From 136139333d34179b3677b950e6c213cb61f535d3 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 23 Aug 2023 18:02:40 +0300
Subject: Update how NCBI genewiki entries are transformed

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/generif.scm | 78 ++++++++++++++++++++++++++++++----------------------
 1 file changed, 45 insertions(+), 33 deletions(-)

(limited to 'examples/generif.scm')

diff --git a/examples/generif.scm b/examples/generif.scm
index d6b8b25..cdb692a 100755
--- a/examples/generif.scm
+++ b/examples/generif.scm
@@ -77,39 +77,6 @@
    (gnt:belongsToSpecies rdfs:domain gnc:GNWikiEntry)
    (gnt:symbol rdfs:domain gnc:GNWikiEntry))
   (triples
-(define-transformer ncbi-genewiki-entries
-  (tables (GeneRIF_BASIC)
-          "GROUP BY GeneId, comment, createtime")
-  (schema-triples
-   (gnt:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry))
-  (triples (ontology 'generif:
-                     (field GeneRIF_BASIC GeneId))
-    (set gnt:geneWikiEntryOfNCBI
-         (blank-node
-          (set gnt:geneWikiEntry
-               (annotate-field (field GeneRIF_BASIC comment)
-                               '^^xsd:string))
-          (multiset dct:source (map (lambda (el) (if (string-null? el)
-                                                     ""
-                                                     (ontology 'pubmed: el)))
-                                    (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
-                                                  #\,)))
-          (set dct:created (annotate-field (time-unix->string
-                                            (field GeneRIF_BASIC createtime) "~5")
-                                           '^^xsd:datetime))))))
-      (string->identifier
-       "generif"
-       (make-version-3-uuid
-         (u8-list->bytevector
-          ;; URL namespace UUID is 6ba7b811-9dad-11d1-80b4-00c04fd430c8
-          '(107 167 184 17 157 173 17 209 128 180
-                0 192 79 212 48 200))
-         (format #f "~a~a~a~a"
-                 (field Species FullName)
-                 (field GeneRIF comment)
-                 (field GeneRIF symbol)
-                 (field GeneRIF createtime))
-         ""))
     (string->identifier
      "generif"
      (make-version-3-uuid
@@ -168,6 +135,51 @@
              ""))
     (set foaf:homepage (field GeneRIF weburl))))
 
+(define-transformer ncbi-genewiki-entries
+        (tables (GeneRIF_BASIC)
+                "GROUP BY GeneId, comment, createtime")
+        (schema-triples
+         (gnc:NCBIWikiEntry rdfs:subClassOf gnc:GeneWikiEntry)
+         (gnc:NCBIWikiEntry rdfs:comment "Represents GeneRIF Entries obtained from NCBI"))
+        (triples
+            (string->identifier
+             "generif"
+             (make-version-3-uuid
+              (u8-list->bytevector
+               ;; URL namespace UUID is 6ba7b811-9dad-11d1-80b4-00c04fd430c8
+               '(107 167 184 17 157 173 17 209 128 180
+                     0 192 79 212 48 200))
+              (format #f "~a~a~a~a~a"
+                      (field GeneRIF_BASIC GeneId)
+                      (field GeneRIF_BASIC VersionId)
+                      (field GeneRIF_BASIC comment)
+                      (field GeneRIF_BASIC symbol)
+                      (field GeneRIF_BASIC createtime))
+              ""))
+          (set rdf:type 'gnc:NCBIWikiEntry)
+          (set rdfs:label
+               (annotate-field (field GeneRIF_BASIC comment)
+                               '^^xsd:string))
+          (set gnt:symbol (field GeneRIF_BASIC symbol))
+          (multiset dct:references
+                    (map
+                     (lambda (el)
+                       (if (string-null? el)
+                           ""
+                           (ontology 'pubmed: el)))
+                     (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids))
+                                   #\,)))
+          (set gnt:hasVersion
+               (format #f "~a" (field GeneRIF_BASIC VersionId)))
+          (set dct:created
+               (let ((createtime (field GeneRIF_BASIC createtime)))
+                 (if (string? createtime)
+                     ""
+                     (annotate-field
+                      (time-unix->string
+                       createtime "~5")
+                      '^^xsd:datetime))))))
+
 
 
 (let* ((option-spec
-- 
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