From a525d36edb35587d2f95142d4e6e7e9a32c0136d Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Tue, 18 Jul 2023 17:16:56 +0300 Subject: Replace gn with gn-term and gn-id where suitable Signed-off-by: Munyoki Kilyungi --- examples/dump-species-metadata.scm | 110 +++++++++++++++++++------------------ 1 file changed, 57 insertions(+), 53 deletions(-) (limited to 'examples') diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index e83893f..48fd425 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -21,53 +21,54 @@ (define-dump dump-species (tables (Species)) (schema-triples - (gn:name rdfs:range rdfs:Literal) - (gn:displayName rdfs:range rdfs:Literal) - (gn:binomialName rdfs:range rdfs:Literal) - (gn:family rdfs:range rdfs:Literal)) + (gn-term:name rdfs:range rdfs:Literal) + (gn-term:displayName rdfs:range rdfs:Literal) + (gn-term:binomialName rdfs:range rdfs:Literal) + (gn-term:family rdfs:range rdfs:Literal)) (triples (string->identifier "" (field Species FullName) - #:ontology "gn-species:" #:separator "" #:proc string-capitalize-first) - (set rdf:type 'gn:species) - (set gn:name (field Species SpeciesName)) - (set gn:displayName (field Species MenuName)) - (set gn:binomialName (field Species FullName)) - (set gn:family (field Species Family)) - (set gn:organism (ontology 'taxon: (field Species TaxonomyId))))) + (set rdf:type 'gn-id:species) + (set gn-term:name (field Species SpeciesName)) + (set gn-term:displayName (field Species MenuName)) + (set gn-term:binomialName (field Species FullName)) + (set gn-term:family (field Species Family)) + (set gn-term:organism (ontology 'taxon: (field Species TaxonomyId))))) (define-dump dump-strain (tables (Strain (left-join Species "ON Strain.SpeciesId = Species.SpeciesId"))) (schema-triples - (gn:strainOfSpecies rdfs:domain gn:strain) - (gn:strainOfSpecies rdfs:range gn:species) - (gn:name rdfs:range rdfs:Literal) - (gn:alias rdfs:range rdfs:Literal) - (gn:symbol rdfs:range rdfs:Literal)) + (gn-term:strainOfSpecies rdfs:domain gn-term:strain) + (gn-term:strainOfSpecies rdfs:range gn-term:species) + (gn-term:name rdfs:range rdfs:Literal) + (gn-term:alias rdfs:range rdfs:Literal) + (gn-term:symbol rdfs:range rdfs:Literal)) (triples (string->identifier - "strain" + "" (regexp-substitute/global #f "[^A-Za-z0-9:]" (field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName)) - 'pre "_" 'post)) - (set rdf:type 'gn:strain) - (set gn:strainOfSpecies + 'pre "_" 'post) + #:separator "" + #:proc string-capitalize-first) + (set rdf:type 'gn-id:strain) + (set gn-term:strainOfSpecies (string->identifier "" (field Species FullName) - #:ontology "gn-species:" #:separator "" #:proc string-capitalize-first)) ;; Name, and maybe a second name - (set gn:name (sanitize-rdf-string (field Strain Name))) - (set gn:name (sanitize-rdf-string (field Strain Name2))) - (set gn:alias (sanitize-rdf-string (field Strain Alias))) - (set gn:symbol (field Strain Symbol)))) + (set gn-term:name (sanitize-rdf-string (field Strain Name))) + (set gn-term:name2 (sanitize-rdf-string (field Strain Name2))) + (set gn-term:alias (sanitize-rdf-string (field Strain Alias))) + (set gn-term:symbol (field Strain Symbol)))) (define-dump dump-mapping-method (tables (MappingMethod)) - (triples (string->identifier "mappingMethod" (field MappingMethod Name)) - (set rdf:type 'gn:mappingMethod))) + (triples + (string->identifier "mappingMethod" (field MappingMethod Name)) + (set rdf:type 'gn-id:mappingMethod))) (define-dump dump-inbred-set (tables (InbredSet @@ -75,30 +76,33 @@ (left-join MappingMethod "ON InbredSet.MappingMethodId=MappingMethod.Id"))) (schema-triples - (gn:fullName rdfs:range rdfs:Literal) - (gn:geneticType rdfs:range rdfs:Literal) - (gn:inbredSetCode rdfs:range rdfs:Literal) - (gn:inbredFamily rdfs:range rdfs:Literal) - (gn:inbredSetOfSpecies rdfs:range gn:species) - (gn:inbredSetType rdfs:range rdfs:Literal) - (gn:phenotype rdfs:range gn:inbredSetType) - (gn:genotype rdfs:range gn:inbredSetType) - (gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod)) - (triples (string->identifier "inbredSet" (field InbredSet Name)) - (set rdf:type 'gn:inbredSet) - (set gn:binomialName (field InbredSet FullName)) - (set gn:geneticType (field InbredSet GeneticType)) - (set gn:inbredFamily (field InbredSet Family)) - (set gn:inbredSetOfMappingMethod (field MappingMethod Name)) - (set gn:inbredSetCode (field InbredSet InbredSetCode)) - (set gn:inbredSetOfSpecies + (gn-term:fullName rdfs:range rdfs:Literal) + (gn-term:geneticType rdfs:range rdfs:Literal) + (gn-term:inbredSetCode rdfs:range rdfs:Literal) + (gn-term:inbredFamily rdfs:range rdfs:Literal) + (gn-term:inbredSetOfSpecies rdfs:range gn:species) + (gn-term:inbredSetType rdfs:range rdfs:Literal) + (gn-term:phenotype rdfs:range gn-term:inbredSetType) + (gn-term:genotype rdfs:range gn-term:inbredSetType) + (gn-term:inbredSetOfMappingMethod rdfs:range gn-term:mappingMethod)) + (triples (string->identifier + "" (field InbredSet Name) + #:separator "" + #:proc string-capitalize-first) + (set rdf:type 'gn-id:inbredSet) + (set gn-term:binomialName (field InbredSet FullName)) + (set gn-term:geneticType (field InbredSet GeneticType)) + (set gn-term:inbredFamily (field InbredSet Family)) + (set gn-term:inbredSetOfMappingMethod (field MappingMethod Name)) + (set gn-term:inbredSetCode (field InbredSet InbredSetCode)) + (set gn-term:inbredSetOfSpecies (string->identifier "" (field Species FullName BinomialName) - #:ontology "gn-species:" + #:ontology "gn-id:" #:separator "" #:proc string-capitalize-first)) - (set gn:genotype + (set gn-term:genotype (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP))) - (set gn:phenotype + (set gn-term:phenotype (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP))))) (define-dump dump-avg-method @@ -106,10 +110,10 @@ ;; the Name field. (tables (AvgMethod)) (schema-triples - (gn:name rdfs:range rdfs:Literal)) + (gn-term:normalization rdfs:range rdfs:Literal)) (triples (string->identifier "avgmethod" (field AvgMethod Name)) - (set rdf:type 'gn:avgMethod) - (set gn:name (field AvgMethod Name)))) + (set rdf:type 'gn-id:avgMethod) + (set gn-term:normalization (field AvgMethod Normalization)))) @@ -118,10 +122,10 @@ (connection %connection-settings) (table-metadata? #f) (prefixes - '(("rdf:" "") + '(("gn-id:" "") + ("gn-term:" "") + ("rdf:" "") ("rdfs:" "") - ("gn:" "") - ("gn-species:" "") ("taxon:" ""))) (inputs (list dump-species -- cgit v1.2.3