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authorMunyoki Kilyungi2023-08-21 14:31:52 +0300
committerMunyoki Kilyungi2023-08-21 14:31:52 +0300
commite25db8edf8615f59d0682841fde8d43367ebfa53 (patch)
tree1050b589e84f77c007470296367e44dbf4106dfb /examples
parent3b9f1f53722e4866309d1555639c347c7bbacc97 (diff)
downloadgn-transform-databases-e25db8edf8615f59d0682841fde8d43367ebfa53.tar.gz
Rename inbredSet -> set
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples')
-rwxr-xr-xexamples/dump-dataset-metadata.scm8
-rwxr-xr-xexamples/dump-genotype.scm2
-rwxr-xr-xexamples/dump-phenotype.scm4
-rwxr-xr-xexamples/dump-probesetfreeze.scm2
-rwxr-xr-xexamples/dump-species-metadata.scm16
5 files changed, 16 insertions, 16 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index 2f03dfd..e732772 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -76,9 +76,9 @@
(gnc:genotypeDataset rdfs:subClassOf gnc:dataset)
(gnc:phenotypeDataset rdfs:subClassOf gnc:dataset)
(gnc:probesetDataset rdfs:subClassOf gnc:dataset)
- (gnt:belongsToInbredSet rdfs:domain gnc:dataset)
- (gnt:belongsToInbredSet a owl:ObjectProperty)
- (gnt:belongsToInbredSet skos:definition "The InbredSet this resource belongs to")
+ (gnt:belongsToSet rdfs:domain gnc:dataset)
+ (gnt:belongsToSet a owl:ObjectProperty)
+ (gnt:belongsToSet skos:definition "The InbredSet this resource belongs to")
(gnt:hasTissue rdfs:domain gnc:dataset)
(gnt:hasTissue a owl:ObjectProperty)
(gnt:hasTissue skos:definition "Tissues this resource has")
@@ -158,7 +158,7 @@
(set gdmt:hasDatasetIdentifierSubType (format #f "GN~a" (field InfoFiles GN_AccesionId)))
(set gdmt:hasRightsInfo (string-downcase
(field DatasetStatus DatasetStatusName)))
- (set gnt:belongsToInbredSet
+ (set gnt:belongsToSet
(string->identifier
"inbredSet" (field InbredSet Name)
#:separator ""
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index d4849d7..04f1af0 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -54,7 +54,7 @@
(set dct:created (annotate-field
(field GenoFreeze CreateTime)
'^^xsd:date))
- (set gnt:belongsToInbredSet
+ (set gnt:belongsToSet
(string->identifier
"inbredSet" (field InbredSet Name)
#:separator ""
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index 35f96b3..f5a8c3c 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -41,7 +41,7 @@
(set dct:created (annotate-field
(field PublishFreeze CreateTime)
'^^xsd:date))
- (set gnt:belongsToInbredSet
+ (set gnt:belongsToSet
(string->identifier
"inbredSet" (field InbredSet Name)
#:separator ""
@@ -82,7 +82,7 @@
(field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
Phenotype)))
(set rdf:type 'gnc:phenotype)
- (set gnt:belongsToInbredSet
+ (set gnt:belongsToSet
(string->identifier
"inbredSet" (field InbredSet Name)
#:separator ""
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index fab41b4..50307bf 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -100,7 +100,7 @@
(string->identifier
"tissue"
(field Tissue Short_Name)))
- (set gnt:belongsToInbredSet
+ (set gnt:belongsToSet
(string->identifier
"inbredSet" (field InbredSet Name)
#:separator ""
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
index ca51ed2..a1c942e 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/dump-species-metadata.scm
@@ -146,25 +146,25 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
(left-join MappingMethod
"ON InbredSet.MappingMethodId=MappingMethod.Id")))
(schema-triples
- (gnc:inbredSet skos:broader gnc:species)
- (gnc:inbredSet skos:definition "A set of terms used to describe an inbred set")
+ (gnc:set skos:broader gnc:species)
+ (gnc:set skos:definition "A set of terms used to describe an set, which can be inbredSet, outbredSet etc etc.")
(gnt:geneticType a owl:ObjectProperty)
- (gnt:geneticType rdfs:domain gnc:inbredSet)
+ (gnt:geneticType rdfs:domain gnc:set)
(gnt:code a owl:ObjectProperty)
- (gnt:code rdfs:domain gnc:inbredSet)
+ (gnt:code rdfs:domain gnc:set)
;; Already defined as an owl prop in dump-species
- (gnt:family rdfs:domain gnc:inbredSet)
+ (gnt:family rdfs:domain gnc:set)
(gnt:phenotype a owl:ObjectProperty)
- (gnt:phenotype rdfs:domain gnc:inbredSet)
+ (gnt:phenotype rdfs:domain gnc:set)
(gnt:genotype a owl:ObjectProperty)
(gnt:genotype rdfs:domain gnt:inbredSet)
(gnt:mappingMethod a owl:ObjectProperty)
- (gnt:mappingMethod rdfs:domain gnc:inbredSet))
+ (gnt:mappingMethod rdfs:domain gnc:set))
(triples (string->identifier
"inbredSet" (field InbredSet Name)
#:separator ""
#:proc string-capitalize-first)
- (set rdf:type 'gnc:inbredSet)
+ (set rdf:type 'gnc:set)
(set rdfs:label (field InbredSet FullName))
(set skos:altLabel (field InbredSet Name))
(set gnt:geneticType (field InbredSet GeneticType))