From 1097dfffa12cb0d0c18f5f4b2c91ecbaf6db2ded Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 28 Jan 2026 23:07:30 +0300
Subject: Move genechip ontology to own file.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dataset-metadata.scm | 30 +----------------
 examples/gene-chip.scm        | 78 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+), 29 deletions(-)
 create mode 100755 examples/gene-chip.scm

diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm
index 38dac9c..23dd48e 100755
--- a/examples/dataset-metadata.scm
+++ b/examples/dataset-metadata.scm
@@ -12,33 +12,6 @@
              (transform special-forms))
 
 
-
-(define-transformer gene-chip
-  (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)
-   (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))
-  (triples (string->identifier "platform" (field GeneChip Name) #:separator "_")
-    (set rdf:type 'gnc:gene_chip)
-    (set rdfs:label (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_geo_series_id
-         (ontology 'geoSeries:
-                   (string-trim-both (field GeneChip GeoPlatform))))))
-
 (define-transformer info-files
   (tables (InfoFiles
            (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
@@ -455,8 +428,7 @@
     (list info-files
           publishfreeze
           genofreeze
-          probesetfreeze
-          gene-chip))
+          probesetfreeze))
    (outputs
     `(#:documentation ,documentation
       #:rdf ,output))))
diff --git a/examples/gene-chip.scm b/examples/gene-chip.scm
new file mode 100755
index 0000000..a0de6b8
--- /dev/null
+++ b/examples/gene-chip.scm
@@ -0,0 +1,78 @@
+#! /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 gene-chip
+  (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)
+   (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))
+  (triples (string->identifier "platform" (field GeneChip Name) #:separator "_")
+    (set rdf:type 'gnc:gene_chip)
+    (set rdfs:label (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_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 "Info files / Investigators 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#>")
+      ("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/>")))
+   (inputs
+    (list gene-chip))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
-- 
cgit 1.4.1