save

cglabrata-homologs/build/resources/main/cglabrata-homologs_keys.properties

@@ -1,7 +1,7 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
-Gene.key=secondaryIdentifier
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
+Gene.key_secondaryidentifier=secondaryIdentifier

cglabrata-homologs/src/main/resources/cglabrata-homologs_keys.properties

@@ -1,7 +1,7 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
-Gene.key=secondaryIdentifier
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
+Gene.key_secondaryidentifier=secondaryIdentifier

cgob-homologs/src/main/resources/cgob-homologs_keys.properties

@@ -1,7 +1,7 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
-Gene.key=secondaryIdentifier
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
+Gene.key_secondaryidentifier=secondaryIdentifier

disease/src/main/resources/disease_keys.properties

@@ -5,8 +5,8 @@ Protein.key_primaryacc=primaryAccession
 Organism.key_taxonid=taxonId
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
-Ontology.key_title=name
+Ontology.key_name=name
 DiseaseEvidenceCode.key_code=code
 Publication.key_pubmed=pubMedId
-DataSet.key_title=name
+DataSet.key_name=name
 DataSource.key_name=name

do/resources/do_keys.properties

@@ -1,6 +1,6 @@
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
-Ontology.key_title=name
-OntologyTermSynonym.key = name, type
-DataSet.key_title=name
+Ontology.key_name=name
+OntologyTermSynonym.key_name_type =name, type
+DataSet.key_name=name
 DataSource.key_name=name

eco/resources/eco_keys.properties

@@ -1,9 +1,9 @@
-DataSet.key = name
-DataSource.key = name
-Organism.key = taxonId
+DataSet.key_name = name
+DataSource.key_name = name
+Organism.key_taxonid = taxonId
 OntologyTerm.key_name_ontology=name, ontology
-Ontology.key_title=name
+Ontology.key_name=name
 OntologyTerm.key_identifier=identifier
-SOTerm.key = name, ontology
-Ontology.key = name
-Publication.key = pubMedId
+SOTerm.key_name_ontology = name, ontology
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId

ensembl-compara/src/main/resources/ensembl-compara_keys.properties

@@ -1,8 +1,9 @@
-DataSet.key=name
-DataSource.key=name
-SOTerm.key=name, ontology
-Organism.key=taxonId
-Ontology.key=name
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+OntologyTerm.key_name_ontology=name, ontology
+Ontology.key_name=name
 Gene.key_primaryidentifier=primaryIdentifier
-Gene.key_symbol=symbol, organism
-Gene.key_secondaryidentifier = secondaryIdentifier, organism
+Gene.key_symbol_org=symbol, organism
+Gene.key_secondaryidentifier = secondaryIdentifier, organism

fungi-homologs/src/main/resources/fungi-homologs_keys.properties

@@ -1,7 +1,7 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
-Gene.key = secondaryIdentifier
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology= name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
+Gene.key_secondaryidentifier = secondaryIdentifier

go-annotation-db/src/main/resources/go-annotation-db_keys.properties

@@ -5,8 +5,8 @@ Protein.key_primaryacc=primaryAccession
 Organism.key_taxonid=taxonId
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
-Ontology.key_title=name
+Ontology.key_name=name
 GOEvidenceCode.key_code=code
 Publication.key_pubmed=pubMedId
-DataSet.key_title=name
+DataSet.key_name=name
 DataSource.key_name=name

go-slim/resources/go-slim_keys.properties

@@ -1,6 +1,6 @@
 OntologyTerm.key_identifier=identifier
-DataSet.key_title=name
+DataSet.key_name=name
 OntologyTerm.key_name_ontology=name, ontology
-OntologyTermSynonym.key = name, type
-DataSet.key_title=name
+OntologyTermSynonym.key_name_type = name, type
+DataSet.key_name=name
 DataSource.key_name=name

go/resources/go_keys.properties

@@ -1,6 +1,6 @@
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
-Ontology.key_title=name
-OntologyTermSynonym.key = name, type
-DataSet.key_title=name
+Ontology.key_name=name
+OntologyTermSynonym.key_name_type=name,type
+DataSet.key_name=name
 DataSource.key_name=name

homolog-genes/src/main/resources/homolog-genes_keys.properties

@@ -1,7 +1,7 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
 Gene.key_primaryidentifier=primaryIdentifier

homologene/src/main/resources/homologene_keys.properties

@@ -4,5 +4,5 @@ SOTerm.key_name_ontology = name, ontology
 Organism.key_taxonid = taxonId
 Ontology.key_name = name
 Publication.key_pubmed = pubMedId
-Gene.key_primaryidentifier=primaryIdentifier
+Gene.key_primaryidentifier=primaryIdentifier, organism
 Gene.key_symbol_org=symbol, organism

mgi-identifiers/src/main/resources/mgi-identifiers_keys.properties

@@ -1,8 +1,8 @@
-DataSet.key_title=name
+DataSet.key_name=name
 DataSource.key_name=name
-Gene.key_symbol=symbol, organism
+Gene.key_symbol_org=symbol, organism
 Gene.key_primaryidentifier=primaryIdentifier
 Gene.key_secondaryidentifier=secondaryIdentifier
-Organism.key_taxon=taxonId
-SOTerm.key=name, ontology
-Ontology.key_title=name
+Organism.key_taxonid=taxonId
+SOTerm.key_name_ontology=name, ontology
+Ontology.key_name=name

ncbi-gene/src/main/resources/ncbi-gene_keys.properties

@@ -1,9 +1,9 @@
-DataSet.key=name
-DataSource.key=name
-SOTerm.key=name, ontology
-Ontology.key=name
-Organism.key=taxonId
-Gene.key=symbol, organism
+DataSet.key_name=name
+DataSource.key_name=name
+SOTerm.key_name_ontology=name, ontology
+Ontology.key_name=name
+Organism.key_taxonid=taxonId
+Gene.key_symbol_org=symbol, organism
 Gene.key_primaryIdentifier=primaryIdentifier
-NcRNA.key=symbol, organism
-Synonym.key_synonym=subject, value
+NcRNA.key_symbol_org=symbol, organism
+Synonym.key_synonym=subject, value

ncbi-gene/src/main/resources/ncbigene_config.properties

@@ -6,9 +6,6 @@
 # worm
 # 6239.xref=
 
-# human
-#9606.xref=Ensembl
-
 # mouse
 10090.xref=MGI
 

omim/src/main/resources/omim_keys.properties

@@ -1,10 +1,9 @@
-DataSet.key=name
-DataSource.key=name
-SOTerm.key=name, ontology
-Organism.key=taxonId
-#Gene.key_primaryIdentifier=primaryIdentifier
+DataSource.key_name=name
+DataSet.key_name=name
+SOTerm.key_name_ontology=name, ontology
+Organism.key_taxon=taxonId
 Gene.key_symbol_org=symbol, organism
 Gene.key_primaryidentifier=primaryIdentifier
-Ontology.key=name
-Publication.key=pubMedId
-Disease.key=identifier
+Ontology.key_name=name
+Publication.key_pubmed=pubMedId
+#Disease.key_primaryIdentifier=primaryIdentifier

panther/src/main/resources/panther_keys.properties

@@ -1,9 +1,9 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmedid = pubMedId
 Gene.key_primaryidentifier=primaryIdentifier
 Gene.key_secondaryidentifier=secondaryIdentifier, organism
-Gene.key_symbol=symbol, organism
+Gene.key_symbol_org=symbol, organism

pombe-homologs/src/main/resources/pombe-homologs_keys.properties

@@ -1,7 +1,7 @@
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
-Gene.key=secondaryIdentifier
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
+Gene.key_secondaryidentifier=secondaryIdentifier

psi-complexes/src/main/resources/psi-complexes_keys.properties

@@ -1,16 +1,15 @@
-DataSet.key_title=name
+DataSet.key_name=name
 DataSource.key_name=name
 Gene.key_primaryidentifier=primaryIdentifier
 Gene.key_secondaryidentifier=secondaryIdentifier
 Gene.key_symbol_org=symbol, organism
 #yes merge - kk;  no merging, I think.
 #Interaction.key_interaction=participant1, participant2
 InteractionTerm.key_identifier=identifier
-Ontology.key_title=name
+Ontology.key_name=name
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
 Organism.key_taxonid=taxonId
 Publication.key_pubmed=pubMedId
 ProteinDomain.key_identifier=primaryIdentifier
-#Protein.key_primaryacc=primaryAccession
 Protein.key_primaryidentifier=primaryIdentifier

psi-mi-ontology/resources/psi-mi-ontology_keys.properties

@@ -1,3 +1,3 @@
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
-Ontology.key_title=name
+Ontology.key_name=name

rgd-identifiers/src/main/resources/rgd-identifiers_keys.properties

@@ -1,6 +1,6 @@
-DataSet.key=name
-DataSource.key=name
-SOTerm.key=name, ontology
-Organism.key=taxonId
-Ontology.key=name
-Gene.key=primaryIdentifier
+DataSource.key_name=name
+DataSet.key_name=name
+SOTerm.key_name_ontology=name, ontology
+Organism.key_taxonid=taxonId
+Ontology.key_name=name
+Gene.key_primaryidentifier=primaryIdentifier

settings.gradle

@@ -19,7 +19,7 @@ include ':bio-source-cglabrata-homologs',
  ':bio-source-mgi-identifiers',
  ':bio-source-rgd-identifiers',
  ':bio-source-omim',
- ':bio-source-treefam',
+ ':bio-source-treefam', ':bio-source-homologene',
  ':bio-source-panther',
  ':bio-source-homologene',
  ':bio-source-ensembl-compara', ':bio-source-go-slim'
@@ -56,6 +56,7 @@ project(':bio-source-rgd-identifiers').projectDir = new File(settingsDir, './rgd
 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')
 
 

sgd-gff/src/main/resources/sgd-gff_keys.properties

@@ -1,9 +1,11 @@
 Gene.key_secondaryidentifier = secondaryIdentifier
 Chromosome.key_primaryidentifier=primaryIdentifier, organism
 BindingSite.key_primaryidentifier=primaryIdentifier
-DataSet.key = name
-DataSource.key = name
-SOTerm.key = name, ontology
-Organism.key = taxonId
-Ontology.key = name
-Publication.key = pubMedId
+DataSet.key_name = name
+DataSource.key_name = name
+SOTerm.key_name_ontology = name, ontology
+Organism.key_taxonid = taxonId
+Ontology.key_name = name
+Publication.key_pubmed = pubMedId
+Gene.key_symbol_org=symbol, organism
+

sgd/src/main/java/org/intermine/bio/dataconversion/SgdConverter.java

@@ -120,7 +120,7 @@ public void process() throws Exception {
 		processGeneChildrenLocations(connection);
 		processProteins(connection);
 
-		processAllPubs(connection);           						
+		processAllPubs(connection);
 		processPubsWithFeatures(connection); 
 
 		processProteinAbundance(connection);

sgd/src/main/resources/sgd_keys.properties

@@ -1,7 +1,7 @@
 Organism.key_taxonid=taxonId
-DataSet.key=name
-DataSource.key=name
-Publication=key_pubmed
+DataSet.key_name=name
+DataSource.key_name=name
+Publication.key_pubmed = pubMedId
 ECOTerm.key=name, ontology
 Gene.key_primaryidentifier=primaryIdentifier
 Chromosome.key_primaryidentifier=primaryIdentifier

treefam/src/main/resources/treefam_keys.properties

@@ -1,10 +1,9 @@
 Gene.key_primaryidentifier=primaryIdentifier
 Gene.key_secondaryidentifier=secondaryIdentifier, organism
-Gene.key_symbol=symbol, organism
+Gene.key_symbol_org=symbol, organism
 Organism.key_taxonid=taxonId
-DataSet.key_title=name
+DataSet.key_name=name
 DataSource.key_name=name
 OrthologueEvidenceCode.key_code=abbreviation
-SOTerm.key=name, ontology
-Ontology.key_title=name
-#Gene.key_symbol_org=symbol, organism
+SOTerm.key_name_ontology=name, ontology
+Ontology.key_name=name