Remodel genechip metadata.

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

2 files changed, 23 insertions, 24 deletions

diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 23dd48e..32dba7a 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -428,7 +428,8 @@
     (list info-files
           publishfreeze
           genofreeze
-          probesetfreeze))
+          probesetfreeze
+          gene-chip))
    (outputs
     `(#:documentation ,documentation
       #:rdf ,output))))
diff --git a/examples/gene-chip.scm b/examples/gene-chip.scm
index a0de6b8..050c984 100755
--- a/examples/gene-chip.scm
+++ b/examples/gene-chip.scm
@@ -12,34 +12,38 @@
              (transform special-forms))
 
 
-
-(define-transformer gene-chip
+(define-transformer gn:platform->metadata
   (tables (GeneChip
            (left-join Species "USING (SpeciesId)")))
   (schema-triples
-   (gnc:gene_chip a skos:Concept)
-   (gnc:gene_chip
-    skos:description
-    "This is a set of controlled terms that are used to describe a given gene chip/platform")
-   (gnt:has_geo_series_id rdfs:domain gnc:platform)
-   (gnt:has_geo_series_id rdfs:domain gnc:gene_chip)
+   (gnc:gene_chip a skos:ConceptScheme)
+   (gnc:gene_chip skos:prefLabel "Gene Chip Vocabulary")
+   (gnc:gene_chip skos:definition "A controlled vocabulary used to describe gene chip and microarray platforms.")
+   (gnt:has_geo_series_id rdf:type owl:ObjectProperty)
+   (gnt:has_geo_series_id rdf:label "has GEO Series ID")
+   (gnt:has_geo_series_id rdfs:domain skos:Concept)
    (gnt:has_go_tree_value a owl:ObjectProperty)
-   (gnt:has_go_tree_value skos:definition "This resource the following GO tree value")
-   (gnt:has_go_tree_value rdfs:domain gnc:gene_chip))
+   (gnt:has_go_tree_value rdfs:label "has GO tree value")
+   (gnt:has_go_tree_value
+    rdfs:comment
+    "Associates a gene chip concept with a Gene Ontology term used for categorization.")
+   (gnt:has_go_tree_value rdfs:domain skos:Concept)
+   (gnt:has_go_tree_value rdfs:range xsd:string))
   (triples (string->identifier "platform" (field GeneChip Name) #:separator "_")
-    (set rdf:type 'gnc:gene_chip)
-    (set rdfs:label (field GeneChip GeneChipName))
+    (set rdf:type 'skos:Concept)
+    (set skos:inScheme (field GeneChip GeneChipName))
     (set skos:prefLabel (field GeneChip Name))
     (set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
                                Title)))
     (set gnt:has_go_tree_value (field GeneChip Go_tree_value))
-    (set xkos:classifiedUnder
-         (string->identifier "" (remap-species-identifiers (field Species Fullname)) #:separator ""))
+    (set gnt:has_species
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
     (set gnt:has_geo_series_id
          (ontology 'geoSeries:
                    (string-trim-both (field GeneChip GeoPlatform))))))
 
 
+
 (let* ((option-spec
         '((settings (single-char #\s) (value #t))
           (output (single-char #\o) (value #t))
@@ -52,25 +56,19 @@
         (call-with-input-file settings
           read)))
   (with-documentation
-   (name "Info files / Investigators Metadata")
+   (name "GeneChip Metadata")
    (connection %connection-settings)
    (table-metadata? #f)
    (prefixes
-    '(("v:" "<http://www.w3.org/2006/vcard/ns#>")
-      ("foaf:" "<http://xmlns.com/foaf/0.1/#term_>")
-      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
-      ("dcat:" "<http://www.w3.org/ns/dcat#>")
+    '(("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
       ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
       ("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
       ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
       ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
       ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
       ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
       ("owl:" "<http://www.w3.org/2002/07/owl#>")
-      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-      ("taxon:" "<http://purl.uniprot.org/taxonomy/>")
-      ("dct:" "<http://purl.org/dc/terms/>")))
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
    (inputs
     (list gene-chip))
    (outputs