[ensembl-dev] Wrong gene description

[Sébastien Moretti]

Hi

it looks there are other descriptions already containing "[Source:" in 
this ftp file.
Will check these ones in my own entries!
Thanks to have reported it back to Xenbase.

Best
Sébastien

> Hi Sébastien,
>
> Ensembl's mapping to Xenbase come from the following file:
>
> ftp://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt
>
> If you look for the record associated with ENSXETG00000008325 you can see the full gene name (which we are using as a description):
>
> Putative ortholog of galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135) (Beta-1,3-glucuronyltransferase 1) (Glucuronosyltransferase-P) (GlcAT-P) (UDP-GlcUA:glycoprotein beta- 1,3-glucuronyltransferase) (GlcUAT-P). [Source:Uniprot/SWISSPROT;Acc:, 1 of 1
>
> The extra "[Source:" section seen in our website is from Xenbase and not added by our pipelines (we do add the Source:Jamboree though). However this micro-format does scream Ensembl. It suggests that Xenbase has imported annotation from us and have not fully stripped this section. I have submitted an issue to Xenbase to see if they can clean up the record.
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Core Software Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 15 Oct 2013, at 08:50, Sébastien Moretti <sebastien.moretti at unil.ch> wrote:
>
>> Hi Magali,
>>
>>
>>> Hi Sebastien,
>>>
>>> Xenbase uses two types of information to describe their gene models.
>>>
>>> The first one is the gene symbol, which corresponds to what we in
>>> Ensembl would call a display name.
>>> The second one is the gene name, which we import as a gene description.
>>>
>>> For the entry you are referring to, the gene symbol is 'unnamed', as
>>> Xenbase have not manually annotated that gene.
>>> This is what the 'Source:UniProt/SWISSPROT' part of the description
>>> refers to.
>>> As this entry as not yet been fully annotated, the description has been
>>> imported from Uniprot.
>>>
>>> We import our xenopus annotations directly from Xenbase, so rely on
>>> their knowledge in the matter.
>>
>> According to Xenbase, the "1 of 1" in [Source:UniProt/SWISSPROT;Acc:, 1 of 1 [Source:Jamboree;Acc:XB-GENE-961613] should be part of the ensembl description core, not in the source part, at the end.
>> And ". [Source:UniProt/SWISSPROT;Acc:" is useless.
>>
>>> As for the space, I believe there is none between 'beta' and '1,3', but
>>> the rendering makes it look like it does.
>>> Looking the ID up on our rest service will show you the exact
>>> description, without additional rendering.
>>> http://beta.rest.ensembl.org/xrefs/id/ENSXETG00000008325?content-type=application/json
>>>
>>>
>>> Hope that helps,
>>> Magali
>>>
>>> On 14/10/13 14:54, Sébastien Moretti wrote:
>>>> Hi
>>>>
>>>> it looks there is a problem with gene description of
>>>> ENSXETG00000008325, at least since release 68.
>>>>
>>>> The source at the end of the description is
>>>>   [Source:UniProt/SWISSPROT;Acc:, 1 of 1
>>>> [Source:Jamboree;Acc:XB-GENE-961613]
>>>> and should be
>>>>   [Source:Jamboree;Acc:XB-GENE-961613]
>>>> "1 of 1" is part of the gene name according to Xenbase.
>>>>
>>>> Also, "beta-" & "1,3-glucuronyltransferase" should not be separated by
>>>> a space I think.
>>>>
>>>>
>>>>
>>>> Putative ortholog of galactosylgalactosylxylosylprotein
>>>> 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135)
>>>> (Beta-1,3-glucuronyltransferase 1) (Glucuronosyltransferase-P)
>>>> (GlcAT-P) (UDP-GlcUA:glycoprotein beta-1,3-glucuronyltransferase)
>>>> (GlcUAT-P), 1 of 1 [Source:Jamboree;Acc:XB-GENE-961613]
>>>>
>>>> Regards

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/