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+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 getopt-long)
+             (ice-9 match)
+             (ice-9 regex)
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
+
+
+(define-transformer gn:platform->metadata
+  (tables (GeneChip
+           (left-join Species "USING (SpeciesId)")))
+  (schema-triples
+   (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 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 '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 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))
+          (documentation (single-char #\d) (value #t))))
+       (options (getopt-long (command-line) option-spec))
+       (settings (option-ref options 'settings #f))
+       (output (option-ref options 'output #f))
+       (documentation (option-ref options 'documentation #f))
+       (%connection-settings
+        (call-with-input-file settings
+          read)))
+  (with-documentation
+   (name "GeneChip Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("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#>")))
+   (inputs
+    (list gn:platform->metadata))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))