[ensembl-dev] Pongo 9600 to 9601

[Gregory Jordan]

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
>
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