From 6e4359319695a6d93de55339b758b6ec6926c5ca Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 14 Aug 2023 16:40:38 +0300
Subject: Use prism, fabio and dct ontologies to represent a publication

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-publication.scm | 52 +++++++++++++++++++++----------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm
index 50e4358..5b1af83 100755
--- a/examples/dump-publication.scm
+++ b/examples/dump-publication.scm
@@ -20,16 +20,6 @@
 
 (define-dump dump-publication
   (tables (Publication))
-  (schema-triples
-   (gnt:pubMedId rdfs:range rdfs:Literal)
-   (gnt:title rdfs:range rdfs:Literal)
-   (gnt:journal rdfs:range rdfs:Literal)
-   (gnt:volume rdfs:range rdfs:Literal)
-   (gnt:pages rdfs:range rdfs:Literal)
-   (gnt:month rdfs:range rdfs:Literal)
-   (gnt:year rdfs:range rdfs:Literal)
-   (gnt:author rdfs:range rdfs:Literal)
-   (gnt:abstract rdfs:range rdfs:Literal))
   (triples
       (let ((pmid (field
                    ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
@@ -39,27 +29,33 @@
             (string->identifier "unpublished"
                                 (number->string publication-id))
             (ontology 'pubmed: pmid)))
-    (set rdf:type 'gnc:publication)
-    (set gnt:pubMedId
+    (set rdf:type 'fabio:ResearchPaper)
+    (set fabio:hasPubMedId
          (ontology 'pubmed: (field ("IFNULL(PubMed_ID, '')" pubmedId))))
-    (set gnt:title (delete-substrings (field Publication Title)
+    (set dct:title (delete-substrings (field Publication Title)
+                                      "Unknown"))
+    (set fabio:Journal (delete-substrings (field Publication Journal)
                                           "Unknown"))
-    (set gnt:journal (delete-substrings (field Publication Journal)
-                                            "Unknown"))
-    (set gnt:volume (delete-substrings (field Publication Volume)
-                                           "Unknown"))
-    (set gnt:pages (delete-substrings (field Publication Pages)
-                                          "Unknown"))
-    (set gnt:month (delete-substrings (field Publication Month)
-                                          "Unknown"))
-    (set gnt:year (field Publication Year))
-    (multiset gn:author
+    (set prism:volume (delete-substrings (field Publication Volume)
+                                                "Unknown"))
+    (set fabio:page (delete-substrings (field Publication Pages)
+                                       "Unknown"))
+    (set prism:publicationDate (annotate-field
+                                (delete-substrings (field Publication Month)
+                                                   "Unknown")
+                                '^^xsd:gMonth))
+    (set fabio:hasPublicationYear
+         (annotate-field
+          (field
+           ("IF(Publication.Year = 0, NULL, Publication.Year)" Year))
+          '^^xsd:gYear))
+    (multiset dct:creator
               ;; The authors field is a comma
               ;; separated list. Split it.
               (map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,)))
-    (set gn:abstract
+    (set dct:abstract
          (sanitize-rdf-string
-          (field ("CAST(CONVERT(BINARY CONVERT(Publication.Abstract USING latin1) USING utf8) AS VARCHAR(100))" Abstract))))))
+          (field Publication Abstract)))))
 
 
 
@@ -69,13 +65,17 @@
  (table-metadata? #f)
  (prefixes
   '(("gnt:" "<http://genenetwork.org/terms/>")
+    ("fabio:" "<http://purl.org/spar/fabio/>")
+    ("dct:" "<http://purl.org/dc/terms/>")
+    ("prism:" "<http://prismstandard.org/namespaces/basic/2.0/>")
     ("gn:" "<http://genenetwork.org/id/>")
     ("gnc:" "<http://genenetwork.org/category/>")
     ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
     ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
     ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")))
  (inputs
   (list dump-publication))
  (outputs
   '(#:documentation "./docs/dump-publication.md"
-    #:rdf "./verified-data/dump-publication.md")))
+    #:rdf "./verified-data/dump-publication.ttl")))
-- 
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