1 files changed, 0 insertions, 77 deletions
diff --git a/examples/species-metadata.scm b/examples/species-metadata.scm
index b330b12..89f2e27 100755
--- a/examples/species-metadata.scm
+++ b/examples/species-metadata.scm
@@ -21,33 +21,6 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-transformer species
-  (tables (Species))
-  (schema-triples
-   (gnc:species a skos:Concept)
-   (gnc:species skos:description "This is a set of controlled terms that are used to describe a given species")
-   (gnc:species skos:broader gnc:family)
-   (gnt:binomialName a owl:ObjectProperty)
-   (gnt:binomialName rdfs:domain gnc:species)
-   (gnt:family a owl:ObjectProperty)
-   (gnt:family rdfs:domain gnc:species)
-   (gnt:family skos:definition "This resource belongs to this family")
-   (gnt:organism a owl:ObjectProperty)
-   (gnt:organism rdfs:domain gnc:species)
-   (gnt:shortName a owl:ObjectProperty)
-   (gnt:shortName rdfs:domain gnc:species))
-  (triples
-      (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                          #:separator ""
-                          #:proc string-capitalize-first)
-    (set rdf:type 'gnc:species)
-    (set skos:label (field Species SpeciesName))
-    (set skos:altLabel (field Species Name))
-    (set rdfs:label (field Species MenuName))
-    (set gnt:binomialName (field Species FullName))
-    (set gnt:family (field Species Family))
-    (set gnt:organism (ontology 'taxon: (field Species TaxonomyId)))))
-
 #!
 
 The ProbeData table contains StrainID.
@@ -132,56 +105,6 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
     (set rdf:type 'gnc:mappingMethod)
     (set rdfs:label (field MappingMethod Name))))
 
-
-(define-transformer inbred-set
-  (tables (InbredSet
-           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
-           (left-join MappingMethod
-                      "ON InbredSet.MappingMethodId=MappingMethod.Id")))
-  (schema-triples
-   (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:set)
-   (gnt:code a owl:ObjectProperty)
-   (gnt:code rdfs:domain gnc:set)
-   ;; Already defined as an owl prop in species
-   (gnt:family rdfs:domain gnc:set)
-   (gnt:phenotype a owl:ObjectProperty)
-   (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:set))
-  (triples (string->identifier
-            "set" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first)
-    (set rdf:type 'gnc:set)
-    (set rdfs:label (field InbredSet FullName))
-    (set skos:altLabel (field InbredSet Name))
-    (set gnt:geneticType (field InbredSet GeneticType))
-    (set gnt:family (field InbredSet Family))
-    (set gnt:mappingMethod (field MappingMethod Name))
-    (set gnt:code (field InbredSet InbredSetCode))
-    (set gnt:belongsToSpecies
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                             #:separator ""
-                             #:proc string-capitalize-first))
-    (set gnt:genotype
-         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
-    (set gnt:phenotype
-         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))
-    (multiset gnt:hasTissue
-              (map
-               (lambda (x)
-                 (string->identifier "tissue"
-                                     x))
-               (string-split-substring
-                (field ("(SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name)"
-                        molecularTrait))
-                "||")))))
-
 (define-transformer avg-method
   ;; The Name and Normalization fields seem to be the same. Dump only
   ;; the Name field.