[ensembl-dev] Pongo 9600 to 9601

[Javier Herrero]

Hi Greg

I am sorry about the problems you had with this change. We didn't noticed this 
earlier as the API (i.e., the Registry) gets the common name from the meta 
table of the core DBs.

We will had a check to our QC suite to make sure the ensembl_common_name and 
ensembl_alias_name entries in the core and in the compara database match.

I am afraid it is a bit late in the release cycle now to get this sorted for 
e!63, but things should be back to normal in e!64.

Thank you for reporting this and sorry again for the inconvenience.

Javier

On Wednesday 15 Jun 2011 15:55:56 Gregory Jordan wrote:
> And to suggest a further change, the 'ensembl alias name' and 'ensembl
> common name' entries in the ncbi_taxa_name table should be updated for the
> new taxon_id (see below). I tracked down this mismatch as the cause of the
> problems in my code, where the Orangutan NCBITaxon appears to have a blank
> Ensembl alias.
> 
> Cheers,
>  Greg
> 
> mysql> select * from ensembl_compara_62.ncbi_taxa_name where name_class
> like "%ensembl%" and taxon_id=9600\G
> *************************** 1. row ***************************
>   taxon_id: 9600
>       name: Orangutan
> name_class: ensembl alias name
> *************************** 2. row ***************************
>   taxon_id: 9600
>       name: orangutan
> name_class: ensembl common name
> 2 rows in set (0.00 sec)
> 
> mysql> select * from ensembl_compara_62.ncbi_taxa_name where name_class
> like "%ensembl%" and taxon_id=9601\G
> Empty set (0.00 sec)
> 
> On Wed, Jun 15, 2011 at 3:44 PM, Gregory Jordan <greg at ebi.ac.uk> wrote:
> > Hi all,
> > 
> > I came across a surprising change in the genome_db table from Compara v61
> > to v62: the orangutan taxon ID and species binomial are not what they
> > used to be!
> > 
> > The change is understandable, as the Sumatran taxon identifier is more
> > appropriate for the genome source, but I was caught off guard (and so was
> > some of my code) by the abrupt change... perhaps some mention of this
> > could go into the Ensembl changelog?
> > 
> > Cheers,
> > 
> >  Greg
> > 
> > mysql> select * from ensembl_compara_62.genome_db where name like
> > "%pongo%"\G;
> > *************************** 1. row ***************************
> > 
> >     genome_db_id: 60
> >     
> >         taxon_id: 9601
> >         
> >             name: pongo_abelii
> >         
> >         assembly: PPYG2
> > 
> > assembly_default: 1
> > 
> >        genebuild: 2007-10-Ensembl
> > 
> > mysql> select * from ensembl_compara_61.genome_db where name like
> > "%pongo%"\G;
> > *************************** 1. row ***************************
> > 
> >     genome_db_id: 60
> >     
> >         taxon_id: 9600
> >         
> >             name: pongo_pygmaeus
> >         
> >         assembly: PPYG2
> > 
> > assembly_default: 1
> > 
> >        genebuild: 2007-10-Ensembl

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK