[ensembl-dev] Schema patch for ensembl ontology 71 -> 72

mr6 at ebi.ac.uk mr6 at ebi.ac.uk
Fri Jan 17 10:01:06 GMT 2014


Hi Jan,

Historically, we did not use to have patch files.
The ontology database is created from scratch every release to contain the
latest set of ontologies.
If some changes were necessary to cope with the data, they were done
directly to the table.sql file.

Since 71, we have decided to create patch files to reflect the changes
done to the schema, as it allows users to patch existing databases, the
way you are currently doing.
Apologies about the mistake in the first one, we will fix this as soon as
possible.

Unfortunately, we have no record of the changes made prior to 71, apart
from the history in table.sql.

I would still recommend taking a direct copy of the release 74 database.
There are a number of GO entries retired every release, which is why we
need to run a fresh import every time.
If you are using EFO terms as well, they did not use to be fully
represented in earlier versions of the ontology database.


Hope this helps,
Magali

>
> Hi,
>
> again. some patching issues - I try to patch an ensembl-ontology  67 db to
> 74.
>
> There are issues with the patch_71_72_e.sql patch  - the table TERM does
> not exist ( but term ) - attached a patch file for the patch.
>
> Also, some other changes are missing ( there are no patch files for 67->
> 68, 68->69, 69->70, 70->71 ).
>
> I've listed the changes below but haven't run any tests with the 74 api
> for this. Did anyone else do ? How does this work with the new ontology_id
> column in the relation and closure tables ?
>
> Maybe I should consider just downloading the new ontology 74 db …
>
> Regards,
>
>    Jan Vogel
>
> File :  ensembl-74/ensembl/misc-scripts/ontology/sql/patch_71_72_e.sql
>
>
> ALTER TABLE TERM ADD COLUMN is_obsolete INT NOT NULL DEFAULT 0;
>
> -- Patch identifier
> INSERT INTO meta (meta_key, meta_value)   VALUES ('patch',
> 'patch_71_72_e.sql|is_obsolete');
>
>
>
>
> Additional changes from 67 -> 74 which are not in patch files:
>
> table term is missing the "is_root" column :
>
> ALTER TABLE term ADD COLUMN is_root INT NOT NULL DEFAULT 0;
>
> table relation and table closure is missing ontology_id column and
> subsequently the indexes have to be updated:
>
> ALTER TABLE relation ADD COLUMN ontology_id INT UNSIGNED NOT  NULL;
> ALTER TABLE closure  ADD COLUMN ontology_id INT UNSIGNED NOT  NULL;
>
> DROP INDEX child_parent_idx ON relation;
> CREATE UNIQUE INDEX child_parent_idx ON relation   (child_term_id,
> parent_term_id, relation_type_id, intersection_of, ontology_id) ;
>
> DROP INDEX child_parent_idx ON closure;
> CREATE UNIQUE INDEX child_parent_idx ON closure    (child_term_id,
> parent_term_id, subparent_term_id, ontology_id)  ;
>
>
>
>
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