[ensembl-dev] homo_sapiens_variation_62_37g

Stuart Meacham sm766 at cam.ac.uk
Fri May 13 09:49:42 BST 2011

Hi guys,

I have a few queries. I am trying to incorporate the latest Ensembl 
release into RoboSNP. Basically I use 5 tables from 
homo_sapiens_variation_62_37g (allele, sample, subsnp_handle, 
transcript_variation and variation_feature). There seems to have been a 
number of seemingly arbitrary changes to the schemas.

For example in the transcript_variation table the consequence_type field 
has been renamed consequence_types, yet this has not been followed 
through in the variation_feature table which still has a field  called 
consequence_type. Also in transcript_variation we find 
peptide_allele_string is now called pep_allele_string. The 
transcript_stable_id is now rather confusingly called feature_stable_id. 
What is the rationale for these changes? I understand you need to update 
things as more, and more refined data, becomes available but shouldn't 
the default policy be 'conservation' so as the break as few things as 



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