webconfig-model.xml 9.37 KB
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<webconfig>
  <class className="org.intermine.model.bio.Author">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </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.Chromosome">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="organism.name"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Comment">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="description"/>
    </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.Gene">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="organism.shortName" />
    </fields>
  </class>

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  <class className="org.intermine.model.bio.Location">
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    <fields>
      <fieldconfig fieldExpr="feature.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="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="organism.name"/>
    </fields>
  </class>

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

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

  <class className="org.intermine.model.bio.OntologyRelation">
    <fields>
      <fieldconfig fieldExpr="relationship"/>
      <fieldconfig fieldExpr="parentTerm.identifier"/>
      <fieldconfig fieldExpr="childTerm.identifier"/>
    </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>
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        <title mainTitles="name"/>
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      </titles>
    </headerconfig>
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="taxonId" />
    </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"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
  </class>

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

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

  <class className="org.intermine.model.bio.Transcript">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false"/>
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
    </fields>
  </class>

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  <class className="org.intermine.model.bio.Homologue">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="homologue.primaryIdentifier" label="DB identifier"/>
      <fieldconfig fieldExpr="homologue.symbol" label="Symbol"/>
      <fieldconfig fieldExpr="homologue.length" label="Length"/>
      <fieldconfig fieldExpr="homologue.chromosome.primaryIdentifier" label="DB identifier"/>
      <fieldconfig fieldExpr="homologue.organism.shortName" label="Short Name"/>
    </fields>
  </class>


  <!-- exporters -->
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  <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>

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

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

    <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="" placement="Proteins" types="Gene,Protein"/>
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  </reportdisplayers>

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  <!-- widgets -->
  <widgets>
    <graphdisplayer id="chromosome_distribution_for_gene" title="Chromosome Distribution" 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="ColumnChart" rangeLabel="Count" domainLabel="Chromosome" filterLabel="Organism" filters="organism.name=[list]" startClass="Gene" typeClass="Gene" categoryPath="chromosome.primaryIdentifier" seriesLabels="Actual,Expected" seriesPath="ActualExpectedCriteria" constraints="organism.name=[Organism]" views="primaryIdentifier, symbol, secondaryIdentifier, organism.name, chromosome.primaryIdentifier,
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                             chromosomeLocation.start, chromosomeLocation.end, chromosomeLocation.strand"/>

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  </widgets>
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</webconfig>