Update overlaps.rst

docs/data-model/overlaps.rst

@@ -1,40 +1,41 @@
 Querying over 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' `SequenceFeature.overlappingFeatures` collection that is a `view` in the postgres database using the `BIOSEG` index to find other features that overlap it.
+.. note::
+
+   Starting with InterMine 1.4 Bioseg is no longer required if you are using Postgres version 9.2 or later.
 
-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. 
+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' `SequenceFeature.overlappingFeatures` collection that is a `view` in the postgres database using the `BIOSEG` index to find other features that overlap it.
 
-To use the overlapping queries in InterMine you need to:
+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. 
 
-Install BIOSEG 
--------------------
+Install BIOSEG (Postgres versions 9.1 and older only)
+--------------------------------------------------------------------------------------------------
 
 `BIOSEG` is a custom index type that you need to add to postgres. See :doc:`/system-requirements/software/postgres/bioseg` for details
 
-Create the BIOSEG index
----------------------------
+Create the 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:
+You need to create the index on the location table in your production database.  This is done simply by adding the `create-location-range-index` post-process step to your `project.xml` file:
 
 .. code-block:: xml
 
-	<post-process name="create-bioseg-location-index"/>
+	<post-process name="create-location-range-index"/>
+
+If you are using an older version of Postgres, this will create a BIOSEG index. Otherwise it will use a native Postgres index.
 
 Create the `overlappingFeatures` view
--------------------------------------------
+--------------------------------------------------------------------------------------------------
 
-Now create the view in 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.  Just add the `create-overlap-view` post-process step, it needs to be after `create-bioseg-location-index`.
+Now 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.  Just add the `create-overlap-view` post-process step, it needs to be after `create-location-range-index`.
 
 .. code-block:: xml
 
 	<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.
-
+Now any queries on the `overlappingFeatures` collections will use this view and the new index.
 
 .. index:: overlaps, region search, bioseg, genome coordinates, overlappingFeatures, create-overlap-view, create-bioseg-location-index