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yeastgenome · May 12, 2020 · 0b29a02 · 0b29a02
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Showing 14 changed files with 73 additions and 645 deletions.
diff --git a/...uild/tmp/expandedArchives/bio-model-4.0.0.jar_6hq9d1x0xascumibripq5gfvi/genomic_model.xml b/...uild/tmp/expandedArchives/bio-model-4.0.0.jar_6hq9d1x0xascumibripq5gfvi/genomic_model.xml
diff --git a/psi-complexes/build.gradle b/psi-complexes/build.gradle
diff --git a/psi-complexes/psi-complexes.properties b/psi-complexes/psi-complexes.properties
diff --git a/psi-complexes/src/main/java/org/intermine/bio/dataconversion/PsiComplexesConverter.java b/psi-complexes/src/main/java/org/intermine/bio/dataconversion/PsiComplexesConverter.java
diff --git a/psi-complexes/src/main/resources/psi-complexes_additions.xml b/psi-complexes/src/main/resources/psi-complexes_additions.xml
diff --git a/psi-complexes/src/main/resources/psi-complexes_keys.properties b/psi-complexes/src/main/resources/psi-complexes_keys.properties
diff --git a/psi-complexes/src/test/java/org/intermine/bio/dataconversion/PsiComplexesConverterTest.java b/psi-complexes/src/test/java/org/intermine/bio/dataconversion/PsiComplexesConverterTest.java
diff --git a/psi-mi-ontology/build.gradle b/psi-mi-ontology/build.gradle
diff --git a/psi-mi-ontology/psi-mi-ontology.properties b/psi-mi-ontology/psi-mi-ontology.properties
diff --git a/psi-mi-ontology/resources/psi-mi-ontology_additions.xml b/psi-mi-ontology/resources/psi-mi-ontology_additions.xml
diff --git a/psi-mi-ontology/resources/psi-mi-ontology_keys.properties b/psi-mi-ontology/resources/psi-mi-ontology_keys.properties
diff --git a/settings.gradle.old b/settings.gradle.old
@@ -0,0 +1,59 @@
+rootProject.name = 'bio-sources'
+
+include ':bio-source-cglabrata-homologs',
+ ':bio-source-cgob-homologs',
+ ':bio-source-disease',
+ ':bio-source-eco',
+ ':bio-source-fungi-homologs',
+ ':bio-source-go-annotation-db',
+        ':bio-source-go-slim',
+':bio-source-homolog-genes',
+ ':bio-source-pombe-homologs',
+ ':bio-source-sgd-complementation',
+ ':bio-source-sgd-gff-utr',
+ ':bio-source-sgd-gff',
+ ':bio-source-sgd-protein-ntermini',
+ ':bio-source-sgd-protein-properties',
+ ':bio-source-sgd',
+ ':bio-source-spell-expression',
+ ':bio-source-ncbi-gene',
+ ':bio-source-mgi-identifiers',
+ ':bio-source-rgd-identifiers',
+ ':bio-source-omim',
+ ':bio-source-treefam',
+ ':bio-source-panther',
+ ':bio-source-homologene',
+ ':bio-source-ensembl-compara',
+//':bio-source-psi-mi-ontology', ':bio-source-psi-complexes'
+
+
+
+project(':bio-source-cglabrata-homologs').projectDir = new File(settingsDir, './cglabrata-homologs')
+project(':bio-source-cgob-homologs').projectDir = new File(settingsDir, './cgob-homologs')
+project(':bio-source-disease').projectDir = new File(settingsDir, './disease')
+project(':bio-source-eco').projectDir = new File(settingsDir, './eco')
+project(':bio-source-fungi-homologs').projectDir = new File(settingsDir, './fungi-homologs')
+project(':bio-source-go-annotation-db').projectDir = new File(settingsDir, './go-annotation-db')
+project(':bio-source-go-slim').projectDir = new File(settingsDir, './go-slim')
+project(':bio-source-homolog-genes').projectDir = new File(settingsDir, './homolog-genes')
+project(':bio-source-pombe-homologs').projectDir = new File(settingsDir, './pombe-homologs')
+project(':bio-source-sgd-complementation').projectDir = new File(settingsDir, './sgd-complementation')
+project(':bio-source-sgd-gff-utr').projectDir = new File(settingsDir, './sgd-gff-utr')
+project(':bio-source-sgd-gff').projectDir = new File(settingsDir, './sgd-gff')
+project(':bio-source-sgd-protein-ntermini').projectDir = new File(settingsDir, './sgd-protein-ntermini')
+project(':bio-source-sgd-protein-properties').projectDir = new File(settingsDir, './sgd-protein-properties')
+project(':bio-source-sgd').projectDir = new File(settingsDir, './sgd')
+project(':bio-source-spell-expression').projectDir = new File(settingsDir, './spell-expression')
+project(':bio-source-ncbi-gene').projectDir = new File(settingsDir, './ncbi-gene')
+project(':bio-source-mgi-identifiers').projectDir = new File(settingsDir, './mgi-identifiers')
+project(':bio-source-rgd-identifiers').projectDir = new File(settingsDir, './rgd-identifiers')
+project(':bio-source-omim').projectDir = new File(settingsDir, './omim')
+project(':bio-source-treefam').projectDir = new File(settingsDir, './treefam')
+project(':bio-source-panther').projectDir = new File(settingsDir, './panther')
+project(':bio-source-homologene').projectDir = new File(settingsDir, './homologene')
+project(':bio-source-ensembl-compara').projectDir = new File(settingsDir, './ensembl_compara')
+//project(':bio-source-psi-mi-ontology').projectDir = new File(settingsDir, './psi-mi-ontology')
+//project(':bio-source-psi-complexes').projectDir = new File(settingsDir, './psi-complexes')
+
+
+
diff --git a/sgd/src/main/java/org/intermine/bio/dataconversion/SgdConverter.java b/sgd/src/main/java/org/intermine/bio/dataconversion/SgdConverter.java
@@ -73,7 +73,7 @@ public class SgdConverter extends BioDBConverter {
 	private static final String TAXON_ID = "4932";
 	private Item organism;
 	private Map<String, String> featureMap = new HashMap();
-	private static final boolean TEST_LOCAL = false;
+	private static final boolean TEST_LOCAL = true;
 	private String licence;
 
 
@@ -114,17 +114,17 @@ public void process() throws Exception {
 
 		processChromosomeSequences(connection);
 		processGenes(connection);
-		/*processNISS(connection);
+		processNISS(connection);
 		processAliases(connection);
 		processCrossReferences(connection);
 		processGeneLocations(connection);
 		processGeneChildrenLocations(connection);
-		processProteins(connection);*/
+		processProteins(connection);
 
 		processAllPubs(connection);
-		processPubsWithFeatures(connection); 
+		processPubsWithFeatures(connection);
 
-		/*processProteinAbundance(connection);
+		processProteinAbundance(connection);
 		processProteinHalfLife(connection);
 		processProteinDomains(connection);
 		processProteinModifications(connection);
@@ -134,7 +134,7 @@ public void process() throws Exception {
 
 		processFunctionSummary(connection);
 		processRegulation(connection);
-		processRegulationSummary(connection);*/
+		processRegulationSummary(connection);
 
 		processAllPathways(connection);
 		processGenePathways(connection);
@@ -1336,7 +1336,7 @@ private void processProteinDomains(Connection connection) throws SQLException, O
 			String method = res.getString("url_type");
 			String interpro = res.getString("interpro_id");
 
-			Item protein = proteins.get(featureNo);					
+			Item protein = proteins.get(featureNo);
 			Item pdomain = getDomain(domainMatch, domainDesc, sstart, send, runDate, method);
 			protein.addToCollection("proteinDomains", pdomain.getIdentifier());
 

diff --git a/yeastmine-global_additions.xml b/yeastmine-global_additions.xml
@@ -94,15 +94,15 @@
 	<collection name="dataSets" referenced-type="DataSet"/>
 </class>
 <class name="Complex" is-interface="true">
-	<attribute name="properties" type="java.lang.String"/>
 	<attribute name="identifier" type="java.lang.String"/>
 	<attribute name="name" type="java.lang.String"/>
 	<attribute name="systematicName" type="java.lang.String"/>
 	<attribute name="function" type="java.lang.String"/>
-	<collection name="publications" referenced-type="Publication"/>
+	<attribute name="properties" type="java.lang.String"/>
+	<collection name="dataSets" referenced-type="DataSet"/>
 	<collection name="allInteractors" referenced-type="Interactor"/>
 	<collection name="goAnnotation" referenced-type="GOAnnotation"/>
-	<collection name="dataSets" referenced-type="DataSet"/>
+	<collection name="publications" referenced-type="Publication"/>
 </class>
 <class name="CrossReference" is-interface="true">
 	<attribute name="dbxreftype" type="java.lang.String"/>
@@ -262,9 +262,9 @@
 	<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"/>
-	<reference name="participant1" referenced-type="BioEntity" reverse-reference="interactions"/>
 	<collection name="details" referenced-type="InteractionDetail" reverse-reference="interaction"/>
 </class>
 <class name="InteractionDetail" is-interface="true">
@@ -628,9 +628,11 @@
 	<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="RNA" extends="BioEntity" is-interface="true"/>
+
 <class name="RRNAGene" extends="NcRNAGene" is-interface="true"/>
+
 <class name="RegulationEvidence" extends="OntologyAnnotation" is-interface="true">
 	<collection name="publications" referenced-type="Publication"/>
 </class>