kasowitz-2
Hello,

I have been working with some mass spec data using software (Scaffold) that only seems willing to use IPI database IDs. I would like to convert these accession numbers to Ensembl or Refseq, and was hoping I could do this using Biomart. From what I can tell however, Biomart can output the IPI ID as an attribute, but I cannot find a filter that will let me input a list of IPI IDs. Am I missing something?

Thanks,
Seth

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Re: [biomart-users] IPI ID Conversion

Arek Kasprzyk
Hi Seth,

The BioMart mapping tool is based on Ensembl data. Probably best to drop an email to Ensembl helpdesk[hidden email]. They will be able to tell you what type of id mapping is supported atm and what they are planning to support in the near future.

a.



On 2 September 2015 at 14:07, Seth Kasowitz <[hidden email]> wrote:
Hello,

I have been working with some mass spec data using software (Scaffold) that only seems willing to use IPI database IDs. I would like to convert these accession numbers to Ensembl or Refseq, and was hoping I could do this using Biomart. From what I can tell however, Biomart can output the IPI ID as an attribute, but I cannot find a filter that will let me input a list of IPI IDs. Am I missing something?

Thanks,
Seth

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Re: [biomart-users] IPI ID Conversion

Thomas Maurel
In reply to this post by Seth Kasowitz-2
Dear Seth,

I am afraid that the IPI IDs have been retired in 2011, we kept them in Ensembl until early 2013. You can still filter on them using our Ensembl Release 70 archive from January 2013: http://jan2013.archive.ensembl.org/biomart/martview.

Hope this helps,
Regards,
Thomas
On 2 Sep 2015, at 14:07, Seth Kasowitz <[hidden email]> wrote:

Hello,

I have been working with some mass spec data using software (Scaffold) that only seems willing to use IPI database IDs. I would like to convert these accession numbers to Ensembl or Refseq, and was hoping I could do this using Biomart. From what I can tell however, Biomart can output the IPI ID as an attribute, but I cannot find a filter that will let me input a list of IPI IDs. Am I missing something?

Thanks,
Seth

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] IPI ID Conversion

Seth Kasowitz-2
Thomas,

Thanks for your help, I was able to convert my protein IDs to Ensembl using the archived release.

Seth

On Monday, 14 September 2015 10:06:29 UTC-4, Thomas Maurel wrote:
Dear Seth,

I am afraid that the IPI IDs have been retired in 2011, we kept them in Ensembl until early 2013. You can still filter on them using our Ensembl Release 70 archive from January 2013: <a href="http://jan2013.archive.ensembl.org/biomart/martview" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fjan2013.archive.ensembl.org%2Fbiomart%2Fmartview\46sa\75D\46sntz\0751\46usg\75AFQjCNGA7oid5ViOeyFPu1CHcm80gvPdgQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fjan2013.archive.ensembl.org%2Fbiomart%2Fmartview\46sa\75D\46sntz\0751\46usg\75AFQjCNGA7oid5ViOeyFPu1CHcm80gvPdgQ&#39;;return true;">http://jan2013.archive.ensembl.org/biomart/martview.

Hope this helps,
Regards,
Thomas
On 2 Sep 2015, at 14:07, Seth Kasowitz <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="pc_nkywXLAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">skas...@...> wrote:

Hello,

I have been working with some mass spec data using software (Scaffold) that only seems willing to use IPI database IDs. I would like to convert these accession numbers to Ensembl or Refseq, and was hoping I could do this using Biomart. From what I can tell however, Biomart can output the IPI ID as an attribute, but I cannot find a filter that will let me input a list of IPI IDs. Am I missing something?

Thanks,
Seth

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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