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yeastgenome · May 2, 2024 · 4b71cdc · 4b71cdc
1 parent 4aea2b4
commit 4b71cdc
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Showing 2 changed files with 54 additions and 58 deletions.
diff --git a/sgd/src/main/java/org/intermine/bio/dataconversion/SgdConverter.java b/sgd/src/main/java/org/intermine/bio/dataconversion/SgdConverter.java
@@ -81,7 +81,7 @@ public class SgdConverter extends BioDBConverter {
 	private static final String H_TAXON_ID = "9606";
 	private Item organism;
 	private Map<String, String> featureMap = new HashMap();
-	private static final boolean LOCAL = true;
+	private static final boolean LOCAL = false;
 	private String licence;
 
 
@@ -151,7 +151,7 @@ public void process() throws Exception {
 		storeAlleles();
 		storeTranscripts();
 
-		if(LOCAL) {
+		if(!LOCAL) {
 
 			 processPhysicalInteractions(connection);
 			 processGeneticInteractions(connection);
@@ -377,6 +377,8 @@ private void processAlleles(Connection connection) throws SQLException,
 			String alleleNo = res.getString("allele");
 			String featureNo = res.getString("locus");
 
+			System.out.println(alleleNo + "\t"+featureNo);
+
 			Item gene = genes.get(featureNo);
 			Item allele = alleles.get(alleleNo);
 
@@ -2653,7 +2655,7 @@ private void processPhysicalInteractions(Connection connection)
 					year, issue, abbreviation, dsId, firstAuthor, dbxrefid, note);*/
 
 		}
-		System.out.println("interaction count is : " + count);
+		System.out.println("physical interaction count is : " + count);
 	}
 
 	/**
@@ -2734,6 +2736,7 @@ private void processGeneticInteractions(Connection connection)
 					year, issue, abbreviation, dsId, firstAuthor, dbxrefid, note);*/
 
 		}
+		System.out.println("genetic interaction count is : " + count);
 	}
 
 	/**
@@ -2745,11 +2748,13 @@ private void processGeneticInteractions(Connection connection)
 
 	private void processGeneticInteractionsWithAlleles(Connection connection)
 			throws SQLException, ObjectStoreException {
+
 		System.out.println("Processing Genetic Interactions with Alleles.....");
 		ResultSet res = PROCESSOR.getGeneticInteractionWithAllelesResults(connection);
+		int count = 0;
 
 		while (res.next()) {
-
+	        count++;
 			String interactionNo = res.getString("interaction_id");
 			String annotationNo = res.getString("annotation_id");
 			String allele1_id =  res.getString("allele1_id");
@@ -2818,6 +2823,7 @@ private void processGeneticInteractionsWithAlleles(Connection connection)
 			}
 
 		}
+		System.out.println("genetic allele interaction count is : " + count);
 	}
 
 	private void processPhenotypes(Connection connection) throws SQLException,

diff --git a/yeastmine-global_additions.xml b/yeastmine-global_additions.xml
@@ -1,26 +1,32 @@
 <model name="genomic" package="org.intermine.model.bio">
 
-	<class name="Allele" extends="SequenceCollection SequenceFeature" is-interface="true" term="http://purl.obolibrary.org/obo/SO:0001023">
-		<attribute name="alleleClass" type="java.lang.String"/>
-		<attribute name="alleleSgdid" type="java.lang.String"/>
-		<attribute name="description" type="java.lang.String"/>
-		<attribute name="name" type="java.lang.String"/>
-		<attribute name="aliasName" type="java.lang.String"/>
-		<reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
-		<reference name="centromere" referenced-type="Centromere" reverse-reference="alleles"/>
-		<reference name="ori" referenced-type="OriginOfReplication" reverse-reference="alleles"/>
-	</class>
-
 	<class name="ARS" extends="OriginOfReplication" is-interface="true">
 	<attribute name="geneSummary" type="java.lang.String"/>
 	<collection name="arsconsensussequences" referenced-type="ARSConsensusSequence" reverse-reference="ars"/>
 </class>
 
-<class name="ARSConsensusSequence" extends="SequenceFeature" is-interface="true">
+	<class name="ARSConsensusSequence" extends="SequenceFeature" is-interface="true">
 	<reference name="xelement" referenced-type="XElement" reverse-reference="arsconsensussequences"/>
 	<reference name="ars" referenced-type="ARS" reverse-reference="arsconsensussequences"/>
 	<reference name="yprimeelement" referenced-type="YPrimeElement" reverse-reference="arsconsensussequences"/>
 </class>
+
+<class name="Allele" extends="SequenceCollection SequenceFeature" is-interface="true" term="http://purl.obolibrary.org/obo/SO:0001023">
+		<attribute name="alleleClass" type="java.lang.String"/>
+		<attribute name="alleleSgdid" type="java.lang.String"/>
+		<attribute name="description" type="java.lang.String"/>
+		<attribute name="name" type="java.lang.String"/>
+		<attribute name="aliasName" type="java.lang.String"/>
+		<reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
+		<reference name="centromere" referenced-type="Centromere" reverse-reference="alleles"/>
+		<reference name="ori" referenced-type="OriginOfReplication" reverse-reference="alleles"/>
+	</class>
+<class name="AlleleInteraction" is-interface="true">
+		<attribute name="pvalue" type="java.lang.Float"/>
+		<attribute name="sgaScore" type="java.lang.Float"/>
+		<reference name="allele1" referenced-type="Allele"/>
+		<reference name="allele2" referenced-type="Allele"/>
+	</class>
 <class name="Annotatable" is-interface="true">
 		<attribute name="primaryIdentifier" type="java.lang.String"/>
 		<collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/>
@@ -37,7 +43,7 @@
 	<reference name="regulator" referenced-type="Gene"/>
 	<reference name="xelement" referenced-type="XElement" reverse-reference="bindingsites"/>
 </class>
-<class name="BioEntity"  extends="Annotatable" is-interface="true">
+<class name="BioEntity" extends="Annotatable" is-interface="true">
 	<attribute name="sgdAlias" type="java.lang.String"/>
 	<attribute name="symbol" type="java.lang.String"/>
 	<attribute name="name" type="java.lang.String"/>
@@ -52,8 +58,8 @@
 	<collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/>
 	<collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/>
 </class>
-<class name="BiologicalRegion" extends="SequenceFeature" is-interface="true"/>
 
+	<class name="BiologicalRegion" extends="SequenceFeature" is-interface="true"/>
 	<class name="BlockedReadingFrame" extends="ProteinCodingGene" is-interface="true">
 	<!--<attribute name="phenotypeSummary" type="java.lang.String"/>
 	<collection name="CDSs" referenced-type="CDS" reverse-reference="blockedreadingframe"/>-->
@@ -72,29 +78,30 @@
 	<reference name="type" referenced-type="OntologyTerm"/>
 	<reference name="feature" referenced-type="BioEntity"/>
 </class>
+
 	<class name="Centromere" extends="SequenceFeature" is-interface="true">
-		<collection name="alleles" referenced-type="Allele" reverse-reference="centromere"/>
+	<collection name="alleles" referenced-type="Allele" reverse-reference="centromere"/>
 	<reference name="centromereDNAElementIs" referenced-type="CentromereDNAElementI" reverse-reference="centromere"/>
 	<reference name="centromereDNAElementIIIs" referenced-type="CentromereDNAElementIII" reverse-reference="centromere"/>
 	<reference name="centromereDNAElementIIs" referenced-type="CentromereDNAElementII" reverse-reference="centromere"/>
 </class>
-
-	<class name="CentromereDNAElementI" extends="SequenceFeature" is-interface="true">
+<class name="CentromereDNAElementI" extends="SequenceFeature" is-interface="true">
 	<reference name="centromere" referenced-type="Centromere" reverse-reference="centromereDNAElementIs"/>
 </class>
+
 <class name="CentromereDNAElementII" extends="SequenceFeature" is-interface="true">
 	<reference name="centromere" referenced-type="Centromere" reverse-reference="centromereDNAElementIIs"/>
 </class>
 
 <class name="CentromereDNAElementIII" extends="SequenceFeature" is-interface="true">
 	<reference name="centromere" referenced-type="Centromere" reverse-reference="centromereDNAElementIIIs"/>
 </class>
-
 <class name="Chromosome" extends="BiologicalRegion" 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="Complement" is-interface="true">
 	<attribute name="source" type="java.lang.String"/>
 	<attribute name="direction" type="java.lang.String"/>
@@ -107,10 +114,6 @@
 	<collection name="dataSets" referenced-type="DataSet"/>
 </class>
 
-<class name="ComplexEvidence" extends="OntologyAnnotation" is-interface="true">
-	<collection name="publications" referenced-type="Publication"/>
-</class>
-
 <class name="Complex" is-interface="true">
 	<attribute name="identifier" type="java.lang.String"/>
 	<attribute name="accession" type="java.lang.String"/>
@@ -126,6 +129,9 @@
 	<collection name="publications" referenced-type="Publication"/>
 </class>
 
+<class name="ComplexEvidence" extends="OntologyAnnotation" is-interface="true">
+	<collection name="publications" referenced-type="Publication"/>
+</class>
 <class name="CrossReference" is-interface="true">
 	<attribute name="dbxreftype" type="java.lang.String"/>
 	<attribute name="identifier" type="java.lang.String"/>
@@ -164,14 +170,14 @@
 </class>
 <class name="DiseaseAnnotation" extends="OntologyAnnotation" is-interface="true">
 	</class>
-<class name="DiseaseEvidence"  extends="OntologyEvidence" is-interface="true">
+<class name="DiseaseEvidence" extends="OntologyEvidence" is-interface="true">
 		<collection name="with" referenced-type="BioEntity"/>
 		<attribute name="withText" type="java.lang.String"/>
 		<attribute name="annotType" type="java.lang.String"/>
 		<reference name="code" referenced-type="DiseaseEvidenceCode"/>
 		<collection name="publications" referenced-type="Publication"/>
 	</class>
-<class name="DiseaseEvidenceCode"  extends="OntologyAnnotationEvidenceCode" is-interface="true">
+<class name="DiseaseEvidenceCode" extends="OntologyAnnotationEvidenceCode" is-interface="true">
 		<attribute name="code" type="java.lang.String"/>
 </class>
 <class name="ECOTerm" extends="OntologyTerm" is-interface="true"/>
@@ -266,19 +272,9 @@
 	<attribute name="includeGene" type="java.lang.Boolean"/>
 	<reference name="gene" referenced-type="Gene" reverse-reference="flankingRegions"/>
 </class>
+
 <class name="GeneGroup" extends="SequenceFeature" is-interface="true"/>
-<!--<class name="Homologue" is-interface="true">
-	<attribute name="source" type="java.lang.String"/>
-	<attribute name="type" type="java.lang.String"/>
-	<attribute name="bootstrapScore" type="java.lang.Integer"/>
-	<reference name="gene" referenced-type="Gene" reverse-reference="homologues"/>
-	<reference name="publication" referenced-type="Publication"/>
-	<reference name="homologue" referenced-type="Gene"/>
-	<collection name="evidence" referenced-type="OrthologueEvidence"/>
-	<collection name="crossReferences" referenced-type="CrossReference"/>
-	<collection name="dataSets" referenced-type="DataSet"/>
-</class>-->
-	<class name="Homologue" is-interface="true">
+<class name="Homologue" is-interface="true">
 		<attribute name="source" type="java.lang.String"/>
 		<attribute name="type" type="java.lang.String"/>
 		<attribute name="algorithms" type="java.lang.String"/>
@@ -299,15 +295,15 @@
 <class name="InteinEncodingRegion" extends="Gene" is-interface="true">
 	<reference name="orf" referenced-type="ORF" reverse-reference="inteinencodingregions"/>
 </class>
+
 <class name="Interaction" is-interface="true">
 	<reference name="participant1" referenced-type="BioEntity" reverse-reference="interactions"/>
 	<reference name="participant2" referenced-type="BioEntity"/>
 	<reference name="complex" referenced-type="Complex"/>
 	<collection name="details" referenced-type="InteractionDetail" reverse-reference="interaction"/>
 	<collection name="alleleinteractions" referenced-type="AlleleInteraction"/>
 </class>
-
-<class name="InteractionDetail" is-interface="true">
+	<class name="InteractionDetail" is-interface="true">
 	<attribute name="phenotype" type="java.lang.String"/>
 	<attribute name="role2" type="java.lang.String"/>
 	<attribute name="type" type="java.lang.String"/>
@@ -326,12 +322,6 @@
 	<collection name="allInteractors" referenced-type="Interactor"/>
 	<collection name="dataSets" referenced-type="DataSet"/>
 </class>
-	<class name="AlleleInteraction" is-interface="true">
-		<attribute name="pvalue" type="java.lang.Float"/>
-		<attribute name="sgaScore" type="java.lang.Float"/>
-		<reference name="allele1" referenced-type="Allele"/>
-		<reference name="allele2" referenced-type="Allele"/>
-	</class>
 <class name="InteractionExperiment" is-interface="true">
 	<attribute name="description" type="java.lang.String"/>
 	<attribute name="hostOrganism" type="java.lang.String"/>
@@ -443,11 +433,6 @@
 	<collection name="evidence" referenced-type="OntologyEvidence"/>
 </class>
 
-	<class name="OntologyEvidence" is-interface="true">
-		<reference name="code" referenced-type="OntologyAnnotationEvidenceCode"/>
-		<collection name="publications" referenced-type="Publication"/>
-	</class>
-
 	<class name="OntologyAnnotationEvidenceCode" is-interface="true">
 		<attribute name="code" type="java.lang.String"/>
 		<attribute name="withText" type="java.lang.String"/>
@@ -456,6 +441,11 @@
 		<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="OntologyRelation" is-interface="true">
 	<attribute name="redundant" type="java.lang.Boolean"/>
@@ -512,7 +502,7 @@
 <class name="PathwaySummary" is-interface="true">
 	<attribute name="summaryType" type="java.lang.String"/>
 	<attribute name="text" type="java.lang.String"/>
-	<collection name="publications" referenced-type="Publication" />
+	<collection name="publications" referenced-type="Publication"/>
 </class>
 <class name="Phenotype" is-interface="true">
 	<attribute name="mutantType" type="java.lang.String"/>
@@ -652,9 +642,7 @@
 	<!--<collection name="CDSs" referenced-type="CDS" reverse-reference="pseudogene"/>-->
 	<collection name="plus1translationalframeshifts" referenced-type="Plus1TranslationalFrameshift" reverse-reference="pseudogene"/>
 </class>
-	<class name="RecombinationEnhancer" extends="Gene" is-interface="true">
-	</class>
-<class name="Publication" is-interface="true">
+	<class name="Publication" is-interface="true">
 	<attribute name="year" type="java.lang.Integer"/>
 	<attribute name="citation" type="java.lang.String"/>
 	<attribute name="issue" type="java.lang.String"/>
@@ -684,11 +672,13 @@
 	<collection name="literatureTopics" referenced-type="LiteratureTopic"/>
 	<collection name="genes" referenced-type="Gene" reverse-reference="publicationAnnotations"/>
 </class>
-
 <class name="RNA" extends="BioEntity" is-interface="true"/>
 
 <class name="RRNAGene" extends="NcRNAGene" is-interface="true"/>
 
+<class name="RecombinationEnhancer" extends="Gene" is-interface="true">
+	</class>
+
 <class name="RegulationEvidence" extends="OntologyAnnotation" is-interface="true">
 	<collection name="publications" referenced-type="Publication"/>
 </class>