Update how datasets are dumped

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

1 files changed, 39 insertions, 47 deletions

diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 0b869b9..56280a7 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -104,52 +104,42 @@
            (left-join GeneChip "USING (GeneChipId)"))
           "WHERE GN_AccesionId IS NOT NULL")
   (schema-triples
-   (gnc:dataset rdf:type dcat:Dataset)
-   (gn:datasetTitle a rdfs:Datatype)
-   (gn:datasetTitle rdfs:comment "The Dataset's Title")
-   (gn:datasetTitle owl:onDatatype xsd:string)
-   (gn:publicationTitle a rdfs:Datatype)
-   (gn:publicationTitle rdfs:comment "The Dataset's Publication Title")
-   (gn:publicationTitle owl:onDatatype xsd:string)
-   (gnc:genotypeDataset rdfs:subClassOf gnc:dataset)
-   (gnc:phenotypeDataset rdfs:subClassOf gnc:dataset)
-   (gnc:probesetDataset rdfs:subClassOf gnc:dataset)
-   (gnt:hasTissue rdfs:domain gnc:dataset)
+   (gnt:hasTissue rdfs:domain dcat:Dataset)
    (gnt:hasTissue a owl:ObjectProperty)
    (gnt:hasTissue skos:definition "Tissues this resource has")
-   (gnt:hasTissueInfo rdfs:domain gnc:dataset)
+   (gnt:hasTissueInfo rdfs:domain dcat:Dataset)
    (gnt:hasTissueInfo a owl:ObjectProperty)
    (gnt:hasTissueInfo skos:definition "Metadata about Tissue for this resource")
-   (gnt:usesNormalization rdfs:domain gnc:dataset)
+   (gnt:usesNormalization rdfs:domain dcat:Dataset)
    (gnt:usesNormalization a owl:ObjectProperty)
    (gnt:usesNormalization skos:definition "Normalization techniques this resource has")
-   (gnt:usesPlatform rdfs:domain gnc:dataset)
+   (gnt:usesPlatform rdfs:domain dcat:Dataset)
    (gnt:usesPlatform a owl:ObjectProperty)
    (gnt:usesPlatform skos:definition "The Platform this resource uses")
-   (gnt:hasGeoSeriesId rdfs:domain gnc:dataset)
+   (gnt:hasGeoSeriesId rdfs:domain dcat:Dataset)
    (gnt:hasGeoSeriesId a owl:ObjectProperty)
    (gnt:hasGeoSeriesId skos:definition "id of record in NCBI database")
-   (gnt:hasExperimentDesignInfo rdfs:domain gnc:dataset)
+   (gnt:hasExperimentDesignInfo rdfs:domain dcat:Dataset)
    (gnt:hasExperimentDesignInfo rdfs:label "Experiment Design")
    (gnt:hasExperimentDesignInfo a owl:ObjectProperty)
    (gnt:hasExperimentDesignInfo skos:definition "Information about how the experiment was designed")
-   (gnt:hasNotes rdfs:domain gnc:dataset)
+   (gnt:hasNotes rdfs:domain dcat:Dataset)
    (gnt:hasNotes a owl:ObjectProperty)
    (gnt:hasNotes rdfs:label "Notes")
    (gnt:hasNotes skos:definition "Extra Notes about this dataset")
-   (gnt:hasDataProcessingInfo rdfs:domain gnc:dataset)
+   (gnt:hasDataProcessingInfo rdfs:domain dcat:Dataset)
    (gnt:hasDataProcessingInfo rdfs:label "About Data Processing")
    (gnt:hasDataProcessingInfo a owl:ObjectProperty)
    (gnt:hasDataProcessingInfo skos:definition "Information about how this dataset was processed")
-   (gnt:hasPlatformInfo rdfs:domain gnc:dataset)
+   (gnt:hasPlatformInfo rdfs:domain dcat:Dataset)
    (gnt:hasPlatformInfo a owl:ObjectProperty)
    (gnt:hasPlatformInfo rdfs:label "About Platfoorm")
    (gnt:hasPlatformInfo skos:definition "Information about the platform that was used with this dataset")
-   (gnt:hasCaseInfo rdfs:domain gnc:dataset)
+   (gnt:hasCaseInfo rdfs:domain dcat:Dataset)
    (gnt:hasCaseInfo rdfs:label "About Case")
    (gnt:hasCaseInfo a owl:ObjectProperty)
    (gnt:hasCaseInfo skos:definition "Information about the cases used in this platform")
-   (gnt:hasAcknowledgement rdfs:domain gnc:dataset)
+   (gnt:hasAcknowledgement rdfs:domain dcat:Dataset)
    (gnt:hasAcknowledgement rdfs:label "Acknowledgement")
    (gnt:hasAcknowledgement a owl:ObjectProperty)
    (gnt:hasAcknowledgement skos:definition "People to acknowledge"))
@@ -159,9 +149,16 @@
                                          'pre "_" 'post)
             #:separator ""
             #:proc string-capitalize-first)
-    (set rdf:type (string->symbol
-                   (field ("IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotypeDataset', IF(ProbeSetFreeze.Name IS NOT NULL, 'gnc:probesetDataset', 'gnc:dataset')))"
-                           rdfType))))
+    (set rdf:type 'dcat:Dataset)
+    (set xkos:classifiedUnder
+         (let ([dataset-type
+                (string-trim-both
+                 (field ("IF(GenoFreeze.Id IS NOT NULL, 'gnc:Genotype', IF(PublishFreeze.Id IS NOT NULL, 'gnc:Phenotype', IF(ProbeSetFreeze.Name IS NOT NULL, 'gnc:Probeset', '')))"
+                         DatasetType)))])
+           (if (not (string-null? dataset-type))
+               (string->symbol
+                dataset-type)
+               "")))
     (set rdfs:label (regexp-substitute/global
                      #f "^[Nn]one$"
                      (field InfoFiles InfoPageName)
@@ -169,26 +166,20 @@
     (set skos:prefLabel
          (field ("IFNULL(GenoFreeze.FullName, IFNULL(PublishFreeze.FullName, ''))"
                  DatasetFullName)))
-    (set skos:prefLabel (field Datasets DatasetName DatasetGroup))
+    (set skos:altLabel (field Datasets DatasetName DatasetGroup))
     (set dct:title
-         (annotate-field
-          (regexp-substitute/global
-           #f "^[Nn]one$"
+         (regexp-substitute/global
+          #f "^[Nn]one$"
+          (or
+           (regexp-substitute/global
+            #f "^Unpublished$" (field Datasets PublicationTitle) "")
            (field InfoFiles InfoFileTitle)
-           ""))
-         '^^gn:datasetTitle)
-    ;; This is the published title
-    (set dct:title
-         (annotate-field
-          (regexp-substitute/global
-           #f "^[Nn]one$"
-           (field Datasets PublicationTitle)
-           ""))
-         '^^gn:publicationTitle)
+           "")
+          ""))
     (set dct:created
          (field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))"
                  createTimeGenoFreeze)))
-    (set dcat:contacttPoint
+    (set dcat:contactPoint
          (investigator-attributes->id (field Investigators FirstName)
                                       (field Investigators LastName)
                                       (field Investigators Email)))
@@ -196,7 +187,7 @@
          (field Organizations OrganizationName))
     (set dct:identifier (format #f "GN~a" (field InfoFiles GN_AccesionId)))
     (set dct:accessRights (string-downcase
-                            (field DatasetStatus DatasetStatusName)))
+                           (field DatasetStatus DatasetStatusName)))
     (set xkos:classifiedUnder
          (string->identifier
           "set" (field InbredSet Name)
@@ -205,7 +196,7 @@
     (set gnt:hasTissue (string->identifier "tissue"
                                            (field Tissue Short_Name)))
     (set gnt:usesNormalization
-         (string->identifier "avgmethod"
+         (string->identifier "avgMethod"
                              ;; If AvgMethodName is NULL, assume N/A.
                              (if (string-blank? (field AvgMethod Name AvgMethodName))
                                  "N/A" (field AvgMethod Name AvgMethodName))))
@@ -265,9 +256,9 @@
                                  'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:phenotypeDataset)
+    (set xkos:classifiedUnder 'gnc:Phenotype)
+    (set dct:title  (field PublishFreeze FullName))
     (set rdfs:label (field PublishFreeze Name))
-    (set skos:prefLabel (field PublishFreeze FullName))
     (set skos:altLabel (field PublishFreeze ShortName))
     (set dct:created (annotate-field
                       (field PublishFreeze CreateTime)
@@ -295,9 +286,9 @@
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotypeDataset)
+    (set xkos:classifiedUnder 'gnc:Genotype)
     (set rdfs:label (field GenoFreeze Name))
-    (set skos:prefLabel (field GenoFreeze FullName))
+    (set dct:title (field GenoFreeze FullName))
     (set skos:altLabel (field GenoFreeze ShortName))
     (set dct:created (annotate-field
                       (field GenoFreeze CreateTime)
@@ -331,9 +322,9 @@
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:probesetDataset)
+    (set xkos:classifiedUnder 'gnc:Probeset)
     (set gnt:usesNormalization
-         (string->identifier "avgmethod"
+         (string->identifier "avgMethod"
                              ;; If AvgMethodName is NULL, assume N/A.
                              (if (string-blank? (field AvgMethod Name AvgMethodName))
                                  "N/A" (field AvgMethod Name AvgMethodName))))
@@ -375,6 +366,7 @@
    (prefixes
     '(("v:" "<http://www.w3.org/2006/vcard/ns#>")
       ("foaf:" "<http://xmlns.com/foaf/0.1/>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
       ("dcat:" "<http://www.w3.org/ns/dcat#>")
       ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
       ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")