[ensembl-dev] Protein feature hit descriptions in older MySQL releases

[Charles Joseph Murphy]

Thanks, Thibaut! I was thinking I would have to do something like that.

> On Mar 3, 2017, at 08:18, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:
> 
> Hi Charlie,
> The reason for this difference is because we changed our pipeline for the protein annotation and now we are filling the hit_description column.
> 
> You should be able to get the “missing" information by searching the website of the domain/feature you are looking at.
> 
> Thanks
> Thibaut
> 
>> On 27 Feb 2017, at 21:38, Charles Joseph Murphy <chm2059 at med.cornell.edu> wrote:
>> 
>> I was looking at the protein_feature.hit_description column for PFAM protein domains. I see there are descriptions for recent releases (e.g. mus_musculus_core_75_38 and homo_sapiens_core_75_37), but not for older releases (e.g. mus_musculus_core_75_38 and homo_sapiens_core_75_37). Instead those older releases just have NULL all protein_feature.hit_description. What is the reason?
>> 
>> Here is an example command I’ am using
>> 
>> mysql -u anonymous -h ensembldb.ensembl.org -e "use homo_sapiens_core_84_38; SELECT translation.translation_id, translation.stable_id, protein_feature.hit_name, protein_feature.seq_start, protein_feature.seq_end, protein_feature.hit_description, analysis.db FROM analysis, analysis_description, protein_feature, translation WHERE protein_feature.translation_id = translation.translation_id AND protein_feature.analysis_id = analysis.analysis_id AND analysis.analysis_id = analysis_description.analysis_id AND analysis.db = 'Pfam';" > pfam_homo_sapiens_core_84_38.txt
>> 
>> Charlie
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