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justinccdev/gist:3ff33dea6bf11456c0d1d36d9772b35d

Created October 19, 2017 14:17
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synbiomine genomic model with terms
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gistfile1.txt
<model name="genomic" package="org.intermine.model.bio">
<class name="Allele" extends="SequenceCollection" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0001023" is-interface="true">
<reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
</class>
<class name="ChromosomalDuplication" extends="ChromosomeStructureVariation" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:1000037" is-interface="true"></class>
<class name="ThreePrimeUTR" extends="UTR" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000205" is-interface="true"></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"/>
</class>
<class name="Transcript" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000673" is-interface="true">
<reference name="gene" referenced-type="Gene" reverse-reference="transcripts"/>
<reference name="protein" referenced-type="Protein" reverse-reference="transcripts"/>
<collection name="terminators" referenced-type="Terminator" reverse-reference="transcript"/>
<collection name="introns" referenced-type="Intron" reverse-reference="transcripts"/>
<collection name="exons" referenced-type="Exon" reverse-reference="transcripts"/>
<collection name="ribosomeEntrySites" referenced-type="RibosomeEntrySite" reverse-reference="transcript"/>
<collection name="CDSs" referenced-type="CDS" reverse-reference="transcript"/>
<collection name="UTRs" referenced-type="UTR" reverse-reference="transcripts"/>
</class>
<class name="PointMutation" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:1000008" is-interface="true"></class>
<class name="SnRNA" extends="NcRNA" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000274" is-interface="true"></class>
<class name="GoldenPathFragment" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000468" is-interface="true"></class>
<class name="Ontology" is-interface="true">
<attribute name="url" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
</class>
<class name="EST" extends="Oligo" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000345" is-interface="true">
<collection name="overlappingESTSets" referenced-type="OverlappingESTSet" reverse-reference="ESTs"/>
</class>
<class name="Enhancer" extends="CRM" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000165" is-interface="true"></class>
<class name="SequenceVariant" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0001060" is-interface="true">
<collection name="genes" referenced-type="Gene"/>
</class>
<class name="RegulatoryRegion" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0005836" is-interface="true">
<reference name="gene" referenced-type="Gene" reverse-reference="regulatoryRegions"/>
</class>
<class name="ChromosomeBand" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000341" is-interface="true"></class>
<class name="ReversePrimer" extends="Primer" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000132" is-interface="true"></class>
<class name="TransposableElementInsertionSite" extends="SequenceFeature" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000368" is-interface="true"></class>
<class name="CRM" extends="RegulatoryRegion" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000727" is-interface="true">
<collection name="TFBindingSites" referenced-type="TFBindingSite" reverse-reference="CRM"/>
</class>
<class name="OverlappingESTSet" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0001262" is-interface="true">
<collection name="ESTs" referenced-type="EST" reverse-reference="overlappingESTSets"/>
</class>
<class name="DataSource" is-interface="true">
<attribute name="description" type="java.lang.String"/>
<attribute name="url" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<collection name="publications" referenced-type="Publication"/>
<collection name="dataSets" referenced-type="DataSet" reverse-reference="dataSource"/>
</class>
<class name="Oligo" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000696" is-interface="true"></class>
<class name="BindingSite" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000409" is-interface="true"></class>
<class name="MicroarrayOligo" extends="Oligo" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000328" is-interface="true"></class>
<class name="ChromosomalTranslocation" extends="ChromosomeStructureVariation" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:1000044" is-interface="true"></class>
<class name="Location" is-interface="true">
<attribute name="strand" type="java.lang.String"/>
<attribute name="start" type="java.lang.Integer"/>
<attribute name="end" type="java.lang.Integer"/>
<reference name="locatedOn" referenced-type="BioEntity" reverse-reference="locatedFeatures"/>
<reference name="feature" referenced-type="BioEntity" reverse-reference="locations"/>
<collection name="dataSets" referenced-type="DataSet"/>
</class>
<class name="SnoRNA" extends="NcRNA" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000275" is-interface="true"></class>
<class name="Intron" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000188" is-interface="true">
<collection name="transcripts" referenced-type="Transcript" reverse-reference="introns"/>
<collection name="genes" referenced-type="Gene" reverse-reference="introns"/>
</class>
<class name="Terminator" extends="RegulatoryRegion" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000141" is-interface="true">
<reference name="transcript" referenced-type="Transcript" reverse-reference="terminators"/>
</class>
<class name="ChromosomeStructureVariation" extends="SequenceCollection" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:1000183" is-interface="true"></class>
<class name="Primer" extends="Oligo" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000112" is-interface="true"></class>
<class name="NaturalTransposableElement" extends="TransposableElement" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000797" is-interface="true"></class>
<class name="Minus10Signal" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000175" is-interface="true"></class>
<class name="MRNA" extends="Transcript" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000234" is-interface="true"></class>
<class name="MiRNA" extends="NcRNA" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000276" is-interface="true"></class>
<class name="ForwardPrimer" extends="Primer" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000121" is-interface="true"></class>
<class name="Plasmid" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000155" is-interface="true"></class>
<class name="OntologyRelation" is-interface="true">
<attribute name="redundant" type="java.lang.Boolean"/>
<attribute name="direct" type="java.lang.Boolean"/>
<attribute name="relationship" type="java.lang.String"/>
<reference name="parentTerm" referenced-type="OntologyTerm"/>
<reference name="childTerm" referenced-type="OntologyTerm"/>
</class>
<class name="ChromosomalInversion" extends="ChromosomeStructureVariation" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:1000030" is-interface="true"></class>
<class name="UTR" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000203" is-interface="true">
<reference name="gene" referenced-type="Gene" reverse-reference="UTRs"/>
<collection name="transcripts" referenced-type="Transcript" reverse-reference="UTRs"/>
</class>
<class name="NcRNA" extends="Transcript" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000655" is-interface="true"></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="TFBindingSite" extends="BindingSite RegulatoryRegion" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000235" is-interface="true">
<reference name="CRM" referenced-type="CRM" reverse-reference="TFBindingSites"/>
</class>
<class name="RRNA" extends="NcRNA" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000252" is-interface="true"></class>
<class name="STS" extends="Oligo" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000331" is-interface="true"></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="Region" extends="SequenceFeature" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000001" is-interface="true"></class>
<class name="OntologyTerm" is-interface="true">
<attribute name="identifier" type="java.lang.String"/>
<attribute name="description" type="java.lang.String"/>
<attribute name="obsolete" type="java.lang.Boolean"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="namespace" 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="Gene" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000704" is-interface="true">
<attribute name="briefDescription" type="java.lang.String"/>
<attribute name="description" type="java.lang.String"/>
...
</class>
<class name="Protein" extends="BioEntity" term="http://semanticscience.org/resource/SIO_010043.rdf" is-interface="true">
<attribute name="md5checksum" type="java.lang.String"/>
<attribute name="primaryAccession" type="java.lang.String"/>
...
</class>
<class name="Organism" is-interface="true">
<attribute name="species" type="java.lang.String"/>
<attribute name="genus" type="java.lang.String"/>
<attribute name="taxonId" type="java.lang.Integer"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="commonName" type="java.lang.String"/>
<attribute name="shortName" type="java.lang.String"/>
</class>
<class name="TransposableElement" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000101" is-interface="true"></class>
<class name="Publication" is-interface="true">
<attribute name="year" type="java.lang.Integer"/>
<attribute name="issue" type="java.lang.String"/>
<attribute name="title" type="java.lang.String"/>
<attribute name="pages" type="java.lang.String"/>
<attribute name="doi" type="java.lang.String"/>
<attribute name="volume" type="java.lang.String"/>
<attribute name="journal" type="java.lang.String"/>
<attribute name="firstAuthor" type="java.lang.String"/>
<attribute name="month" type="java.lang.String"/>
<attribute name="abstractText" type="java.lang.String"/>
<attribute name="pubMedId" type="java.lang.String"/>
<collection name="authors" referenced-type="Author" reverse-reference="publications"/>
<collection name="bioEntities" referenced-type="BioEntity" reverse-reference="publications"/>
<collection name="meshTerms" referenced-type="MeshTerm" reverse-reference="publications"/>
</class>
<class name="GeneFlankingRegion" extends="SequenceFeature" is-interface="true">
<attribute name="direction" type="java.lang.String"/>
<attribute name="distance" type="java.lang.String"/>
<attribute name="includeGene" type="java.lang.Boolean"/>
<reference name="gene" referenced-type="Gene" reverse-reference="flankingRegions"/>
</class>
<class name="ChromosomalDeletion" extends="ChromosomeStructureVariation" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:1000029" is-interface="true"></class>
<class name="BioEntity" is-interface="true">
<attribute name="symbol" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<attribute name="primaryIdentifier" type="java.lang.String"/>
<attribute name="secondaryIdentifier" 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="publications" referenced-type="Publication" reverse-reference="bioEntities"/>
<collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/>
</class>
<class name="SequenceFeature" extends="BioEntity" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000110" 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="sequenceOntologyTerm" referenced-type="SOTerm"/>
<reference name="chromosomeLocation" referenced-type="Location"/>
<reference name="sequence" referenced-type="Sequence"/>
<reference name="chromosome" referenced-type="Chromosome"/>
<collection name="overlappingFeatures" referenced-type="SequenceFeature"/>
<collection name="childFeatures" referenced-type="SequenceFeature"/>
</class>
<class name="RibosomeEntrySite" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000139" is-interface="true">
<reference name="transcript" referenced-type="Transcript" reverse-reference="ribosomeEntrySites"/>
</class>
<class name="RepeatRegion" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000657" 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="Comment" is-interface="true">
<attribute name="description" type="java.lang.String"/>
<attribute name="type" type="java.lang.String"/>
</class>
<class name="SOTerm" extends="OntologyTerm" is-interface="true"></class>
<class name="IntergenicRegion" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000605" is-interface="true">
<collection name="adjacentGenes" referenced-type="Gene"/>
</class>
<class name="PCRProduct" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000006" is-interface="true"></class>
<class name="OntologyTermSynonym" is-interface="true">
<attribute name="type" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
</class>
<class name="Chromosome" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000340" is-interface="true"></class>
<class name="CDNAClone" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000317" is-interface="true"></class>
<class name="FivePrimeUTR" extends="UTR" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000204" is-interface="true"></class>
<class name="CDS" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000316" is-interface="true">
<reference name="gene" referenced-type="Gene" reverse-reference="CDSs"/>
<reference name="transcript" referenced-type="Transcript" reverse-reference="CDSs"/>
<reference name="protein" referenced-type="Protein" reverse-reference="CDSs"/>
</class>
<class name="Exon" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000147" is-interface="true">
<reference name="gene" referenced-type="Gene" reverse-reference="exons"/>
<collection name="transcripts" referenced-type="Transcript" reverse-reference="exons"/>
</class>
<class name="Operon" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000178" is-interface="true"></class>
<class name="TmRNA" extends="NcRNA" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000584" is-interface="true"></class>
<class name="SequenceCollection" extends="BioEntity" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0001260" is-interface="true">
<reference name="sequenceOntologyTerm" referenced-type="SOTerm"/>
</class>
<class name="Sequence" is-interface="true">
<attribute name="md5checksum" type="java.lang.String"/>
<attribute name="residues" type="org.intermine.objectstore.query.ClobAccess"/>
<attribute name="length" type="int"/>
</class>
<class name="DataSet" is-interface="true">
<attribute name="description" type="java.lang.String"/>
<attribute name="url" type="java.lang.String"/>
<attribute name="name" 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="ChromosomalTransposition" extends="ChromosomeStructureVariation" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000453" is-interface="true"></class>
<class name="TRNA" extends="NcRNA" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000253" is-interface="true"></class>
<class name="Author" is-interface="true">
<attribute name="firstName" type="java.lang.String"/>
<attribute name="initials" type="java.lang.String"/>
<attribute name="lastName" type="java.lang.String"/>
<attribute name="name" type="java.lang.String"/>
<collection name="publications" referenced-type="Publication" reverse-reference="authors"/>
</class>
<class name="Minus35Signal" extends="Region" term="http://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:0000176" is-interface="true"></class>
</model>
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