[ensembl-dev] gene description

[Andy Yates]

Hi Yin,

After some investigations carried out by Ensembl Genomes & Ensembl we can confirm that this is a bug which had been patched in Ensembl Genomes. Due to Ensembl's release cycle procedure the patched drosophila DB was not used for the new release; we will take their patched data for our next release. Since Ensembl Genomes holds the fixed descriptions my best suggestion is to use their dumps if possible. Otherwise you should manually correct for these bad descriptions using the URI::Encode module from Perl (or an equivalent module in your language of choice).

Best regards,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 15 May 2012, at 05:56, yin huang wrote:

> Hi,all
> 
> I find these error basically appear in species 'Fruitfly' in ensembl release 67 download from ftp://ftp.ebi.ac.uk/pub/software/ensembl/EBeyeXML/ensembl/ .Hope to see as soon as possible to correct data.
> 
> I find the same error in gene description as follow:
> 
> homogentisate 1%2c2-dioxygenase
> absent%2c small%2c or homeotic discs 1
> jumonji%2c at rich interactive domain 2
> selenide%2cwater dikinase
> modifier of rpr and grim%2c ubiquitously expressed
> atp synthase%2c subunit b
> inositol 1%2c4%2c5-triphosphate kinase 1
> gdp-mannose 4%2c6-dehydratase
> gdp-4-keto-6-deoxy-d-mannose 3%2c5-epimerase/4-reductase
> atp synthase%2c subunit d
> scavenger receptor class c%2c type iii
> breast cancer 2%2c early onset homolog
> absent%2c small%2c or homeotic discs 2
> alpha1%2c6-fucosyltransferase
> scavenger receptor class c%2c type ii
> na%2ck-atpase interacting
> inositol 1%2c4%2c5-triphosphate kinase 2
> inositol 1%2c4%2c5%2c-tris-phosphate receptor
> fructose-1%2c6-bisphosphatase
> forkhead box%2c sub-group o
> scavenger receptor class c%2c type i
> scavenger receptor class c%2c type iv
> 
> 
> 2012/5/15 Javier Herrero <jherrero at ebi.ac.uk>
> Hi Yin
> 
> This seems to be an error: http://flybase.org/reports/FBgn0050169.html
> 
> I guess there is a problem with the parser, thank you for reporting this.
> 
> Javier
> 
> Sent from my Kindle Fire
> 
> 
> 
> From: yin huang <abelhuangyin at gmail.com>
> Sent: Tue May 15 04:54:03 GMT+01:00 2012
> To: dev at ensembl.org
> Subject: [ensembl-dev] gene description
> 
> Hi,all
>     I find that some gene description has char '%'。
>     follow url：
>     http://www.ensembl.org/Drosophila_melanogaster/Search/Details?species=Drosophila_melanogaster;idx=Gene;end=1;q=breast%20cancer%202%252c%20early%20onset%20homolog
> 
>     error or correct?
>     who can help me? Thank you very much.
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/