From e1f390b7fab33d33fa3d813a74ae8b7d935c929b Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 15 Aug 2023 18:26:34 +0300
Subject: Introduce phenotype/genotype/probeset Dataset as a category

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-dataset-metadata.scm | 7 ++++---
 examples/dump-genotype.scm         | 6 +++++-
 examples/dump-phenotype.scm        | 4 +++-
 examples/dump-probesetfreeze.scm   | 7 +++----
 4 files changed, 15 insertions(+), 9 deletions(-)

(limited to 'examples')

diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index 3d2e1f9..e099bac 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -73,8 +73,9 @@
           "WHERE GN_AccesionId IS NOT NULL")
   (schema-triples
    (gnc:dataset rdf:type gdmt:Dataset)
-   (gnc:genotype rdfs:subClassOf gnc:dataset)
-   (gnc:phenotype rdfs:subClassOf gnc:dataset)
+   (gnc:genotypeDataset rdfs:subClassOf gnc:dataset)
+   (gnc:phenotypeDataset rdfs:subClassOf gnc:dataset)
+   (gnc:probesetDataset rdfs:subClassOf gnc:dataset)
    (gnt:belongsToInbredSet rdfs:domain gnc:dataset)
    (gnt:belongsToInbredSet a owl:ObjectProperty)
    (gnt:belongsToInbredSet skos:definition "The InbredSet this resource belongs to")
@@ -124,7 +125,7 @@
             #:separator ""
             #:proc string-capitalize-first)
     (set rdf:type (string->symbol
-                   (field ("IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotype', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotype', 'gnc:dataset'))"
+                   (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 rdfs:label (regexp-substitute/global
                      #f "^[Nn]one$"
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 4ac836d..ed23e80 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -37,7 +37,7 @@
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotype)
+    (set rdf:type 'gnc:genotypeDataset)
     (set rdfs:label (field GenoFreeze Name))
     (set skos:prefLabel (field GenoFreeze FullName))
     (set skos:altLabel (field GenoFreeze ShortName))
@@ -54,6 +54,10 @@
            (left-join InbredSet "ON InbredSet.InbredSetId = GenoFreeze.InbredSetId")
            (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")))
   (schema-triples
+   (gnc:genotype a skos:Concept)
+   (gnc:genotype
+    skos:description
+    "This is a set of controlled terms that are used to describe a given genotype")
    (gnt:chr a owl:ObjectProperty)
    (gnt:chr skos:description "This resource is located on a given chromosome")
    (gnt:chr rdfs:domain gnc:genotype)
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index f73f19f..ed10b24 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -34,7 +34,7 @@
                                  'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:phenotype)
+    (set rdf:type 'gnc:phenotypeDataset)
     (set rdfs:label (field PublishFreeze Name))
     (set skos:prefLabel (field PublishFreeze FullName))
     (set skos:altLabel (field PublishFreeze ShortName))
@@ -59,6 +59,8 @@
           ;; I.e. traits that have no associated vectors
           "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND PublishFreeze.Id IS NOT NULL")
   (schema-triples
+   (gnc:phenotype a skos:Concept)
+   (gnc:phenotype skos:description "This is a set of controlled terms that are used to describe a given phenotype")
    (gnt:abbreviation a owl:ObjectProperty)
    (gnt:abbreviation rdfs:domain gnc:phenotype)
    (gnt:abbreviation skos:definition "The abbreviation used for this resource")
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index 86e614d..f528139 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -69,7 +69,6 @@
            (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
           "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
   (schema-triples
-   (gnc:probeset rdfs:subClassOf gnc:dataset)
    (gnt:usesNormalization rdfs:domain gnc:probeset)
    (gnt:usesDataScale rdfs:domain gnc:probeset)
    (gnt:usesDataScale a owl:ObjectProperty)
@@ -83,16 +82,16 @@
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:probeset)
+    (set rdf:type 'gnc:probesetDataset)
     (set gnt:usesNormalization
          (string->identifier "avgmethod"
                              ;; If AvgMethodName is NULL, assume N/A.
                              (if (string-blank? (field AvgMethod Name AvgMethodName))
                                  "N/A" (field AvgMethod Name AvgMethodName))))
     (set dct:title (field ProbeSetFreeze FullName))
-    (set rdfs:label (field ProbeSetFreeze Name))
+    (set rdfs:label (field ProbeSetFreeze ShortName))
+    (set skos:prefLabel (field ProbeSetFreeze Name))
     (set skos:altLabel (field ProbeSetFreeze Name2))
-    (set skos:prefLabel (field ProbeSetFreeze ShortName))
     (set dct:created (annotate-field
                       (field ProbeSetFreeze CreateTime)
                       '^^xsd:datetime))
-- 
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