Update how genotypes are dumped

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

1 files changed, 64 insertions, 27 deletions

diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 50cafb6..4ac836d 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -25,10 +25,6 @@
            (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
            (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
           "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
-  (schema-triples
-   (gnt:datasetOfInbredSet rdfs:subPropertyOf gnc:inbredSet)
-   (gnc:genotypeDataset rdfs:subPropertyOf gnc:dataset)
-   (gnt:shortName rdfs:subPropertyOf gnc:genotypeDataset))
   (triples
       (string->identifier
        ""
@@ -41,59 +37,98 @@
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotypeDataset)
-    (set gnt:name (field GenoFreeze Name))
-    (set gnt:fullName (field GenoFreeze FullName))
-    (set gnt:shortName (field GenoFreeze ShortName))
+    (set rdf:type 'gnc:genotype)
+    (set rdfs:label (field GenoFreeze Name))
+    (set skos:prefLabel (field GenoFreeze FullName))
+    (set skos:altLabel (field GenoFreeze ShortName))
     (set dct:created (annotate-field
                       (field GenoFreeze CreateTime)
                       '^^xsd:date))
-    (set gnt:datasetOfInbredSet
+    (set gnt:belongsToInbredSet
          (string->identifier "" (field InbredSet Name InbredSetName)))))
 
 (define-dump dump-genotypes
   (tables (Geno
            (left-join GenoXRef "ON Geno.Id = GenoXRef.GenoId")
            (left-join GenoFreeze "ON GenoFreeze.Id = GenoXRef.GenoFreezeId")
+           (left-join InbredSet "ON InbredSet.InbredSetId = GenoFreeze.InbredSetId")
            (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")))
   (schema-triples
-   (gnc:genotype rdfs:range rdfs:Literal)
-   (gnt:genotypeDataset rdfs:subPropertyOf gn:dataset))
+   (gnt:chr a owl:ObjectProperty)
+   (gnt:chr skos:description "This resource is located on a given chromosome")
+   (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:mbMm8 a owl:ObjectProperty)
+   (gnt:mbMm8 skos:definition "TODO")
+   (gnt:mbMm8 rdfs:domain gnc:genotype)
+   (gnt:mb2016 a owl:ObjectProperty)
+   (gnt:mb2016 skos:definition "TODO")
+   (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:hasSource a owl:ObjectProperty)
+   (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
+    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:cM a owl:ObjectProperty)
+   (gnt:cM rdfs:domain gnc:genotype)
+   (gnt:cM skos:definition "The centimorgan for this resource")
+   (gnt:usedForMapping a owl:ObjectProperty)
+   (gnt:usedForMapping rdfs:domain gnc:genotype)
+   (gnt:usedForMapping
+    skos:definition "This indicates whether this resource is used for mapping"))
   (triples
       (string->identifier
        ""
        (regexp-substitute/global
         #f "[^A-Za-z0-9:]"
-        (field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name)" abbrev))
+        (field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, '_')), Geno.Name)" abbrev))
         'pre "_" 'post)
        #:separator ""
        #:proc string-capitalize-first)
     (set rdf:type 'gnc:genotype)
-    (set gnt:name (sanitize-rdf-string (field Geno Name)))
-    (set gnt:markerName (sanitize-rdf-string (field Geno Marker_Name)))
+    (set skos:prefLabel (sanitize-rdf-string (field Geno Name)))
     (set gnt:chr (field Geno Chr))
-    (set gnt:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
-    (set gnt:sequence (field Geno Sequence))
-    (set gnt:source (field Geno Source))
-    (set gnt:source2 (field Geno Source2))
-    (set gnt:genotypeOfDataset
+    (set gnt:mb (annotate-field
+                 (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
+    (set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8))
+                                   '^^xsd:double))
+    (set gnt:mb2016
+         (annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016))
+                         '^^xsd:double))
+    (set gnt:hasSequence (field Geno Sequence))
+    (set gnt:hasSource (field Geno Source))
+    ;; Only dump Source2 if it differs from Source
+    (set gnt:hasAltSourceName
+         (field ("IF((Source2 = Source), NULL, Source2)"
+                 Source2)))
+    (set gnt:belongsToDataset
          (string->identifier
           ""
           (regexp-substitute/global
-                     #f "[^A-Za-z0-9:]"
-                     (field ("IFNULL(GenoFreeze.Name, '')" DatasetName))
-                     'pre "_" 'post)
+           #f "[^A-Za-z0-9:]"
+           (field ("IFNULL(GenoFreeze.Name, '')" DatasetName))
+           'pre "_" 'post)
           #:separator ""
-          #:proc string-capitalize-first)
-         )
+          #:proc string-capitalize-first))
     (set gnt:chrNum
          (annotate-field
-          (field ("IFNULL(Geno.chr_num, '')" chr_num))
+          (field Geno chr_num)
           '^^xsd:int))
-    (set gn:comments (field ("CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255))" Comments)))
+    (set rdfs:comments (field Geno Comments))
     (set gnt:cM
          (annotate-field
-          (field ("IFNULL(GenoXRef.cM, '')" Chr_mm8))
+          (field GenoXRef cM)
           '^^xsd:int))))
 
 
@@ -109,6 +144,8 @@
     ("gnt:" "<http://genenetwork.org/term/>")
     ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
     ("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#>")
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
  (inputs
   (list dump-genofreeze