Changeset 1110


Ignore:
Timestamp:
Nov 9, 2010, 6:53:25 PM (6 years ago)
Author:
work@…
Message:
  • bootstrapping tried to insert duplicate ontologies...
File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/grails-app/conf/BootStrapTemplates.groovy

    r1046 r1110  
    2020         */
    2121        public static void initTemplateOntologies() {
    22 
    23                 // add Subject>species ontology
    24                 println ".adding NCBI species ontology"
    25                 def speciesOntology = new Ontology(
    26                         name: 'NCBI organismal classification',
    27                         description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',
    28                         url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',
    29                         versionNumber: '1.2',
    30                         ncboId: '1132',
    31                         ncboVersionedId: '38802'
    32                 ).with { if (!validate()) { errors.each { println it} } else save()}
    33 
    34                 // add Sample>material ontology
    35                 println ".adding BRENDA source material ontology"
    36                 def brendaOntology = new Ontology(
    37                         name: 'BRENDA tissue / enzyme source',
    38                         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.',
    39                         url: 'http://www.brenda-enzymes.info',
    40                         versionNumber: '1.3',
    41                         ncboId: '1005',
    42                         ncboVersionedId: '40643'
    43                 ).with { if (!validate()) { errors.each { println it} } else save()}
    44 
    45                 // add NCI ontology which is used in Mouse genotype template field
    46                 def nciOntology = new Ontology(
    47                         name: 'NCI Thesaurus',
    48                         description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.',
    49                         url: 'http://ncicb.nci.nih.gov/core/EVS',
    50                         versionNumber: '10.01',
    51                         ncboId: '1032',
    52                         ncboVersionedId: '42693'
    53                 ).with { if (!validate()) { errors.each { println it} } else save()}
    54 
    55                 // add CHEBI ontology which is used in Mouse genotype template field
    56                 def chebiOntology = new Ontology(
    57                         name: 'Chemical entities of biological interest',
    58                         description: 'A structured classification of chemical compounds of biological relevance.',
    59                         url: 'http://www.ebi.ac.uk/chebi',
    60                         versionNumber: '1.68',
    61                         ncboId: '1007',
    62                         ncboVersionedId: '42878'
    63                 ).with { if (!validate()) { errors.each { println it} } else save()}
    64                
     22                def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
     23                def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
     24                def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
     25                def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)         
    6526        }
    6627
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