Querying over genomic ranges

InterMine includes functionality for querying features with overlapping genome coordinates. We have an index that is created on the Location table. This is used by a 'virtual' SequenceFeature.overlappingFeatures collection that is a view in the postgres database using the native Postgres index to find other features that overlap it.

In modMine (the InterMine for the modENCODE project), we also create GeneFlankingRegion features to represent specific distances upstream and downstream of genes to query for genes that are nearby other features.

Create the index

You need to create the index on the location table in your production database by adding the create-location-range-index post-process step to your project.xml file like so:

<post-process name="create-location-range-index"/>

Create the overlappingFeatures view

Create the SequenceFeature.overlappingFeatures view in the database. This allows you to query for any features that overlap any other types of features in the web interface or query API. Add the create-overlap-view post-process step, which needs to be located after create-location-range-index in your project XML file.

<post-process name="create-overlap-view" />

Now any queries on the overlappingFeatures collections will use this view and the new index.