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<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="description"/>
</fields>
</class>
<class className="org.intermine.model.bio.Complex">
<headerconfig>
<titles>
<title mainTitles="identifier|name"/>
</titles>
</headerconfig>
<fields>
<fieldconfig fieldExpr="identifier"/>
<fieldconfig fieldExpr="name"/>
</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"/>
<fieldconfig fieldExpr="name"/>
</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.jpeg"
/>
</customlinks>
</headerconfig>
<inlinelist>
<table path="synonyms.value" showInHeader="true" lineLength="100" />
<table path="probeSets.primaryIdentifier" showLinksToObjects="true" />
</inlinelist>
<fields>
<fieldconfig fieldExpr="secondaryIdentifier"/>
<fieldconfig fieldExpr="symbol"/>
<fieldconfig fieldExpr="primaryIdentifier"/>
<fieldconfig fieldExpr="organism.name"/>
</fields>
<bagdisplayers>
<displayer src="friendlyMineLinkDisplayer.tile" showOnLeft="false" />
<displayer src="esynListDisplayer.tile" showOnLeft="true" />
</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="participant1.primaryIdentifier" />
<fieldconfig fieldExpr="participant2.primaryIdentifier" />
</fields>
</class>
<class className="org.intermine.model.bio.InteractionDetail">
<fields>
<fieldconfig fieldExpr="type"/>
<fieldconfig fieldExpr="relationshipType"/>
<fieldconfig fieldExpr="name"/>
<fieldconfig fieldExpr="role1"/>
<fieldconfig fieldExpr="role2"/>
</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" label="Organism Name"/>
</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.RNAiScreen">
<headerconfig>
<titles>
<title mainTitles="name" />
</titles>
</headerconfig>
<fields>
<fieldconfig fieldExpr="name"/>
<fieldconfig fieldExpr="publication.title"/>
</fields>
</class>
<class className="org.intermine.model.bio.RNAiResult">
<fields>
<fieldconfig fieldExpr="rnaiScreen.name" label="Screen" />
<fieldconfig fieldExpr="gene.symbol" label="Gene" />
<fieldconfig fieldExpr="phenotype"/>
<fieldconfig fieldExpr="score"/>
<fieldconfig fieldExpr="conditions"/>
<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.RNASeqResult">
<fields>
<fieldconfig fieldExpr="stage"/>
<fieldconfig fieldExpr="expressionScore"/>
<fieldconfig fieldExpr="expressionLevel"/>
</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,ontologyAnnotation"
placement="Function"
types="Gene"/>
<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': ['Panther 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"/>
<!-- update to new model
<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,InteractionDetail.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.EsynDisplayer"
jspName="model/esynDisplayer.jsp"
replacesFields=""
placement="Interactions"
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"/>
<reportdisplayer javaClass="org.intermine.bio.web.displayer.FlyBaseExpressionDisplayer"
jspName="model/flybaseExpressionDisplayer.jsp"
replacesFields="rnaSeqResults"
placement="Expression"
types="Gene"/>
<reportdisplayer javaClass="org.intermine.bio.web.displayer.PathwayDescriptionDisplayer"
jspName="model/pathwayDescriptionDisplayer.jsp"
showImmediately="true"
replacesFields="description"
placement="summary"
types="Pathway"/>
</reportdisplayers>
<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="SequenceFeature"
typeClass="SequenceFeature"
categoryPath="chromosome.primaryIdentifier"
seriesLabels="Actual,Expected"
seriesPath="ActualExpectedCriteria"
constraints="organism.name=[Organism]"
views="primaryIdentifier, symbol, secondaryIdentifier, organism.name, chromosome.primaryIdentifier,
chromosomeLocation.start, chromosomeLocation.end, chromosomeLocation.strand"/>
<graphdisplayer id="flyatlas_for_gene"
title="Gene Expression in the Fly (FlyAtlas)"
description="For each tissue in the 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."
graphType="BarChart"
domainLabel="Tissue"
rangeLabel="Up (+) or Down (-) gene count"
startClass="FlyAtlasResult"
typeClass="Gene"
listPath="FlyAtlasResult.genes"
categoryPath="tissue.name"
seriesPath="affyCall"
seriesValues="Up,Down"
seriesLabels="Up,Down"
constraints="presentCall != 0,
presentCall != 1,
presentCall != 2"
views="genes.secondaryIdentifier,genes.symbol,genes.name,genes.organism.name,
tissue.name,enrichment,affyCall,mRNASignal,mRNASignalSEM,presentCall"/>
<graphdisplayer id="flyatlas_for_probeset"
title="Gene Expression in Fly Tissues (FlyAtlas Data)"
description="For each tissue, 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."
graphType="BarChart"
domainLabel="Tissue"
rangeLabel="Up (+) or Down (-) gene count"
startClass="FlyAtlasResult"
typeClass="ProbeSet"
listPath="FlyAtlasResult.material"
categoryPath="tissue.name"
seriesPath="affyCall"
seriesValues="Up,Down"
seriesLabels="Up,Down"
constraints="presentCall != 0,
presentCall != 1,
presentCall != 2"
views="material.secondaryIdentifier,material.symbol,material.name,material.organism.name,
tissue.name,enrichment,affyCall,mRNASignal,mRNASignalSEM,presentCall"/>
<graphdisplayer id="flyfish"
title="mRNA subcellular localisation (fly-FISH)"
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;."
graphType="ColumnChart"
domainLabel="Stage"
rangeLabel="Gene count"
startClass="Gene"
typeClass="Gene"
listPath=""
categoryPath="mRNAExpressionResults.stageRange"
seriesPath="mRNAExpressionResults.expressed"
seriesValues="true,false"
seriesLabels="Expressed,Not Expressed"
constraints="mRNAExpressionResults.dataSet.name=fly-Fish data set"
views="primaryIdentifier,secondaryIdentifier,name,organism.name,
mRNAExpressionResults.stageRange,mRNAExpressionResults.expressed"/>
<!-- <graphdisplayer id="mouse_human_orthologue_pair"
title="Mouse-human orthologue pair"
description="dots would be where there is a mouse-human orthologue pair "
graphType="ScatterChart"
domainLabel="Chromosome location for humans"
rangeLabel="Chromosome location for mouses"
startClass="Gene"
typeClass="Gene"
categoryPath="organism.name"
seriesPath="homologues.homologue.organism.name"
seriesValues=""
seriesLabels=""
constraints="organism.name=Homo sapiens,homologues.homologue.organism.name=Mus musculus"
views="primaryIdentifier,secondaryIdentifier,name,organism.name"/> -->
<graphdisplayer id="bdgp"
title="BDGP expression patterns"
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;. "
graphType="ColumnChart"
domainLabel="Stage"
rangeLabel="Gene count"
startClass="Gene"
typeClass="Gene"
listPath=""
categoryPath="mRNAExpressionResults.stageRange"
seriesPath="mRNAExpressionResults.expressed"
seriesValues="true,false"
seriesLabels="Expressed,Not Expressed"
constraints="mRNAExpressionResults.dataSet.name=BDGP in situ data set"
views="primaryIdentifier,secondaryIdentifier,name,organism.name,
mRNAExpressionResults.stageRange,mRNAExpressionResults.expressed"/>
<enrichmentwidgetdisplayer id="miranda_enrichment"
title="MiRNA Enrichment"
description="MiRNAs enriched for items in this list."
label="MiRNAs"
startClass="Gene"
startClassDisplay="symbol"
enrich="transcripts[MRNA].miRNAinteractions.mirnagene.symbol"
typeClass="Gene"
views="symbol,transcripts[MRNA].miRNAinteractions.mirnagene.symbol"/>
<enrichmentwidgetdisplayer id="protein_features"
title="UniProt Features"
description="UniProt features enriched for proteins in this list."
label="Feature"
startClass="Protein"
startClassDisplay="primaryIdentifier"
enrich="features.type"
enrichIdentifier="features.type"
constraints="organism.name=[list]"
typeClass="Protein"
views="primaryIdentifier, primaryAccession, organism.name,
features.feature.name, features.type,features.description,
features.begin, features.end"/>
<enrichmentwidgetdisplayer id="uniprot_keywords"
title="UniProt Keywords"
description="UniProt keywords enriched for proteins in this list."
label="Keyword"
startClass="Protein"
startClassDisplay="primaryIdentifier"
enrich="keywords.name"
constraints="organism.name=[list]"
typeClass="Protein"
views="primaryIdentifier, primaryAccession, organism.name,
keywords.name, keywords.description"/>
<enrichmentwidgetdisplayer id="go_enrichment_for_gene"
title="Gene Ontology Enrichment"
description="GO terms enriched for items in this list."
label="GO Term"
filterLabel="Ontology"
filters="biological_process,cellular_component,molecular_function"
startClass="Gene"
startClassDisplay="primaryIdentifier"
enrich="goAnnotation.ontologyTerm.parents.name"
enrichIdentifier="goAnnotation.ontologyTerm.parents.identifier"
constraints="goAnnotation.ontologyTerm.parents.namespace=[Ontology],organism.name=[list],
primaryIdentifier != null, goAnnotation.qualifier = null,
goAnnotation.ontologyTerm.parents.identifier != go:0008150,
goAnnotation.ontologyTerm.parents.identifier != go:0003674,
goAnnotation.ontologyTerm.parents.identifier != go:0005575"
typeClass="Gene"
views="secondaryIdentifier,symbol,primaryIdentifier,organism.name,
goAnnotation.ontologyTerm.identifier, goAnnotation.ontologyTerm.name,
goAnnotation.ontologyTerm.parents.identifier,goAnnotation.ontologyTerm.parents.name"
externalLink="http://amigo.geneontology.org/amigo/term/"
correctionCoefficient="org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient"/>
<enrichmentwidgetdisplayer id="prot_dom_enrichment_for_gene"
title="Protein Domain Enrichment"
description="Protein Domains enriched for items in this list."
label="Protein Domain"
startClass="Gene"
startClassDisplay="primaryIdentifier"
enrich="proteins.proteinDomainRegions.proteinDomain.name"
enrichIdentifier="proteins.proteinDomainRegions.proteinDomain.primaryIdentifier"
constraints="organism.name=[list]"
typeClass="Gene"
views="secondaryIdentifier,symbol,primaryIdentifier,organism.name,
proteins.proteinDomainRegions.proteinDomain.primaryIdentifier,proteins.proteinDomainRegions.proteinDomain.name"
externalLink="http://www.ebi.ac.uk/interpro/IEntry?ac="/>
<enrichmentwidgetdisplayer id="prot_dom_enrichment_for_protein"
title="Protein Domain Enrichment"
description="Protein Domains enriched for items in this list."
label="Protein Domain"
startClass="Protein"
startClassDisplay="primaryIdentifier"
enrich="proteinDomainRegions.proteinDomain.name"
enrichIdentifier="proteinDomainRegions.proteinDomain.primaryIdentifier"
constraints="organism.name=[list]"
typeClass="Protein"
views="primaryIdentifier,organism.name,proteinDomainRegions.proteinDomain.primaryIdentifier,
proteinDomainRegions.proteinDomain.name"
externalLink="http://www.ebi.ac.uk/interpro/entry/"/>
<enrichmentwidgetdisplayer id="bdgp_enrichment"
title="BDGP Enrichment"
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."
label="Terms"
startClass="Gene"
startClassDisplay="primaryIdentifier"
enrich="mRNAExpressionResults.mRNAExpressionTerms[MRNAExpressionTerm].name"
constraints="mRNAExpressionResults.expressed = true, mRNAExpressionResults.dataSet.name = BDGP in situ data set"
typeClass="Gene"
views="secondaryIdentifier, symbol, organism.name, mRNAExpressionResults.stageRange,
mRNAExpressionResults.mRNAExpressionTerms.name, mRNAExpressionResults.dataSet.name"
constraintsForView="mRNAExpressionResults.expressed = true, mRNAExpressionResults.dataSet.name = BDGP in situ data set"/>
<enrichmentwidgetdisplayer id="publication_enrichment"
title="Publication Enrichment"
description="Publications enriched for genes in this list."
label="Publication"
startClass="Gene"
startClassDisplay="primaryIdentifier"
enrich="publications.title"
enrichIdentifier="publications.pubMedId"
constraints="organism.name=[list],primaryIdentifier != null"
typeClass="Gene"
views="secondaryIdentifier, symbol, organism.name,
publications.title, publications.firstAuthor,
publications.journal, publications.year, publications.pubMedId"
externalLink="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids="/>
<enrichmentwidgetdisplayer id="pathway_enrichment"
title="Pathway Enrichment"
description="Pathways enriched for genes in this list - data from KEGG and Reactome"
label="Pathways"
filterLabel="DataSet"
filters="All,KEGG pathways data set,Reactome data set"
startClass="Gene"
startClassDisplay="primaryIdentifier"
enrich="pathways.name"
enrichIdentifier="pathways.identifier"
constraints="pathways.dataSets.name=[DataSet],organism.taxonId=[list], primaryIdentifier != null"
typeClass="Gene"
views="secondaryIdentifier, symbol, organism.name, pathways.identifier, pathways.name, pathways.dataSets.name"/>
<bagtabledisplayer id="orthologues" title="Orthologues" pathStrings="Gene.homologues[type!=paralogue].homologue.organism"
description="Counts of genes in list with orthologues."
displayFields="name"
exportField="primaryIdentifier"
typeClass="Gene"
columnTitle="Genes"
views="secondaryIdentifier, symbol, organism.shortName,
homologues.homologue.primaryIdentifier,
homologues.homologue.symbol,
homologues.homologue.organism.shortName,
homologues.type"/>
</widgets>
</webconfig>