Rename 'gn-id' prefix to 'gn'

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

4 files changed, 34 insertions, 33 deletions

diff --git a/dump/triples.scm b/dump/triples.scm
index c168f3e..2b43d68 100644
--- a/dump/triples.scm
+++ b/dump/triples.scm
@@ -23,7 +23,7 @@
 
 (define* (string->identifier prefix str
                              #:optional #:key
-                             (ontology "gn-id:")
+                             (ontology "gn:")
                              (separator "_")
                              (proc string-downcase))
   "Convert STR to a turtle identifier after replacing illegal
diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm
index ff46d3d..6f349d6 100755
--- a/examples/dump-publication.scm
+++ b/examples/dump-publication.scm
@@ -21,15 +21,15 @@
 (define-dump dump-publication
   (tables (Publication))
   (schema-triples
-   (gn:pubMedId rdfs:range rdfs:Literal)
-   (gn:title rdfs:range rdfs:Literal)
-   (gn:journal rdfs:range rdfs:Literal)
-   (gn:volume rdfs:range rdfs:Literal)
-   (gn:pages rdfs:range rdfs:Literal)
-   (gn:month rdfs:range rdfs:Literal)
-   (gn:year rdfs:range rdfs:Literal)
-   (gn:author rdfs:range rdfs:Literal)
-   (gn:abstract rdfs:range rdfs:Literal))
+   (gn-term:pubMedId rdfs:range rdfs:Literal)
+   (gn-term:title rdfs:range rdfs:Literal)
+   (gn-term:journal rdfs:range rdfs:Literal)
+   (gn-term:volume rdfs:range rdfs:Literal)
+   (gn-term:pages rdfs:range rdfs:Literal)
+   (gn-term:month rdfs:range rdfs:Literal)
+   (gn-term:year rdfs:range rdfs:Literal)
+   (gn-term:author rdfs:range rdfs:Literal)
+   (gn-term:abstract rdfs:range rdfs:Literal))
   (triples
       (let ((pmid (field
                    ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
@@ -40,18 +40,19 @@
                                 (number->string publication-id))
             (ontology 'publication: pmid)))
     (set rdf:type 'gn:publication)
-    (set gn:pubMedId (ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
-    (set gn:title (delete-substrings (field Publication Title)
-                                     "Unknown"))
-    (set gn:journal (delete-substrings (field Publication Journal)
-                                       "Unknown"))
-    (set gn:volume (delete-substrings (field Publication Volume)
-                                      "Unknown"))
-    (set gn:pages (delete-substrings (field Publication Pages)
-                                     "Unknown"))
-    (set gn:month (delete-substrings (field Publication Month)
-                                     "Unknown"))
-    (set gn:year (field Publication Year))
+    (set gn-term:pubMedId
+         (ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
+    (set gn-term:title (delete-substrings (field Publication Title)
+                                          "Unknown"))
+    (set gn-term:journal (delete-substrings (field Publication Journal)
+                                            "Unknown"))
+    (set gn-term:volume (delete-substrings (field Publication Volume)
+                                           "Unknown"))
+    (set gn-term:pages (delete-substrings (field Publication Pages)
+                                          "Unknown"))
+    (set gn-term:month (delete-substrings (field Publication Month)
+                                          "Unknown"))
+    (set gn-term:year (field Publication Year))
     (multiset gn:author
               ;; The authors field is a comma
               ;; separated list. Split it.
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
index 48fd425..41d5847 100755
--- a/examples/dump-species-metadata.scm
+++ b/examples/dump-species-metadata.scm
@@ -29,7 +29,7 @@
       (string->identifier "" (field Species FullName)
                           #:separator ""
                           #:proc string-capitalize-first)
-    (set rdf:type 'gn-id:species)
+    (set rdf:type 'gn:species)
     (set gn-term:name (field Species SpeciesName))
     (set gn-term:displayName (field Species MenuName))
     (set gn-term:binomialName (field Species FullName))
@@ -53,7 +53,7 @@
              'pre "_" 'post)
             #:separator ""
             #:proc string-capitalize-first)
-    (set rdf:type 'gn-id:strain)
+    (set rdf:type 'gn:strain)
     (set gn-term:strainOfSpecies
          (string->identifier "" (field Species FullName)
                           #:separator ""
@@ -68,7 +68,7 @@
   (tables (MappingMethod))
   (triples
       (string->identifier "mappingMethod" (field MappingMethod Name))
-    (set rdf:type 'gn-id:mappingMethod)))
+    (set rdf:type 'gn:mappingMethod)))
 
 (define-dump dump-inbred-set
   (tables (InbredSet
@@ -89,7 +89,7 @@
             "" (field InbredSet Name)
             #:separator ""
             #:proc string-capitalize-first)
-    (set rdf:type 'gn-id:inbredSet)
+    (set rdf:type 'gn:inbredSet)
     (set gn-term:binomialName (field InbredSet FullName))
     (set gn-term:geneticType (field InbredSet GeneticType))
     (set gn-term:inbredFamily (field InbredSet Family))
@@ -97,7 +97,7 @@
     (set gn-term:inbredSetCode (field InbredSet InbredSetCode))
     (set gn-term:inbredSetOfSpecies
          (string->identifier "" (field Species FullName BinomialName)
-                             #:ontology "gn-id:"
+                             #:ontology "gn:"
                              #:separator ""
                              #:proc string-capitalize-first))
     (set gn-term:genotype
@@ -112,7 +112,7 @@
   (schema-triples
    (gn-term:normalization rdfs:range rdfs:Literal))
   (triples (string->identifier "avgmethod" (field AvgMethod Name))
-    (set rdf:type 'gn-id:avgMethod)
+    (set rdf:type 'gn:avgMethod)
     (set gn-term:normalization (field AvgMethod Normalization))))
 
 
@@ -122,9 +122,9 @@
  (connection %connection-settings)
  (table-metadata? #f)
  (prefixes
-  '(("gn-id:" "<http://genenetwork.org/terms/>")
-    ("gn-term:" "<http://genenetwork.org/terms/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+  '(("gn:" "<http://genenetwork.org/id/>")
+    ("gn-term:" "<http://genenetwork.org/term/>")
+    ("rdf:" "<https://www.w3.org/1999/02/22-rdf-syntax-ns#>")
     ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
     ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
  (inputs
diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm
index 376129c..ff6792e 100755
--- a/examples/dump-tissue.scm
+++ b/examples/dump-tissue.scm
@@ -27,7 +27,7 @@
   ;; Hopefully the Short_Name field is distinct and can be used as an
   ;; identifier.
   (triples (string->identifier "tissue" (field Tissue Short_Name))
-	   (set rdf:type 'gn-id:tissue)
+	   (set rdf:type 'gn:tissue)
 	   (set gn-term:name (field Tissue Name))))
 
 
@@ -37,7 +37,7 @@
  (connection %connection-settings)
  (table-metadata? #f)
  (prefixes
-  '(("gn-id:" "<http://genenetwork.org/terms/>")
+  '(("gn:" "<http://genenetwork.org/id/>")
     ("gn-term:" "<http://genenetwork.org/terms/>")
     ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
     ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))