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<?xml version="1.0"?>
<model name="genomic" package="org.intermine.model.bio">
<class name="Annotatable" is-interface="true">
<attribute name="primaryIdentifier" type="java.lang.String"/>
<collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
<collection name="publications" referenced-type="Publication" reverse-reference="entities"/>
</class>
<class name="Author" is-interface="true">
<attribute name="firstName" type="java.lang.String"/>
<attribute name="lastName" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="initials" type="java.lang.String"/>
<collection name="publications" referenced-type="Publication" reverse-reference="authors"/>
</class>
<class name="BioEntity" is-interface="true" extends="Annotatable">
<attribute name="secondaryIdentifier" type="java.lang.String"/>
<attribute name="symbol" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<reference name="organism" referenced-type="Organism"/>
<collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/>
<collection name="locations" referenced-type="Location" reverse-reference="feature" />
<collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
<collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/>
<collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/>
<collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/>
</class>
<class name="Chromosome" extends="SequenceFeature" is-interface="true"/>
<class name="Comment" is-interface="true">
<attribute name="description" type="java.lang.String"/>
<attribute name="type" type="java.lang.String"/>
</class>
<class name="CrossReference" is-interface="true">
<attribute name="identifier" type="java.lang.String"/>
<reference name="source" referenced-type="DataSource"/>
<reference name="subject" referenced-type="BioEntity" reverse-reference="crossReferences" />
</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="publications" referenced-type="Publication"/>
<collection name="dataSets" referenced-type="DataSet" reverse-reference="dataSource"/>
</class>
<class name="DataSet" is-interface="true">
<attribute name="name" type="java.lang.String"/>
<attribute name="url" type="java.lang.String"/>
<attribute name="description" type="java.lang.String"/>
<attribute name="version" type="java.lang.String"/>
<reference name="dataSource" referenced-type="DataSource" reverse-reference="dataSets"/>
<reference name="publication" referenced-type="Publication"/>
<collection name="bioEntities" referenced-type="BioEntity" reverse-reference="dataSets"/>
</class>
<class name="Gene" extends="SequenceFeature" is-interface="true">
<attribute name="description" type="java.lang.String"/>
<attribute name="briefDescription" type="java.lang.String"/>
<collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
</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="MeshTerm" is-interface="true">
<attribute name="name" type="java.lang.String"/>
<collection name="publications" referenced-type="Publication" reverse-reference="meshTerms"/>
</class>
<class name="Ontology" is-interface="true">
<attribute name="name" type="java.lang.String"/>
<attribute name="url" type="java.lang.String"/>
</class>
<class name="OntologyAnnotationEvidenceCode" is-interface="true">
<attribute name="code" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="url" type="java.lang.String"/>
</class>
<class name="OntologyEvidence" is-interface="true">
<reference name="code" referenced-type="OntologyAnnotationEvidenceCode"/>
<collection name="publications" referenced-type="Publication"/>
</class>
<class name="OntologyTerm" is-interface="true">
<attribute name="identifier" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="description" type="java.lang.String"/>
<attribute name="namespace" type="java.lang.String"/>
<attribute name="obsolete" type="java.lang.Boolean"/>
<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="OntologyRelation" is-interface="true">
<reference name="parentTerm" referenced-type="OntologyTerm" />
<reference name="childTerm" referenced-type="OntologyTerm" />
<attribute name="relationship" type="java.lang.String"/>
<attribute name="direct" type="java.lang.Boolean"/>
<attribute name="redundant" type="java.lang.Boolean"/>
</class>
<class name="OntologyAnnotation" is-interface="true">
<attribute name="qualifier" type="java.lang.String"/>
<reference name="subject" referenced-type="Annotatable" reverse-reference="ontologyAnnotations"/>
<reference name="ontologyTerm" referenced-type="OntologyTerm" reverse-reference="ontologyAnnotations"/>
<collection name="dataSets" referenced-type="DataSet" />
<collection name="evidence" referenced-type="OntologyEvidence"/>
</class>
<class name="OntologyTermSynonym" is-interface="true">
<attribute name="name" type="java.lang.String"/>
<attribute name="type" type="java.lang.String"/>
</class>
<class name="Organism" is-interface="true">
<attribute name="genus" type="java.lang.String"/>
<attribute name="taxonId" type="java.lang.String"/>
<attribute name="species" type="java.lang.String"/>
<attribute name="commonName" type="java.lang.String"/>
<attribute name="shortName" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="annotationVersion" type="java.lang.String"/>
<attribute name="assemblyVersion" type="java.lang.String"/>
<collection name="strains" referenced-type="Strain"/>
</class>
<class name="Protein" extends="BioEntity" is-interface="true">
<attribute name="md5checksum" type="java.lang.String"/>
<attribute name="primaryAccession" type="java.lang.String"/>
<attribute name="length" type="java.lang.Integer"/>
<attribute name="molecularWeight" type="java.lang.Double"/>
<reference name="sequence" referenced-type="Sequence"/>
<collection name="genes" referenced-type="Gene" reverse-reference="proteins"/>
</class>
<class name="Publication" is-interface="true">
<attribute name="title" type="java.lang.String"/>
<attribute name="doi" type="java.lang.String"/>
<attribute name="issue" type="java.lang.String"/>
<attribute name="pubMedId" type="java.lang.String"/>
<attribute name="pages" type="java.lang.String"/>
<attribute name="month" type="java.lang.String"/>
<attribute name="year" type="java.lang.Integer"/>
<attribute name="volume" type="java.lang.String"/>
<attribute name="journal" type="java.lang.String"/>
<attribute name="firstAuthor" type="java.lang.String"/>
<attribute name="abstractText" type="java.lang.String"/>
<collection name="authors" referenced-type="Author" reverse-reference="publications" />
<collection name="entities" referenced-type="Annotatable" reverse-reference="publications" />
<collection name="meshTerms" referenced-type="MeshTerm" reverse-reference="publications" />
</class>
<class name="SOTerm" extends="OntologyTerm" is-interface="true"/>
<class name="Sequence" is-interface="true">
<attribute name="residues" type="org.intermine.objectstore.query.ClobAccess"/>
<attribute name="length" type="int"/>
<attribute name="md5checksum" type="java.lang.String"/>
</class>
<class name="SequenceCollection" extends="BioEntity" is-interface="true">
<reference name="sequenceOntologyTerm" referenced-type="SOTerm"/>
</class>
<class name="SequenceFeature" extends="BioEntity" is-interface="true">
<attribute name="score" type="java.lang.Double"/>
<attribute name="scoreType" type="java.lang.String"/>
<attribute name="length" type="java.lang.Integer"/>
<reference name="sequence" referenced-type="Sequence"/>
<reference name="chromosome" referenced-type="Chromosome" />
<reference name="chromosomeLocation" referenced-type="Location" />
<reference name="sequenceOntologyTerm" referenced-type="SOTerm"/>
<reference name="strain" referenced-type="Strain" reverse-reference="features" />
<collection name="overlappingFeatures" referenced-type="SequenceFeature" />
<collection name="childFeatures" referenced-type="SequenceFeature" />
</class>
<class name="Strain" extends="BioEntity" is-interface="true">
<attribute name="annotationVersion" type="java.lang.String"/>
<attribute name="assemblyVersion" type="java.lang.String"/>
<collection name="features" referenced-type="SequenceFeature" reverse-reference="strain" />
</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="SyntenyBlock" is-interface="true">
<collection name="syntenicRegions" referenced-type="SyntenicRegion" reverse-reference="syntenyBlock" />
<collection name="dataSets" referenced-type="DataSet" />
<collection name="publications" referenced-type="Publication" />
</class>
<class name="SyntenicRegion" extends="SequenceFeature" is-interface="true">
<reference name="syntenyBlock" referenced-type="SyntenyBlock" reverse-reference="syntenicRegions"/>
</class>
</model>