Rename things.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 19 insertions, 23 deletions

diff --git a/examples/molecular-traits.scm b/examples/molecular-traits.scm
index 6ece7b5..47efb98 100755
--- a/examples/molecular-traits.scm
+++ b/examples/molecular-traits.scm
@@ -11,15 +11,15 @@
              (transform triples)
              (transform special-forms))
 
-(define-transformer tissue
+(define-transformer molecular-entities
   (tables (Tissue))
   (schema-triples
-   (gnc:tissue a owl:Class)
-   (gnc:tissue a skos:Concept)
-   (gnc:tissue rdfs:subClassOf obo:UBERON_0000479)
-   (gnc:tissue rdfs:label "Tissue (GN)"))
+   (gnc:molecular_trait a owl:Class)
+   (gnc:molecular_trait a skos:Concept)
+   (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479)
+   (gnc:molecular_trait rdfs:label "Molecular Trait.   This describes a melecular trait of a given species.  We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups."))
   (triples (string->identifier "tissue" (field Tissue Short_Name) #:separator "_")
-    (set rdf:type 'gnc:tissue)
+    (set rdf:type 'gnc:molecular_trait)
     (set skos:prefLabel (field Tissue Name))
     (set skos:altLabel (field Tissue Short_Name))))
 
@@ -31,30 +31,26 @@
            (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
           "WHERE ProbeSetFreeze.public > 0 GROUP BY Species.Name, Tissue.Short_Name")
   (schema-triples
-   (gnc:molecular_trait a owl:Class)
-   (gnc:molecular_trait a skos:Concept)
-   (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479)
-   (gnc:molecular_trait rdfs:label "Molecular Trait.   This describe a melecular trait of a given species.  We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups.")
-   (gnt:has_tissue rdf:type owl:ObjectProperty)
-   (gnt:has_tissue rdfs:domain gnc:molecular_traits)
-   (gnt:has_tissue rdfs:range gnc:tissue)
-   (gnt:has_tissue rdfs:label "has tissue"))
+   (gnt:has_molecular_trait rdf:type owl:ObjectProperty)
+   (gnt:has_molecular_trait rdfs:domain gnc:set)
+   (gnt:has_molecular_trait rdfs:range gnc:molecular_traits)
+   (gnt:has_molecular_trait rdfs:label "has molecular trait"))
   (triples (string->identifier
             (format #f "trait_~a" (field Species Name))
             (field Tissue Short_Name)
             #:separator "_")
-    (set rdf:type 'gnc:molecular_trait)
+    (set rdf:type 'gnc:molecular_entity)
     (set gnt:has_strain
          (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))
     (set gnt:has_species
          (string->identifier "" (remap-species-identifiers (field Species Fullname))))
-    (multiset gnt:has_dataset
+    (multiset gnt:has_probeset_data
               (map (cut string->identifier "dataset" <> #:separator "_")
                    (string-split
                     (field ("GROUP_CONCAT(ProbeSetFreeze.Name SEPARATOR ',')"
                             dataset_name))
                     #\,)))
-    (set gnt:has_tissue
+    (set gnt:has_molecular_trait
          (string->identifier "tissue"
                              (field Tissue Short_Name)
                              #:separator "_"))))
@@ -67,12 +63,12 @@
            (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
           "WHERE ProbeSetFreeze.public > 0 GROUP BY Species.Name, Tissue.Short_Name")
   (schema-triples
-   (gnt:has_molecular_trait rdf:type owl:ObjectProperty)
-   (gnt:has_molecular_trait rdfs:domain gnc:set)
-   (gnt:has_molecular_trait rdfs:range gnc:molecular_traits)
-   (gnt:has_molecular_trait rdfs:label "has molecular trait"))
+      (gnc:molecular_entity a owl:Class)
+   (gnc:molecular_entity a skos:Concept)
+   (gnc:molecular_entity rdfs:subClassOf obo:UBERON_0000479)
+   (gnc:molecular_entity rdfs:label "This points this to resource which has molecular trait."))
   (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
-    (set gnt:has_molecular_trait
+    (set gnt:has_molecular_entity
          (string->identifier (format #f "trait_~a"
                                      (field Species Name))
                              (field Tissue Short_Name) #:separator "_"))))
@@ -106,7 +102,7 @@
       ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
    (inputs
     (list
-     tissue
+     molecular-entities
      molecular-traits
      list-molecular-traits))
    (outputs