From 8c9da8e40fe211984191caa22e3849fc4c8e954e Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 28 Aug 2023 14:22:37 +0300
Subject: Update how genotypes are transformed

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/genotype.scm | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

(limited to 'examples')

diff --git a/examples/genotype.scm b/examples/genotype.scm
index 830da0a..9dc155a 100755
--- a/examples/genotype.scm
+++ b/examples/genotype.scm
@@ -29,36 +29,31 @@
   (tables (Geno
            (left-join Species "USING (SpeciesId)")))
   (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)
+   (gnt:chr rdfs:domain gnc:Genotype)
    (gnt:mb a owl:ObjectProperty)
    (gnt:mb skos:definition "The size of this resource in Mb")
-   (gnt:mb rdfs:domain gnc:genotype)
+   (gnt:mb rdfs:domain gnc:Genotype)
    (gnt:mbMm8 a owl:ObjectProperty)
    (gnt:mbMm8 skos:definition "TODO")
-   (gnt:mbMm8 rdfs:domain gnc:genotype)
+   (gnt:mbMm8 rdfs:domain gnc:Genotype)
    (gnt:mb2016 a owl:ObjectProperty)
    (gnt:mb2016 skos:definition "TODO")
-   (gnt:mb2016 rdfs:domain gnc:genotype)
+   (gnt:mb2016 rdfs:domain gnc:Genotype)
    (gnt:hasSequence a owl:ObjectProperty)
    (gnt:hasSequence skos:definition "This resource has a given sequence")
-   (gnt:hasSequence rdfs:domain gnc:genotype)
+   (gnt:hasSequence rdfs:domain gnc:Genotype)
    (gnt:hasSource a owl:ObjectProperty)
-   (gnt:hasSource rdfs:domain gnc:genotype)
+   (gnt:hasSource rdfs:domain gnc:Genotype)
    (gnt:hasSource skos:definition "This resource was obtained from this given source")
    (gnt:hasAltSourceName a owl:ObjectProperty)
-   (gnt:hasAltSourceName rdfs:domain gnc:genotype)
+   (gnt:hasAltSourceName rdfs:domain gnc:Genotype)
    (gnt:hasAltSourceName
     skos:definition
     "The alternative name this resource was obtained from")
    (gnt:chrNum a owl:ObjectProperty)
-   (gnt:chrNum rdfs:domain gnc:genotype)
-   (gnt:chrNum skos:definition "The chromosome number for this resource")
+   (gnt:chrNum rdfs:domain gnc:Genotype)
    (gnt:chrNum skos:definition "The chromosome number for this resource"))
   (triples
       (string->identifier
@@ -69,7 +64,7 @@
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotype)
+    (set rdf:type 'gnc:Genotype)
     (set skos:prefLabel (sanitize-rdf-string (field Geno Name)))
     (set gnt:chr (field Geno Chr))
     (set gnt:mb (annotate-field
@@ -85,7 +80,7 @@
     (set gnt:hasAltSourceName
          (field ("IF((Source2 = Source), NULL, Source2)"
                  Source2)))
-    (set gnt:belongsToSpecies
+    (set xkos:classifiedUnder
          (string->identifier
           "" (remap-species-identifiers (field Species Fullname))
           #:separator ""
@@ -122,6 +117,7 @@
       ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
       ("owl:" "<http://www.w3.org/2002/07/owl#>")
       ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
       ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
    (inputs
     (list genotypes))
-- 
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