[ensembl-dev] inconsistent common_name key in ensembl

[PATERSON Trevor]

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> 

Bioinformatics 
The Roslin Institute
The Royal (Dick) School of Veterinary Studies
University of Edinburgh
Scotland EH25 9PS
phone +44 (0)131 5274197
http://bioinformatics.roslin.ed.ac.uk/ <http://bioinformatics.roslin.ed.ac.uk/> 

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