Update phenotype and publishfreeze dump

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

1 files changed, 24 insertions, 29 deletions

diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index 9a1651a..cd6ca95 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -54,11 +54,15 @@
            (left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
            (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
   (schema-triples
-   (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset)
-   (gnt:publicationDescription rdfs:range rdfs:Literal)
-   (gnt:originalDescription rdfs:range rdfs:Literal)
-   (gnt:prePublicationDescription rdfs:range rdfs:Literal)
-   (gnt:postPublicationAbbreviation rdfs:range rdfs:Literal)
+   (gnt:originalDescription a owl:ObjectProperty)
+   (gnt:originalDescription rdfs:domain gnc:phenotype)
+   (gnt:originalDescription skos:definition "The original description of this resource")
+   (gnt:prePublicationDescription a owl:ObjectProperty)
+   (gnt:prePublicationDescription rdfs:domain gnc:phenotype)
+   (gnt:prePublicationDescription skos:definition "The pre publication details of this resource")
+   (gnt:abbreviation a owl:ObjectProperty)
+   (gnt:abbreviation rdfs:domain gnc:phenotype)
+   (gnt:abbreviation skos:definition "The abbreviation used for this resource")
    (gnt:labCode rdfs:range rdfs:Literal)
    (gnt:submitter rdfs:range rdfs:Literal)
    (gnt:owner rdfs:range rdfs:Literal)
@@ -71,49 +75,40 @@
   (triples (string->identifier
             ""
             (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                        (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
-                                        'pre "_" 'post)
+                                      (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
+                                      'pre "_" 'post)
             #:separator ""
             #:proc string-capitalize-first)
     (set rdf:type 'gnc:phenotype)
-    (set gnt:name (sanitize-rdf-string
-                  (field
-                   ("CAST(CONVERT(BINARY CONVERT(IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) USING latin1) USING utf8) AS VARCHAR(100))"
-                    PhenotypeName))))
+    (set rdfs:label (sanitize-rdf-string
+                     (field
+                      ("IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)"
+                       PhenotypeName))))
     ;; There is no row with an empty post-publication description so
     ;; use this field as the main publication description
-    (set gnt:publicationDescription
+    (set dct:description
          (sanitize-rdf-string
-          (field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
-                  postPubDescr))))
-    (set gnt:originalDescription (sanitize-rdf-string
-                                 (delete-substrings
-                                  (field Phenotype Original_description)
-                                  "Original post publication description: ")))
-    (set gnt:prePublicationDescription
-         (sanitize-rdf-string
-          (field
-           ("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
-            prePubDesc))))
+          (field Phenotype  Post_publication_description)))
     (set gnt:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
     (set gnt:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
     (set gnt:labCode (field Phenotype Lab_code))
-    (set gnt:submitter (sanitize-rdf-string (field Phenotype Submitter)))
+    (set gdmt:hasDistributorInfo
+         (sanitize-rdf-string (field Phenotype Submitter)))
     (set gnt:owner (sanitize-rdf-string (field Phenotype Owner)))
     (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
-                                 '^^xsd:double))
+                                  '^^xsd:double))
     (set gnt:locus (field PublishXRef Locus))
-    (set gnt:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
-    (set gnt:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
+    (set gnt:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:double))
+    (set gnt:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:double))
     (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
-    (set gnt:phenotypeOfDataset
+    (set gnt:belongsToDataset
          (string->identifier
           ""
           (field
            ("IFNULL(InfoFiles.InfoPageName, IFNULL(PublishFreeze.Name, ''))" DatasetName))
           #:separator ""
           #:proc string-capitalize-first))
-    (set gnt:phenotypeOfPublication
+    (set dct:isReferencedBy
          (let ((pmid (field
                       ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
                        pmid)))