[ensembl-dev] Homology Member - schema change

[Matthieu Muffato]

Dear Trevor

The full list of changes is available online at 
http://www.ensembl.org/info/website/news.html

Unfortunately, the first change you are mentioning hasn't been reported 
to the declaration of intentions and is therefore not on that page.
Here is the list of the additional schema changes that you can find in 
Compara:
  - cigar_start and cigar_end columns dropped from gene_tree_member, 
protein_tree_member_score, homology_member
  - peptide_align_feature_id dropped from homology_member
  - stable_id dropped from homology
  - analysis_id dropped from the peptide_align_feature_* tables

About the changes in the core meta tables, this is a "declared" 
intention that was half-pushed in release 67 and will be completed in 
release 68. Here is the original intention:

"
The following meta keys are retired
     species.short_name
     species.ensembl_common_name
     species.ensembl_alias_name
The following meta keys will be added
     species.url
     species.display_name
"

In the future, we will make sure that the Compara schema changes are all 
reported.

Best regards,
Matthieu

On 17/05/12 18:09, PATERSON Trevor wrote:
> There doesn't seem to be the usual clear documentation of schema changes
> with release 67.
> Maybe I am looking in the wrong place??
> so far i have found that a few fields ( that always seem to be null
> anyway) have been dropped from the compara.homology_member table
> i.e cigar_start, cigar_end, peptide_align_feature_id
> also in core.meta the names of the keys used to store various names for
> display and aliases etc have changed...
> Can anyone point me at a place where schema changes are documented for
> release67?
> ta
> trevor
>
> **Trevor Paterson PhD ***