ontology and evidence - mystery

build.gradle

@@ -67,7 +67,8 @@ subprojects {
     // uncomment to specify an extra additions file for your bio-sources
     // this file will be merged with the additions file for each data source
     // and included in each source JAR.
-     bioSourceDBModelConfig {
+
+    bioSourceDBModelConfig {
         globalAdditionsFile = "yeastmine-global_additions.xml"
      }
 

disease/src/main/resources/disease_additions.xml

@@ -1,7 +1,5 @@
 <?xml version="1.0"?>
-<!-- This file details any extensions needed to the data model to store data from this source, everything else is automatically generated from the model description so this is all we need to do to add to the model. -->
 
 <classes>
-    <!-- add any <class> elements here-->
 
 </classes>

go-annotation-db/src/main/java/org/intermine/bio/dataconversion/GoAnnotationDbConverter.java

@@ -205,7 +205,8 @@ public void processGOAnnotations(Connection connection) throws SQLException, Obj
 				if (allEvidenceForAnnotation == null ) { //|| !StringUtils.isEmpty(withText)
 					String goTermIdentifier = newGoTerm(goId, dataSource, dataSourceCode);
 					Evidence evidence = new Evidence(newStrEvidence, pubRefId, withText, organism,
-							dataSource, dataSourceCode); 
+							dataSource, dataSourceCode);
+					System.out.print("evidence");
 					allEvidenceForAnnotation = new LinkedHashSet<Evidence>();
 					allEvidenceForAnnotation.add(evidence);
 					goTermGeneToEvidence.put(key, allEvidenceForAnnotation);

go-annotation-db/src/main/resources/go-annotation-db_additions.xml

@@ -1,7 +1,5 @@
 <?xml version="1.0"?>
-<!-- This file details any extensions needed to the data model to store data from this source, everything else is automatically generated from the model description so this is all we need to do to add to the model. -->
 
 <classes>
-    <!-- add any <class> elements here-->
 
 </classes>

settings.gradle

@@ -6,7 +6,6 @@ include ':bio-source-cglabrata-homologs',
  ':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',
@@ -23,9 +22,7 @@ include ':bio-source-cglabrata-homologs',
  ':bio-source-treefam',
  ':bio-source-panther',
  ':bio-source-homologene',
- ':bio-source-ensembl-compara',
- ':bio-source-go',
- ':bio-source-do'
+ ':bio-source-ensembl-compara', ':bio-source-go-slim'
 
 
 
@@ -53,17 +50,13 @@ 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-go').projectDir = new File(settingsDir, './go')
-project(':bio-source-do').projectDir = new File(settingsDir, './do')
 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-ensembl-compara').projectDir = new File(settingsDir, './ensembl-compara')
-project(':bio-source-do').projectDir = new File(settingsDir, './do')
-project(':bio-source-go').projectDir = new File(settingsDir, './go')
 
 
 

sgd-complementation/src/main/resources/sgd-complementation_additions.xml

@@ -1,7 +1,4 @@
 <?xml version="1.0"?>
-<!-- This file details any extensions needed to the data model to store data from this source, everything else is automatically generated from the model description so this is all we need to do to add to the model. -->
-
 <classes>
-    <!-- add any <class> elements here>-->
 
 </classes>