Default exporters in bio project

  • tab/csv - tab or comma separated
  • GFF3
  • BED
  • Galaxy - export data in tab or BED format to Galaxy server

Appears on these pages:

  • Query results page
  • List analysis page
  • Genomic Region Search results page

Create a custom exporter

You can add additional export options to your InterMine by creating a custom exporter.

  1. Write Java classes to handle the data

    see BEDHttpExporter.java and BEDExporter.java

  2. Add the class to your webconfig-model.xml file:

<tableExportConfig id="bed" className="org.intermine.bio.web.export.BEDHttpExporter"/>
  1. update Struts config
# struts-config-model.xml
<action path="/bedExportAction" name="bedExportForm" type="org.intermine.web.struts.TableExportAction" parameter="method"/>

# tiles-defs-model.xml
<definition name="bedExportOptions.tile" path="/model/bedExportOptions.jsp" controllerUrl="/initSequenceFeatureExportOptions.do" />

# struts-config-model-form.xml
<form-bean name="bedExportForm" type="org.intermine.bio.web.struts.BEDExportForm"/>


By default, SequenceFeature and Protein can be exported as FASTA format

fasta.export.classes = SequenceFeature,Protein

Exporter description

exporter.galaxy.description = Export to Galaxy
exporter.sequence.description=Export in FASTA format
exporter.gff3.description=Export in GFF3 format
exporter.bed.description=Export in BED format