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| Line 1: |
Line 1: |
| − | <model name="genomic" package="org.intermine.model.bio">
| + | {{delete| reason }} |
| − | <class name="DatabaseReference" is-interface="true">
| |
| − | <attribute name="identifier" type="java.lang.String"/>
| |
| − | <reference name="subject" referenced-type="Publication" reverse-reference="crossReferences"/>
| |
| − | <reference name="source" referenced-type="DataSource"/>
| |
| − | </class>
| |
| − | <class name="DataSource" is-interface="true">
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <attribute name="url" type="java.lang.String"/>
| |
| − | <attribute name="description" type="java.lang.String"/>
| |
| − | <collection name="dataSets" referenced-type="DataSet" reverse-reference="dataSource"/>
| |
| − | </class>
| |
| − | <class name="ChromosomalDuplication" extends="ChromosomeStructureVariation" is-interface="true"></class>
| |
| − | <class name="ReversePrimer" extends="Primer" is-interface="true"></class>
| |
| − | <class name="SequenceCollection" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="IntergenicRegion" extends="SequenceFeature" is-interface="true">
| |
| − | <collection name="adjacentGenes" referenced-type="Gene"/>
| |
| − | </class>
| |
| − | <class name="SnoRNA" extends="NcRNA" is-interface="true"></class>
| |
| − | <class name="Exon" extends="SequenceFeature" is-interface="true">
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="exons"/>
| |
| − | <collection name="transcripts" referenced-type="Transcript" reverse-reference="exons"/>
| |
| − | </class>
| |
| − | <class name="MiRNA" extends="NcRNA" is-interface="true"></class>
| |
| − | <class name="NaturalTransposableElement" extends="TransposableElement" is-interface="true"></class>
| |
| − | <class name="CRM" extends="RegulatoryRegion" is-interface="true">
| |
| − | <collection name="TFBindingSites" referenced-type="TFBindingSite" reverse-reference="CRM"/>
| |
| − | </class>
| |
| − | <class name="NcRNA" extends="Transcript" is-interface="true"></class>
| |
| − | <class name="Oligo" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="SNP" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="Protein" extends="BioEntity" is-interface="true">
| |
| − | <attribute name="molecularWeight" type="java.lang.Float"/>
| |
| − | <attribute name="md5checksum" type="java.lang.String"/>
| |
| − | <attribute name="length" type="java.lang.Integer"/>
| |
| − | <attribute name="geneName" type="java.lang.String"/>
| |
| − | <attribute name="primaryAccession" type="java.lang.String"/>
| |
| − | <reference name="sequence" referenced-type="Sequence"/>
| |
| − | <collection name="CDSs" referenced-type="CDS" reverse-reference="protein"/>
| |
| − | <collection name="genes" referenced-type="Gene" reverse-reference="proteins"/>
| |
| − | <collection name="transcripts" referenced-type="Transcript" reverse-reference="protein"/>
| |
| − | </class>
| |
| − | <class name="ExpressionPattern" is-interface="true">
| |
| − | <attribute name="subcellularLocalization" type="java.lang.String"/>
| |
| − | <attribute name="primaryIdentifier" type="java.lang.String"/>
| |
| − | <attribute name="pattern" type="java.lang.String"/>
| |
| − | <attribute name="reporterGene" type="java.lang.String"/>
| |
| − | <attribute name="remark" type="java.lang.String"/>
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="expressionPatterns"/>
| |
| − | <collection name="GOTerms" referenced-type="OntologyTerm"/>
| |
| − | <collection name="anatomyTerms" referenced-type="AnatomyTerm"/>
| |
| − | <collection name="lifeStages" referenced-type="LifeStage" reverse-reference="expressionPatterns"/>
| |
| − | </class>
| |
| − | <class name="EST" extends="Oligo" is-interface="true">
| |
| − | <collection name="overlappingESTSets" referenced-type="OverlappingESTSet" reverse-reference="ESTs"/>
| |
| − | </class>
| |
| − | <class name="Primer" extends="Oligo" is-interface="true"></class>
| |
| − | <class name="ChromosomalTranslocation" extends="ChromosomeStructureVariation" is-interface="true"></class>
| |
| − | <class name="Enhancer" extends="CRM" is-interface="true"></class>
| |
| − | <class name="GOAnnotation" extends="OntologyAnnotation" is-interface="true">
| |
| − | <attribute name="annotationExtension" type="java.lang.String"/>
| |
| − | <collection name="evidence" referenced-type="GOEvidence"/>
| |
| − | </class>
| |
| − | <class name="RRNA" extends="NcRNA" is-interface="true"></class>
| |
| − | <class name="ChromosomalInversion" extends="ChromosomeStructureVariation" is-interface="true"></class>
| |
| − | <class name="Phenotype" extends="OntologyTerm" is-interface="true">
| |
| − | <collection name="children" referenced-type="OntologyTerm"/>
| |
| − | <collection name="observedIn" referenced-type="BioEntity" reverse-reference="phenotypesObserved"/>
| |
| − | <collection name="notObservedIn" referenced-type="BioEntity" reverse-reference="phenotypesNotObserved"/>
| |
| − | </class>
| |
| − | <class name="DataSet" is-interface="true">
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <attribute name="version" type="java.lang.String"/>
| |
| − | <attribute name="url" type="java.lang.String"/>
| |
| − | <attribute name="description" type="java.lang.String"/>
| |
| − | <reference name="dataSource" referenced-type="DataSource" reverse-reference="dataSets"/>
| |
| − | <collection name="bioEntities" referenced-type="BioEntity" reverse-reference="dataSets"/>
| |
| − | </class>
| |
| − | <class name="Gene" extends="SequenceFeature" is-interface="true">
| |
| − | <attribute name="briefDescription" type="java.lang.String"/>
| |
| − | <attribute name="operon" type="java.lang.String"/>
| |
| − | <attribute name="description" type="java.lang.String"/>
| |
| − | <reference name="referenceAllele" referenced-type="Allele"/>
| |
| − | <reference name="downstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
| |
| − | <reference name="upstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
| |
| − | <collection name="expressionClusters" referenced-type="ExpressionCluster" reverse-reference="genes"/>
| |
| − | <collection name="regulatoryRegions" referenced-type="RegulatoryRegion" reverse-reference="gene"/>
| |
| − | <collection name="goAnnotation" referenced-type="GOAnnotation"/>
| |
| − | <collection name="transcripts" referenced-type="Transcript" reverse-reference="gene"/>
| |
| − | <collection name="CDSs" referenced-type="CDS" reverse-reference="gene"/>
| |
| − | <collection name="flankingRegions" referenced-type="GeneFlankingRegion" reverse-reference="gene"/>
| |
| − | <collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
| |
| − | <collection name="UTRs" referenced-type="UTR" reverse-reference="gene"/>
| |
| − | <collection name="exons" referenced-type="Exon" reverse-reference="gene"/>
| |
| − | <collection name="expressionPatterns" referenced-type="ExpressionPattern" reverse-reference="gene"/>
| |
| − | <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
| |
| − | <collection name="introns" referenced-type="Intron" reverse-reference="genes"/>
| |
| − | <collection name="strains" referenced-type="Strain" reverse-reference="gene"/>
| |
| − | </class>
| |
| − | <class name="Transcript" extends="SequenceFeature" is-interface="true">
| |
| − | <reference name="protein" referenced-type="Protein" reverse-reference="transcripts"/>
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="transcripts"/>
| |
| − | <collection name="introns" referenced-type="Intron" reverse-reference="transcripts"/>
| |
| − | <collection name="UTRs" referenced-type="UTR" reverse-reference="transcripts"/>
| |
| − | <collection name="exons" referenced-type="Exon" reverse-reference="transcripts"/>
| |
| − | <collection name="CDSs" referenced-type="CDS" reverse-reference="transcripts"/>
| |
| − | </class>
| |
| − | <class name="Sequence" is-interface="true">
| |
| − | <attribute name="md5checksum" type="java.lang.String"/>
| |
| − | <attribute name="length" type="int"/>
| |
| − | <attribute name="residues" type="org.intermine.objectstore.query.ClobAccess"/>
| |
| − | </class>
| |
| − | <class name="OntologyTermSynonym" is-interface="true">
| |
| − | <attribute name="type" type="java.lang.String"/>
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | </class>
| |
| − | <class name="ForwardPrimer" extends="Primer" is-interface="true"></class>
| |
| − | <class name="PCRProduct" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="GOTerm" extends="OntologyTerm" is-interface="true"></class>
| |
| − | <class name="MicroarrayOligo" extends="Oligo" is-interface="true"></class>
| |
| − | <class name="TRNA" extends="NcRNA" is-interface="true"></class>
| |
| − | <class name="GOEvidenceCode" is-interface="true">
| |
| − | <attribute name="code" type="java.lang.String"/>
| |
| − | </class>
| |
| − | <class name="CDS" extends="SequenceFeature" is-interface="true">
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="CDSs"/>
| |
| − | <reference name="protein" referenced-type="Protein" reverse-reference="CDSs"/>
| |
| − | <collection name="transcripts" referenced-type="Transcript" reverse-reference="CDSs"/>
| |
| − | </class>
| |
| − | <class name="SOTerm" extends="OntologyTerm" is-interface="true"></class>
| |
| − | <class name="MRNA" extends="Transcript" is-interface="true"></class>
| |
| − | <class name="MeshTerm" is-interface="true">
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <collection name="publications" referenced-type="Publication" reverse-reference="meshTerms"/>
| |
| − | </class>
| |
| − | <class name="GOEvidence" is-interface="true">
| |
| − | <attribute name="withText" type="java.lang.String"/>
| |
| − | <reference name="code" referenced-type="GOEvidenceCode"/>
| |
| − | <collection name="publications" referenced-type="Publication"/>
| |
| − | <collection name="with" referenced-type="BioEntity"/>
| |
| − | </class>
| |
| − | <class name="TransposableElement" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="Comment" is-interface="true">
| |
| − | <attribute name="type" type="java.lang.String"/>
| |
| − | <attribute name="description" type="java.lang.String"/>
| |
| − | </class>
| |
| − | <class name="ChromosomeStructureVariation" extends="SequenceCollection" is-interface="true"></class>
| |
| − | <class name="RegulatoryRegion" extends="SequenceFeature" is-interface="true">
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="regulatoryRegions"/>
| |
| − | </class>
| |
| − | <class name="TransposableElementInsertionSite" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="UTR" extends="SequenceFeature" is-interface="true">
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="UTRs"/>
| |
| − | <collection name="transcripts" referenced-type="Transcript" reverse-reference="UTRs"/>
| |
| − | </class>
| |
| − | <class name="ChromosomalDeletion" extends="ChromosomeStructureVariation" is-interface="true"></class>
| |
| − | <class name="OverlappingESTSet" extends="SequenceFeature" is-interface="true">
| |
| − | <collection name="ESTs" referenced-type="EST" reverse-reference="overlappingESTSets"/>
| |
| − | </class>
| |
| − | <class name="Synonym" is-interface="true">
| |
| − | <attribute name="value" type="java.lang.String"/>
| |
| − | <reference name="subject" referenced-type="BioEntity" reverse-reference="synonyms"/>
| |
| − | <collection name="dataSets" referenced-type="DataSet"/>
| |
| − | </class>
| |
| − | <class name="Allele" extends="SequenceCollection" is-interface="true">
| |
| − | <attribute name="method" type="java.lang.String"/>
| |
| − | <attribute name="naturalVariant" type="java.lang.String"/>
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
| |
| − | </class>
| |
| − | <class name="PointMutation" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="GeneFlankingRegion" extends="SequenceFeature" is-interface="true">
| |
| − | <attribute name="includeGene" type="java.lang.Boolean"/>
| |
| − | <attribute name="distance" type="java.lang.String"/>
| |
| − | <attribute name="direction" type="java.lang.String"/>
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="flankingRegions"/>
| |
| − | </class>
| |
| − | <class name="ThreePrimeUTR" extends="UTR" is-interface="true"></class>
| |
| − | <class name="ChromosomeBand" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="Organism" is-interface="true">
| |
| − | <attribute name="taxonId" type="java.lang.Integer"/>
| |
| − | <attribute name="shortName" type="java.lang.String"/>
| |
| − | <attribute name="genus" type="java.lang.String"/>
| |
| − | <attribute name="species" type="java.lang.String"/>
| |
| − | <attribute name="commonName" type="java.lang.String"/>
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | </class>
| |
| − | <class name="OntologyTerm" is-interface="true">
| |
| − | <attribute name="identifier" type="java.lang.String"/>
| |
| − | <attribute name="obsolete" type="java.lang.Boolean"/>
| |
| − | <attribute name="namespace" type="java.lang.String"/>
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <attribute name="description" type="java.lang.String"/>
| |
| − | <reference name="ontology" referenced-type="Ontology"/>
| |
| − | <collection name="relations" referenced-type="OntologyRelation"/>
| |
| − | <collection name="synonyms" referenced-type="OntologyTermSynonym"/>
| |
| − | <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="ontologyTerm"/>
| |
| − | <collection name="parents" referenced-type="OntologyTerm"/>
| |
| − | <collection name="dataSets" referenced-type="DataSet"/>
| |
| − | <collection name="crossReferences" referenced-type="OntologyTerm"/>
| |
| − | </class>
| |
| − | <class name="Intron" extends="SequenceFeature" is-interface="true">
| |
| − | <collection name="transcripts" referenced-type="Transcript" reverse-reference="introns"/>
| |
| − | <collection name="genes" referenced-type="Gene" reverse-reference="introns"/>
| |
| − | </class>
| |
| − | <class name="GoldenPathFragment" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="CDNAClone" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="AnatomyTerm" is-interface="true">
| |
| − | <attribute name="primaryIdentifier" type="java.lang.String"/>
| |
| − | <attribute name="definition" type="java.lang.String"/>
| |
| − | <attribute name="synonym" type="java.lang.String"/>
| |
| − | <collection name="parents" referenced-type="AnatomyTerm"/>
| |
| − | <collection name="children" referenced-type="AnatomyTerm"/>
| |
| − | <collection name="attributeOf" referenced-type="ExpressionPattern"/>
| |
| − | <collection name="lifeStages" referenced-type="LifeStage" reverse-reference="anatomyTerms"/>
| |
| − | </class>
| |
| − | <class name="Publication" is-interface="true">
| |
| − | <attribute name="pages" type="java.lang.String"/>
| |
| − | <attribute name="year" type="java.lang.Integer"/>
| |
| − | <attribute name="volume" type="java.lang.String"/>
| |
| − | <attribute name="issue" type="java.lang.String"/>
| |
| − | <attribute name="month" type="java.lang.String"/>
| |
| − | <attribute name="pubMedId" type="java.lang.String"/>
| |
| − | <attribute name="doi" type="java.lang.String"/>
| |
| − | <attribute name="journal" type="java.lang.String"/>
| |
| − | <attribute name="title" type="java.lang.String"/>
| |
| − | <attribute name="firstAuthor" type="java.lang.String"/>
| |
| − | <attribute name="abstractText" type="java.lang.String"/>
| |
| − | <collection name="meshTerms" referenced-type="MeshTerm" reverse-reference="publications"/>
| |
| − | <collection name="bioEntities" referenced-type="BioEntity" reverse-reference="publications"/>
| |
| − | <collection name="crossReferences" referenced-type="DatabaseReference" reverse-reference="subject"/>
| |
| − | <collection name="authors" referenced-type="Author" reverse-reference="publications"/>
| |
| − | </class>
| |
| − | <class name="CloneInsertEnd" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="FivePrimeUTR" extends="UTR" is-interface="true"></class>
| |
| − | <class name="ChromosomalTransposition" extends="ChromosomeStructureVariation" is-interface="true"></class>
| |
| − | <class name="SequenceFeature" extends="BioEntity" is-interface="true">
| |
| − | <attribute name="length" type="java.lang.Integer"/>
| |
| − | <attribute name="scoreType" type="java.lang.String"/>
| |
| − | <attribute name="score" type="java.lang.Double"/>
| |
| − | <reference name="chromosome" referenced-type="Chromosome"/>
| |
| − | <reference name="chromosomeLocation" referenced-type="Location"/>
| |
| − | <reference name="sequence" referenced-type="Sequence"/>
| |
| − | <reference name="sequenceOntologyTerm" referenced-type="SOTerm"/>
| |
| − | <collection name="overlappingFeatures" referenced-type="SequenceFeature"/>
| |
| − | </class>
| |
| − | <class name="OntologyAnnotation" is-interface="true">
| |
| − | <attribute name="qualifier" type="java.lang.String"/>
| |
| − | <reference name="ontologyTerm" referenced-type="OntologyTerm" reverse-reference="ontologyAnnotations"/>
| |
| − | <reference name="subject" referenced-type="BioEntity" reverse-reference="ontologyAnnotations"/>
| |
| − | <collection name="dataSets" referenced-type="DataSet"/>
| |
| − | <collection name="publications" referenced-type="Publication"/>
| |
| − | </class>
| |
| − | <class name="OntologyRelation" is-interface="true">
| |
| − | <attribute name="relationship" type="java.lang.String"/>
| |
| − | <attribute name="redundant" type="java.lang.Boolean"/>
| |
| − | <attribute name="direct" type="java.lang.Boolean"/>
| |
| − | <reference name="childTerm" referenced-type="OntologyTerm"/>
| |
| − | <reference name="parentTerm" referenced-type="OntologyTerm"/>
| |
| − | </class>
| |
| − | <class name="Strain" extends="SequenceFeature" is-interface="true">
| |
| − | <reference name="gene" referenced-type="Gene" reverse-reference="strains"/>
| |
| − | </class>
| |
| − | <class name="SequenceVariant" is-interface="true">
| |
| − | <collection name="genes" referenced-type="Gene"/>
| |
| − | </class>
| |
| − | <class name="TFBindingSite" extends="BindingSite RegulatoryRegion" is-interface="true">
| |
| − | <reference name="CRM" referenced-type="CRM" reverse-reference="TFBindingSites"/>
| |
| − | </class>
| |
| − | <class name="ExpressionCluster" is-interface="true">
| |
| − | <attribute name="algorithm" type="java.lang.String"/>
| |
| − | <attribute name="primaryIdentifier" type="java.lang.String"/>
| |
| − | <attribute name="description" type="java.lang.String"/>
| |
| − | <collection name="genes" referenced-type="Gene" reverse-reference="expressionClusters"/>
| |
| − | </class>
| |
| − | <class name="SnRNA" extends="NcRNA" is-interface="true"></class>
| |
| − | <class name="LifeStage" is-interface="true">
| |
| − | <attribute name="otherName" type="java.lang.String"/>
| |
| − | <attribute name="publicName" type="java.lang.String"/>
| |
| − | <attribute name="primaryIdentifier" type="java.lang.String"/>
| |
| − | <attribute name="definition" type="java.lang.String"/>
| |
| − | <attribute name="remark" type="java.lang.String"/>
| |
| − | <collection name="containedIn" referenced-type="LifeStage"/>
| |
| − | <collection name="precededBy" referenced-type="LifeStage"/>
| |
| − | <collection name="followedBy" referenced-type="LifeStage"/>
| |
| − | <collection name="subStages" referenced-type="LifeStage"/>
| |
| − | <collection name="anatomyTerms" referenced-type="AnatomyTerm" reverse-reference="lifeStages"/>
| |
| − | <collection name="expressionPatterns" referenced-type="ExpressionPattern" reverse-reference="lifeStages"/>
| |
| − | </class>
| |
| − | <class name="BioEntity" is-interface="true">
| |
| − | <attribute name="secondaryIdentifier" type="java.lang.String"/>
| |
| − | <attribute name="symbol" type="java.lang.String"/>
| |
| − | <attribute name="primaryIdentifier" type="java.lang.String"/>
| |
| − | <attribute name="lastUpdated" type="java.util.Date"/>
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <reference name="organism" referenced-type="Organism"/>
| |
| − | <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/>
| |
| − | <collection name="publications" referenced-type="Publication" reverse-reference="bioEntities"/>
| |
| − | <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
| |
| − | <collection name="phenotypesObserved" referenced-type="Phenotype" reverse-reference="observedIn"/>
| |
| − | <collection name="phenotypesNotObserved" referenced-type="Phenotype" reverse-reference="notObservedIn"/>
| |
| − | <collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/>
| |
| − | <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/>
| |
| − | <collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/>
| |
| − | <collection name="locations" referenced-type="Location" reverse-reference="feature"/>
| |
| − | </class>
| |
| − | <class name="Chromosome" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="Location" is-interface="true">
| |
| − | <attribute name="start" type="java.lang.Integer"/>
| |
| − | <attribute name="end" type="java.lang.Integer"/>
| |
| − | <attribute name="strand" type="java.lang.String"/>
| |
| − | <reference name="feature" referenced-type="BioEntity" reverse-reference="locations"/>
| |
| − | <reference name="locatedOn" referenced-type="BioEntity" reverse-reference="locatedFeatures"/>
| |
| − | <collection name="dataSets" referenced-type="DataSet"/>
| |
| − | </class>
| |
| − | <class name="CrossReference" is-interface="true">
| |
| − | <attribute name="identifier" type="java.lang.String"/>
| |
| − | <reference name="subject" referenced-type="BioEntity" reverse-reference="crossReferences"/>
| |
| − | <reference name="source" referenced-type="DataSource"/>
| |
| − | </class>
| |
| − | <class name="BindingSite" extends="SequenceFeature" is-interface="true"></class>
| |
| − | <class name="Author" is-interface="true">
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <attribute name="lastName" type="java.lang.String"/>
| |
| − | <attribute name="initials" type="java.lang.String"/>
| |
| − | <attribute name="firstName" type="java.lang.String"/>
| |
| − | <collection name="publications" referenced-type="Publication" reverse-reference="authors"/>
| |
| − | </class>
| |
| − | <class name="Ontology" is-interface="true">
| |
| − | <attribute name="name" type="java.lang.String"/>
| |
| − | <attribute name="url" type="java.lang.String"/>
| |
| − | </class>
| |
| − | </model>
| |
