source: trunk/flymine/webapp/resources/webapp/WEB-INF/webconfig-model.xml @ 29382

<webconfig>

  <class className="org.intermine.model.bio.AGambiaeLifeCycle" label="A. gambiae Life Cycle"/>

  <class className="org.intermine.model.bio.Allele">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="alleleClass"/>
      <fieldconfig fieldExpr="organism.name" label="Organism" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Author">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.BindingSite">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="factor.primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.BioEntity">
    <headerconfig>
      <titles>
        <title mainTitles="symbol|primaryIdentifier" numberOfMainTitlesToShow="1" subTitles="*organism.shortName*" />
      </titles>
    </headerconfig>
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier" label="DB identifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Component">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.CDNAClone">
    <fields>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.CDS">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol" showInResults="false" showInInlineCollection="false"/>
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInInlineCollection="false"/>
      <fieldconfig fieldExpr="organism.name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Chromosome">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="organism.name"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
  </class>


  <class className="org.intermine.model.bio.ChromosomeStructureVariation">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="available"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Comment">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="text"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.CrossReference">
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="source.name"/>
      <fieldconfig fieldExpr="subject.primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.DataSet">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.DataSource">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
    <tabledisplayer src="/model/dataSourceShort.jsp"/>
  </class>

  <class className="org.intermine.model.bio.Disease">
    <fields>
      <fieldconfig fieldExpr="identifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Exon">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInInlineCollection="false"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.FlyAtlasResult">
    <fields>
      <fieldconfig fieldExpr="affyCall"/>
      <fieldconfig fieldExpr="enrichment"/>
      <fieldconfig fieldExpr="mRNASignal" label="mRNA Signal"/>
      <fieldconfig fieldExpr="mRNASignalSEM" label="mRNA Signal SEM"/>
      <fieldconfig fieldExpr="presentCall"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Gene">
    <headerconfig>
      <customlinks>
        <customlink
          url="http://flybase.org/reports/{primaryIdentifier}.html"
          image="flybase_logo_link.png"
        />
      </customlinks>
    </headerconfig>
    <inlinelist>
      <table path="synonyms.value" showInHeader="true" lineLength="100" />
      <table path="probeSets.primaryIdentifier" showLinksToObjects="true" />
      <table path="pathways.name" showLinksToObjects="true" />
    </inlinelist>
    <fields>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="name"/>
    </fields>
    <bagdisplayers>
      <displayer src="friendlyMineLinkDisplayer.tile" showOnLeft="false" />
   </bagdisplayers>
  </class>

  <class className="org.intermine.model.bio.GOAnnotation">
    <fields>
      <fieldconfig fieldExpr="subject.secondaryIdentifier"/>
      <fieldconfig fieldExpr="subject.name"/>
      <fieldconfig fieldExpr="subject.symbol"/>
      <fieldconfig fieldExpr="ontologyTerm.identifier" />
      <fieldconfig fieldExpr="ontologyTerm.name" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.GOEvidenceCode">
    <fields>
      <fieldconfig fieldExpr="code"/>
    </fields>
  </class>

    <class className="org.intermine.model.bio.GOTerm">
    <headerconfig>
      <titles>
      <title mainTitles="identifier|name" subTitles="ontology.name" />
      </titles>
    </headerconfig>
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="description" showInResults="false" showInInlineCollection="false" doNotTruncate="true" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Homologue">
    <fields>
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInResults="false" showInInlineCollection="false" />
      <fieldconfig fieldExpr="homologue.primaryIdentifier"/>
      <fieldconfig fieldExpr="homologue.organism.shortName"/>
      <fieldconfig fieldExpr="type"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Image">
    <fields>
      <fieldconfig fieldExpr="url" displayer="/model/imageDisplayer.jsp" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Interaction">
   <fields>
     <fieldconfig fieldExpr="gene.primaryIdentifier"/>
     <fieldconfig fieldExpr="shortName"/>
     <fieldconfig fieldExpr="confidenceText"/>
     <fieldconfig fieldExpr="confidence"/>
     <fieldconfig fieldExpr="role"/>
    </fields>

  </class>
  <class className="org.intermine.model.bio.InteractionExperiment">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="description"/>
    </fields>
  </class>
  <class className="org.intermine.model.bio.InteractionTerm">
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Location">
    <fields>
      <fieldconfig fieldExpr="locatedOn.primaryIdentifier"/>
      <fieldconfig fieldExpr="start"/>
      <fieldconfig fieldExpr="end"/>
      <fieldconfig fieldExpr="strand"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.SequenceFeature">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier" />
      <fieldconfig fieldExpr="organism.name" name="Organism"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.MicroArrayExperiment">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="description" sectionOnRight="true" sectionTitle="Description" openByDefault="true"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.MicroArrayResult">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="value"/>
      <fieldconfig fieldExpr="scale"/>
      <fieldconfig fieldExpr="isControl"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.MicroArrayAssay">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="sample1"/>
      <fieldconfig fieldExpr="sample2"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.MicroarrayOligo">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="length"/>
      <fieldconfig fieldExpr="tm"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.MRNAExpressionResult">
    <fields>
      <fieldconfig fieldExpr="stageRange"/>
      <fieldconfig fieldExpr="expressed"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.MRNAExpressionTerm" label="mRNA Expression Term">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="type"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Mutagen">
    <fields>
      <fieldconfig fieldExpr="description"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.NaturalTransposableElement">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Ontology">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.OntologyRelation">
    <fields>
      <fieldconfig fieldExpr="relationship"/>
      <fieldconfig fieldExpr="parentTerm.name"/>
      <fieldconfig fieldExpr="parentTerm.identifier"/>
      <fieldconfig fieldExpr="childTerm.name"/>
      <fieldconfig fieldExpr="childTerm.identifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.OntologyTerm">
    <headerconfig>
      <titles>
      <title mainTitles="identifier|name" subTitles="ontology.name" />
      </titles>
    </headerconfig>
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="description" doNotTruncate="true" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.OntologyTermSynonym">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="type"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Organism">
    <headerconfig>
      <titles>
      <title mainTitles="name"/>
      </titles>
    </headerconfig>
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="taxonId" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.OrthologueEvidence">
    <fields>
      <fieldconfig fieldExpr="evidenceCode.name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.OrthologueEvidenceCode">
    <fields>
      <fieldconfig fieldExpr="abbreviation"/>
      <fieldconfig fieldExpr="name" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Pathway">
    <headerconfig>
        <titles>
            <title mainTitles="identifier|name" />
        </titles>
    </headerconfig>
    <fields>
      <fieldconfig fieldExpr="identifier" />
      <fieldconfig fieldExpr="name" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.PhenotypeAnnotation">
    <fields>
      <fieldconfig fieldExpr="annotationType"/>
      <fieldconfig fieldExpr="description"/>
      <fieldconfig fieldExpr="allele.primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Primer">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.ProbeSet">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Protein">
    <inlinelist>
      <table path="synonyms.value" showLinksToObjects="true" />
    </inlinelist>
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="primaryAccession"/>
      <fieldconfig fieldExpr="organism.name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.ProteinDomain">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="shortName"/>
      <fieldconfig fieldExpr="type"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.ProteinStructure">
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="technique"/>
      <fieldconfig fieldExpr="classification"/>
      <fieldconfig fieldExpr="resolution" />
      <fieldconfig fieldExpr="prosaQScore"/>
      <fieldconfig fieldExpr="prosaZScore"/>
      <fieldconfig fieldExpr="start"/>
      <fieldconfig fieldExpr="end"/>
      <fieldconfig fieldExpr="alignment" doNotTruncate="true" showInResults="false" showInInlineCollection="false" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Protocol">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="description" doNotTruncate="true"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Publication">
    <headerconfig>
  <titles>
    <title mainTitles="title" />
 </titles>
    </headerconfig>
    <inlinelist>
      <table path="authors.name" showLinksToObjects="true" />
    </inlinelist>
    <fields>
      <fieldconfig fieldExpr="firstAuthor"/>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="year"/>
      <fieldconfig fieldExpr="journal"/>
      <fieldconfig fieldExpr="volume"/>
      <fieldconfig fieldExpr="pages"/>
      <fieldconfig fieldExpr="pubMedId"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.RegulatoryRegion">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Reporter">
    <fields>
      <fieldconfig fieldExpr="controlType"/>
      <fieldconfig fieldExpr="isControl"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.RNAiPhenotype">
    <fields>
      <fieldconfig fieldExpr="comment"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="code"/>
    </fields>
  </class>


  <class className="org.intermine.model.bio.RNAiScreen">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="publication.title"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.RNAiScreenHit">
    <fields>
      <fieldconfig fieldExpr="result"/>
      <fieldconfig fieldExpr="pcrProduct.primaryIdentifier" label="PCR Product"/>
      <fieldconfig fieldExpr="rnaiScreen" showInInlineCollection="false" showInSummary="false" showInResults="false" label="RNAi Screen"/>
      <fieldconfig fieldExpr="pcrProduct" showInInlineCollection="false" showInSummary="false" showInResults="false" label="PCR Product"/>
      <fieldconfig fieldExpr="rnaiScreen.name" label="Screen" />
      <fieldconfig fieldExpr="rnaiScreen.publication.pubMedId" label="PubMed ID"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Sample">
    <fields>
      <fieldconfig fieldExpr="materialType"/>
      <fieldconfig fieldExpr="organism.name" label="Organism"/>
      <fieldconfig fieldExpr="primaryCharacteristicType"/>
      <fieldconfig fieldExpr="primaryCharacteristic"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.SampleCharacteristic">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="value"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Sequence">
    <fields>
      <fieldconfig fieldExpr="residues" fieldExporter="org.intermine.bio.web.export.ResidueFieldExporter"
                   sectionOnRight="true" sectionTitle="Residues" openByDefault="true"
                   showInSummary="false" showInResults="false" showInInlineCollection="false"/>
      <fieldconfig fieldExpr="length"/>
    </fields>
    <tabledisplayer src="/model/sequenceShortDisplayer.jsp"/>
  </class>

   <class className="org.intermine.model.bio.Stock">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="stockCenter"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Synonym">
    <fields>
      <fieldconfig fieldExpr="value"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.TFBindingSite">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="gene.symbol" label="Gene"/>
      <fieldconfig fieldExpr="factor.primaryIdentifier" label="Factor"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Transcript">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="gene.symbol" label="Gene" showInSummary="false" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.TransposableElement">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="insertedElement.symbol"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.TransposableElementInsertionSite">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="cytoLocation"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.TreatmentParameter">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="value"/>
      <fieldconfig fieldExpr="units"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Treatment">
    <fields>
      <fieldconfig fieldExpr="action"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.UniProtFeature" label="Uniprot Feature">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="description"/>
      <fieldconfig fieldExpr="begin"/>
      <fieldconfig fieldExpr="end"/>
    </fields>
  </class>

<!-- exporters -->
  <tableExportConfig id="sequence" className="org.intermine.bio.web.export.SequenceHttpExporter"/>
  <tableExportConfig id="gff3" className="org.intermine.bio.web.export.GFF3HttpExporter"/>
  <tableExportConfig id="bed" className="org.intermine.bio.web.export.BEDHttpExporter"/>

  <reportdisplayers>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer"
                     jspName="model/cytoscapeNetworkDisplayer.jsp"
                     replacesFields="interactions"
                     placement="Interactions"
                     types="Gene,Protein"/>

   <reportdisplayer javaClass="org.flymine.web.displayer.DrosophilaHomologueDisplayer"
                    jspName="model/drosophilaHomologueDisplayer.jsp"
                    replacesFields=""
                    placement="Homology"
                    types="Gene"/>

    <reportdisplayer javaClass="org.flymine.web.displayer.FlyAtlasDisplayer"
                     jspName="model/flyAtlasDisplayer.jsp"
                     replacesFields="microArrayResults"
                     placement="Expression"
                     types="Gene"/>

   <reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
                     jspName="model/geneOntologyDisplayer.jsp"
                     replacesFields="goAnnotation,ontologyAnnotations"
                     placement="Function"
                     types="Gene"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.GBrowseDisplayer"
                     jspName="model/gbrowseDisplayer.jsp"
                     replacesFields=""
                     placement="Genes"
                     types="SequenceFeature"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneStructureDisplayer"
                     jspName="model/geneStructureDisplayer.jsp"
                     replacesFields="transcripts,exons,CDSs,introns,UTRs,fivePrimeUTR,threePrimeUTR"
                     placement="Genes"
                     types="Gene,Transcript,Exon,Intron,UTR,CDS"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.HomologueDisplayer"
                     jspName="model/homologueDisplayer.jsp"
                     replacesFields="homologues"
                     placement="Homology"
                     parameters="{'dataSets': ['TreeFam data set', 'KEGG orthologues data set']}"
                     types="Gene"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.JMOLDisplayer"
                     jspName="model/JMOLDisplayer.jsp"
                     replacesFields=""
                     placement="summary"
                     types="ProteinStructure"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer"
                     jspName="model/overlappingFeaturesDisplayer.jsp"
                     replacesFields="overlappingFeatures"
                     placement="Genes"
                     types="SequenceFeature"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer"
                     jspName="model/regulatoryRegionsDisplayer.jsp"
                     replacesFields="regulatoryRegions"
                     placement="Regulation"
                     types="Gene"/>

    <reportdisplayer javaClass="org.flymine.web.displayer.RNAiDisplayer"
                     jspName="model/rnaiDisplayer.jsp"
                     replacesFields="rnaiResults"
                     placement="Regulation"
                     types="Gene"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.SequenceFeatureDisplayer"
                     jspName="model/sequenceFeatureDisplayer.jsp"
                     replacesFields="chromosome,chromosomeLocation,sequence,length,sequenceOntologyTerm,locations,cytoLocation"
                     placement="summary"
                     types="SequenceFeature"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.UniProtCommentsDisplayer"
                     jspName="model/uniProtCommentsDisplayer.jsp"
                     replacesFields="comments"
                     placement="Function"
                     types="Protein"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer"
                     jspName="model/publicationAnnotationsDisplayer.jsp"
                     replacesFields=""
                     placement="summary"
                     parameters="Gene,Protein,Interaction.experiment,GOAnnotation.evidence"
                     types="Publication"/>

    <!-- currently only works with classes with publications collection -->
    <reportdisplayer javaClass="org.intermine.bio.web.displayer.PublicationCountsDisplayer"
                     jspName="model/publicationCountsDisplayer.jsp"
                     replacesFields="publications"
                     placement="Genes"
                     types="BioEntity"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.MinePathwaysDisplayer"
                     jspName="model/minePathwaysDisplayer.jsp"
                     replacesFields="pathways"
                     placement="summary"
                     types="Gene"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.DiseaseDisplayer"
                     jspName="model/diseaseDisplayer.jsp"
                     replacesFields=""
                     placement="summary"
                     types="Gene"/>

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.ProteinStructureATMDisplayer"
                     jspName="model/proteinStructureATMDisplayer.jsp"
                     replacesFields="atm"
                     placement="summary"
                     types="ProteinStructure"/>

     <reportdisplayer javaClass="org.intermine.bio.web.displayer.ProteinSequenceDisplayer"
                     jspName="model/proteinSequenceDisplayer.jsp"
                     replacesFields="sequence"
                     placement="summary"
                     types="Protein"/>

  </reportdisplayers>

   <widgets>
      <graphdisplayer id="chromosome_distribution" title="Chromosome Distribution"
        domainLabel="Chromosome"
        rangeLabel="Count"
        dataSetLoader="org.intermine.bio.web.widget.ChromosomeDistributionDataSetLdr"
        link="org.intermine.bio.web.widget.ChromosomeDistributionGraphURLGenerator"
        description="Actual: number of items in this list found on each chromosome.  Expected: given the total number of items on the chromosome and the number of items in this list, the number of items expected to be found on each chromosome."
        graphType="BarChart"
        extraAttributeClass="org.intermine.bio.util.BioUtil"
        typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.SequenceFeature,org.intermine.model.bio.TransposableElementInsertionSite"
       />
<!--
      <graphdisplayer id="feature_length" title="Feature Length"
                              domainLabel="Length"
                              rangeLabel=" "
                              dataSetLoader="org.intermine.bio.web.widget.FeatureLengthDataSetLdr"
                              description="The distribution of feature lengths in this list compared to lengths of all features of this type."
                              graphType="XYLineChart"
                              extraAttributeClass="org.intermine.bio.util.BioUtil"
                              typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.Protein,org.intermine.model.bio.Exon,org.intermine.model.bio.Transcript"
/>
-->
      <graphdisplayer id="flyatlas" title="Gene Expression in the Adult Fly (FlyAtlas)" domainLabel="Tissue" rangeLabel="Up (+) or Down (-) gene count" dataSetLoader="org.flymine.web.widget.FlyAtlasDataSetLdr"
                      link="org.flymine.web.widget.FlyAtlasGraphURLGenerator"
                      description="For each tissue in the adult fly, the number of genes from this list for which the levels of expression are significantly high (Up) or low (Down) according to &lt;a href=&quot;http://www.flyatlas.org/&quot; target=&quot;_new&quot;&gt;FlyAtlas&lt;/a&gt; AffyCall."
                      typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.ProbeSet"
                      graphType="StackedBarChart" />

      <graphdisplayer id="flyfish" title="mRNA subcellular localisation (fly-FISH)" domainLabel="Stage" rangeLabel="Gene count" dataSetLoader="org.flymine.web.widget.FlyFishDataSetLdr"
                      link="org.flymine.web.widget.FlyFishGraphURLGenerator"
                      description="Expression patterns of Drosophila mRNAs at the subcellular level during early embryogenesis - data from  &lt;a href=&quot;http://fly-fish.ccbr.utoronto.ca/&quot; target=&quot;_new&quot;&gt;Fly-FISH&lt;/a&gt;.  Note that not all genes have been assayed by &lt;a href=&quot;http://fly-fish.ccbr.utoronto.ca/&quot; target=&quot;_new&quot;&gt;Fly-FISH&lt;/a&gt;."
                      typeClass="org.intermine.model.bio.Gene"
                      graphType="BarChart" />

      <graphdisplayer id="bdgp" title="BDGP expression patterns"
                      link="org.flymine.web.widget.BDGPinsituGraphURLGenerator"
                      dataSetLoader="org.flymine.web.widget.BDGPinsituDataSetLdr"
                      description="Expression patterns of Drosophila mRNAs during embryogenesis - data from  &lt;a href=&quot;http://www.fruitfly.org/cgi-bin/ex/insitu.pl&quot; target=&quot;_new&quot;&gt;BGDP&lt;/a&gt;.  Note that not all genes have been assayed by &lt;a href=&quot;http://www.fruitfly.org/cgi-bin/ex/insitu.pl&quot; target=&quot;_new&quot;&gt;BGDP&lt;/a&gt;. "
                      domainLabel="Stage"
                      rangeLabel="Gene count"
                      typeClass="org.intermine.model.bio.Gene"
                      graphType="BarChart" />

      <enrichmentwidgetdisplayer id="miranda_enrichment" title="MiRNA Enrichment"
                                 link="org.flymine.web.widget.MirandaURLQuery"
                                 dataSetLoader="org.flymine.web.widget.MirandaLdr"
                                 description="MiRNAs enriched for items in this list."
                                 label="MiRNAs"
                                 typeClass="org.intermine.model.bio.Gene" />

      <enrichmentwidgetdisplayer id="protein_features" title="UniProt Features"
                                 link="org.intermine.bio.web.widget.UniProtFeaturesURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.UniProtFeaturesLdr"
                                 label="Feature"
                                 description="UniProt features enriched for proteins in this list."
                                 typeClass="org.intermine.model.bio.Protein" />

      <enrichmentwidgetdisplayer id="uniprot_keywords" title="UniProt Keywords"
                                 link="org.intermine.bio.web.widget.UniProtKeywordsURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.UniProtKeywordsLdr"
                                 label="Keyword"
                                 description="UniProt keywords enriched for proteins in this list."
                                 typeClass="org.intermine.model.bio.Protein" />

      <enrichmentwidgetdisplayer id="go_enrichment" title="Gene Ontology Enrichment"
                                 link="org.intermine.bio.web.widget.GoStatURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.GoStatLdr"
                                 description="GO terms enriched for items in this list."
                                 label="GO Term"
                                 filters="biological_process,cellular_component,molecular_function"
                                 filterLabel="Ontology"
                                 typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.Protein"
                                 externalLink="http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" />

      <enrichmentwidgetdisplayer id="prot_dom_enrichment" title="Protein Domain Enrichment"
                                 link="org.intermine.bio.web.widget.ProteinDomainURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.ProteinDomainLdr"
                                 label="Protein Domain"
                                 description="Protein Domains enriched for items in this list."
                                 typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.Protein"
                                 externalLink="http://www.ebi.ac.uk/interpro/IEntry?ac=" />

      <enrichmentwidgetdisplayer id="publication_enrichment" title="Publication Enrichment"
                                 link="org.intermine.bio.web.widget.PublicationURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.PublicationLdr"
                                 label="Publication"
                                 description="Publications enriched for genes in this list."
                                 externalLink="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids="
                                 typeClass="org.intermine.model.bio.Gene"
                                 externalLinkLabel="PubMed:" />

      <enrichmentwidgetdisplayer id="bdgp_enrichment" title="BDGP Enrichment"
                                 link="org.flymine.web.widget.BDGPURLQuery"
                                 dataSetLoader="org.flymine.web.widget.BDGPLdr"
                                 label="Terms"
                                 description="ImaGO terms enriched for genes in this list - data from &lt;a href=&quot;http://www.fruitfly.org/cgi-bin/ex/insitu.pl&quot; target=&quot;_new&quot;&gt;BDGP&lt;/a&gt;.  Note that not all genes have been assayed by BDGP."
                                 typeClass="org.intermine.model.bio.Gene" />

      <enrichmentwidgetdisplayer id="pathway_enrichment" title="Pathway Enrichment"
                                 link="org.intermine.bio.web.widget.PathwayURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.PathwayLdr"
                                 label="Pathways"
                                 filters="All datasets,KEGG,Reactome"
                                 filterLabel="DataSet"
                                 description="Pathways enriched for genes in this list - data from KEGG and Reactome"
                                 typeClass="org.intermine.model.bio.Gene" />

    </widgets>
</webconfig>