[ensembl-dev] inconsistent common_name key in ensembl

[Glenn Proctor]

Thanks for this Trevor, we'll try and address this in release 62 (it's
too late to go into release 61 now).

Glenn.


On Wed, Jan 26, 2011 at 4:50 PM, PATERSON Trevor
<trevor.paterson at roslin.ed.ac.uk> wrote:
>
> Around the time of release 59 there was an attempt to rationalize some of the meta_key
> values used in the 'core.meta' table and to list these in the 'ensembl_production.meta_key' table.
>
> but I think there are still some inconsistencies that have slipped through the net
>
> 'ensembl_production_60.meta_key' table includes two similarly named keys:
> 'species.common_name' and 'species.ensembl_common_name'
>
> from the perlAPI it appears that the 'common_name' key should be used
> ( see Bio::EnsEMBL::DBSQL MetaContainer.get_common_name() )
>
> however this key is not always present in the core.meta table, so the Perl function returns null
> (e.g. for Zebra Finch, this has a 'species.ensembl_common_name' but not a 'species.common_name' key )
>
> I suspect there could be some rationalisation of these two keys to fix this
>
> Currently the perl method Bio::EnsEMBL::DBSQL MetaContainer.get_short_name() seems a more
> reliable alternative to get a "common name"
>
> Trevor
>
>
> Trevor Paterson PhD
> email trevor.paterson at roslin.ed.ac.uk <mailto:trevor.paterson at roslin.ed.ac.uk>
>
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