Created by: tgrego
Requirements
- Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
- Review the contributing guidelines for this repository; remember in particular:
- do not modify code without testing for regression
- provide simple unit tests to test the changes
- if you change the schema you must patch the test databases as well, see Updating the schema
- the PR must not fail unit testing
Description
Using one or more sentences, describe in detail the proposed changes. This adds so_term column to the biotype column and to the Biotype objects. Production master_biotype table needs updating (https://github.com/Ensembl/ensembl-production/pull/218) Core Features have also been updated to include feature_so_term method, in the likelihood of feature_so_acc. Features of compara, regulation and variation need updating through separate pull requests to follow.
Use case
Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. Biotype objects will now report the so_term in addition to the so_acc, thus an ontology database dependency is avoided. Features will also report the so_term.
Benefits
If applicable, describe the advantages the changes will have. Improved Biotype objects and no need for ontology database to look up so terms.
Possible Drawbacks
If applicable, describe any possible undesirable consequence of the changes. A bit more data in the biotype table.
Testing
Have you added/modified unit tests to test the changes? yes
If so, do the tests pass/fail? pass
Have you run the entire test suite and no regression was detected? yes