Make species identifiers consistent.

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

4 files changed, 18 insertions, 6 deletions

diff --git a/examples/classification.scm b/examples/classification.scm
index 13b086a..8eb440a 100755
--- a/examples/classification.scm
+++ b/examples/classification.scm
@@ -48,7 +48,10 @@
    (gnc:Species xkos:depth "3")
    (gnc:Species xkos:specializes gnc:Set))
   (triples "gnc:Species"
-    (set skos:member (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
+    (set skos:member
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))))
 
 (define-transformer classification-scheme-set
   (tables (InbredSet))
@@ -63,7 +66,8 @@
           "set" (field InbredSet Name InbredSetName)))))
 
 (define-transformer species
-  (tables (Species))
+  (tables (Species
+           (left-join InbredSet "USING (FamilyOrder)")))
   (schema-triples
    (gnt:family a owl:ObjectProperty)
    (gnt:family rdfs:domain gnc:Species)
@@ -72,7 +76,9 @@
    (gnt:shortName rdfs:domain gnc:Species)
    (gnt:shortName skos:definition "The short name of a given resource"))
   (triples
-      (string->identifier "" (remap-species-identifiers (field Species Fullname)))
+      (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first)
     (set skos:inScheme 'gnc:ResourceClassificationScheme)
     (set rdfs:label (remap-species-identifiers (field Species Fullname)))
     (set skos:prefLabel (field Species MenuName))
diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 1c02bb3..26ca7f2 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -81,7 +81,9 @@
                                Title)))
     (set gnt:hasGOTreeValue (field GeneChip Go_tree_value))
     (set xkos:classifiedUnder
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))
     (set gnt:hasGeoSeriesId
          (ontology 'geoSeries:
                    (string-trim-both (field GeneChip GeoPlatform))))))
diff --git a/examples/genbank.scm b/examples/genbank.scm
index 65eed0c..dc40d67 100755
--- a/examples/genbank.scm
+++ b/examples/genbank.scm
@@ -36,7 +36,9 @@
             (field Genbank Id))
     (set gnt:hasSequence (field Genbank Sequence))
     (set xkos:classifiedUnder
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))))))
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))))
 
 
 
diff --git a/examples/strains.scm b/examples/strains.scm
index 5ef6f03..8552229 100755
--- a/examples/strains.scm
+++ b/examples/strains.scm
@@ -79,7 +79,9 @@ At this point it is not very clear how Name, Name2, Symbol and Alias are used.
              'pre "_" 'post))
     (set rdf:type 'gnc:strain)
     (set xkos:classifiedUnder
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))
     ;; Name, and maybe a second name
     (set rdfs:label (sanitize-rdf-string (field Strain Name)))
     (set skos:altLabel (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2))))