Changeset 1341

Timestamp:

Jan 6, 2011, 5:33:32 PM (12 years ago)

Author:

business@…

Message:

fix for development environment to circumvent BioPortal? problems

File:

• trunk/grails-app/conf/BootStrapTemplates.groovy (modified) (1 diff)

trunk/grails-app/conf/BootStrapTemplates.groovy

@@ -21 +21 @@
         public static void initTemplateOntologies() {
                 "inserting initial ontologies".grom()
+
+                // add Species ontology which is used for a.o. the Subject domain field 'species'
+                def speciesOntology = new Ontology(
+                        name: 'NCBI organismal classification',
+                        description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',
+                        url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',
+                        versionNumber: '1.2',
+                        ncboId: '1132',
+                        ncboVersionedId: '38802'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                // add Sample>material ontology
+                def brendaOntology = new Ontology(
+                        name: 'BRENDA tissue / enzyme source',
+                        description: 'A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.',
+                        url: 'http://www.brenda-enzymes.info',
+                        versionNumber: '1.3',
+                        ncboId: '1005',
+                        ncboVersionedId: '40643'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                // add NCI ontology which is used in Mouse genotype template field
+                def nciOntology = new Ontology(
+                        name: 'NCI Thesaurus',
+                        description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.',
+                        url: 'http://ncicb.nci.nih.gov/core/EVS',
+                        versionNumber: '10.03',
+                        ncboId: '1032',
+                        ncboVersionedId: '42838'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                // add CHEBI ontology which is used for describing chemicals in e.g. events
+                def chebiOntology = new Ontology(
+                        name: 'Chemical entities of biological interest',
+                        description: 'A structured classification of chemical compounds of biological relevance.',
+                        url: 'http://www.ebi.ac.uk/chebi',
+                        versionNumber: '1.73',
+                        ncboId: '1007',
+                        ncboVersionedId: '44746'
+                ).with { if (!validate()) { errors.each { println it} } else save()}
+
+                /* These ontologies can be added dynamically, fetching the description and such from BioPortal.
+                   However, because the BioPortal REST services are currently down,
+                   added the above as a fix which allows running offline from BioPortal,
+                   and commenting out the following lines.
+
                 def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
                 def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
                 def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
-                def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)          
+                def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)
+                */
         }
+
 
         /**