Changeset 1341

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Timestamp:
06-01-11 17:33:32 (3 years ago)
Author:
business@…
Message:

fix for development environment to circumvent BioPortal? problems

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1 modified

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  • 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        /**