Queries on genomic ranges

InterMine includes functionality for querying features with overlapping genome coordinates. We have a custom BIOSEG index for postgres that is created on the Location table. This is used by a 'virtual' LocatedSequenceFeature.overlappingFeatures collection that is a view in the postgres database using the BIOSEG 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.

To use the overlapping queries in InterMine you need to:

1. Install BIOSEG

BIOSEG is a custom index type that you need to add to postgres - installation instructions.

2. Create the BIOSEG index

You need to create the bioseg index on the location table in your production database. This is done simply by adding the create-bioseg-location-index post-process step to your project.xml file:

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

3. Create the overlappingFeatures view

Now create the view in the LocatedSequenceFeature.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. Just add the create-overlap-view post-process step, it needs to be after create-bioseg-location-index.

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

See FlyMine's project.xml for an example of including these steps.

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