Changeset 1341


Ignore:
Timestamp:
Jan 6, 2011, 5:33:32 PM (6 years ago)
Author:
business@…
Message:

fix for development environment to circumvent BioPortal? problems

File:
1 edited

Legend:

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

    r1245 r1341  
    2121        public static void initTemplateOntologies() {
    2222                "inserting initial ontologies".grom()
     23
     24                // add Species ontology which is used for a.o. the Subject domain field 'species'
     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                def brendaOntology = new Ontology(
     36                        name: 'BRENDA tissue / enzyme source',
     37                        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.',
     38                        url: 'http://www.brenda-enzymes.info',
     39                        versionNumber: '1.3',
     40                        ncboId: '1005',
     41                        ncboVersionedId: '40643'
     42                ).with { if (!validate()) { errors.each { println it} } else save()}
     43
     44                // add NCI ontology which is used in Mouse genotype template field
     45                def nciOntology = new Ontology(
     46                        name: 'NCI Thesaurus',
     47                        description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.',
     48                        url: 'http://ncicb.nci.nih.gov/core/EVS',
     49                        versionNumber: '10.03',
     50                        ncboId: '1032',
     51                        ncboVersionedId: '42838'
     52                ).with { if (!validate()) { errors.each { println it} } else save()}
     53
     54                // add CHEBI ontology which is used for describing chemicals in e.g. events
     55                def chebiOntology = new Ontology(
     56                        name: 'Chemical entities of biological interest',
     57                        description: 'A structured classification of chemical compounds of biological relevance.',
     58                        url: 'http://www.ebi.ac.uk/chebi',
     59                        versionNumber: '1.73',
     60                        ncboId: '1007',
     61                        ncboVersionedId: '44746'
     62                ).with { if (!validate()) { errors.each { println it} } else save()}
     63
     64                /* These ontologies can be added dynamically, fetching the description and such from BioPortal.
     65                   However, because the BioPortal REST services are currently down,
     66                   added the above as a fix which allows running offline from BioPortal,
     67                   and commenting out the following lines.
     68
    2369                def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
    2470                def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
    2571                def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
    26                 def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)         
     72                def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)
     73                */
    2774        }
     75
    2876
    2977        /**
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