Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

combine core and otherfeatures gene models #26

Open
ajo2995 opened this issue Feb 23, 2016 · 1 comment
Open

combine core and otherfeatures gene models #26

ajo2995 opened this issue Feb 23, 2016 · 1 comment
Assignees

Comments

@ajo2995
Copy link
Member

ajo2995 commented Feb 23, 2016

For maize we have the rejected set of gene models in the otherfeatures db and the filtered set in the core db. There is no overlap in the gene stable_ids in maize.
In triticum aestivum, for example, there are additional non-canonical transcripts stored in the otherfeatures database. These share the same gene stable ids as in the core db.

The gene dumping script should query both core and otherfeatures databases for a species so the set of models can be merged if necessary.

@ajo2995 ajo2995 self-assigned this Feb 23, 2016
@ajo2995
Copy link
Member Author

ajo2995 commented Feb 24, 2016

For now, we are going to explicitly ignore the triticum aestivum otherfeatures db. Previously, they were being ignored implicitly because of the way we were importing genes into mongodb (with mongoimport).

The otherfeatures models for maize and rice will be loaded (different stable_id's prevent conflicts). The db_type field in the solr docs can be used to distinguish the models from core and otherfeatures in the search result list or effect the order of the matching genes by boosting the score of core models over otherfeatures models. Also we can tweak the suggestions to prioritize core over otherfeatures

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant