From 522a382af147fac45659afee7a48e10947bddcab Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Fri, 6 Feb 2026 06:31:02 +0300
Subject: Add dna markers and snps.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/genotype.scm | 70 +++++++++++++++++++++++++++++++++++++++++++++++++++
 examples/ontology.scm | 23 ++++++++++++++++-
 2 files changed, 92 insertions(+), 1 deletion(-)
 create mode 100755 examples/genotype.scm

(limited to 'examples')

diff --git a/examples/genotype.scm b/examples/genotype.scm
new file mode 100755
index 0000000..4a91b63
--- /dev/null
+++ b/examples/genotype.scm
@@ -0,0 +1,70 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (rnrs programs)
+             (rnrs io ports)
+             (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:markers/snps->metadata
+  (tables (Geno
+           (inner-join Species "ON Geno.SpeciesId = Species.Id"))
+          "WHERE Species.Name != 'monkey'")
+  (triples (string->identifier "marker" (field Geno Name) #:separator "_")
+    (set gnt:has_species
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
+    (set rdf:type 'gnc:dna_marker)
+    (set skos:prefLabel (field Geno Name))
+    (set skos:altLabel (field Geno Marker_Name))
+    (set gnt:chr (field Geno Chr))
+    (set gnt:mb (annotate-field (field Geno Mb) '^^xsd:doubleg))
+    (set gnt:sequence (field Geno Sequence))
+    (set gnt:source (field Geno Source))
+    (set rdfs:comment (field Geno Comments))))
+
+
+
+(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 "Phenotypes Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("dcat:" "<http://www.w3.org/ns/dcat#>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
+      ("gnd:" "<https://cd.genenetwork.org/lmdb/v1/data/traits/>")
+      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
+      ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ("qb:" "<http://purl.org/linked-data/cube#>")
+      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
+      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
+   (inputs
+    (list gn:markers/snps->metadata))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
+
diff --git a/examples/ontology.scm b/examples/ontology.scm
index 3d58ecb..4be8bd1 100755
--- a/examples/ontology.scm
+++ b/examples/ontology.scm
@@ -237,6 +237,9 @@
       (triple 'gnt:has_phenotype_data 'skos:definition "This resource has phenotype data.")
 
       ;; Genotypes
+      (triple 'gnc:dna_marker 'a 'owl:Class)
+      (triple 'gnc:dna_marker 'a 'skos:Concept)
+      (triple 'gnc:dna_marker 'rdfs:label "A DNA Marker or SNP")
       (triple 'gnt:has_genotype_data 'rdf:type 'owl:ObjectProperty)
       (triple 'gnt:has_genotype_data 'rdfs:label "this resources has genotype data.")
       (triple 'gnt:has_genotype_data 'rdfs:comment "Associates a resource with its genotype data.")
@@ -246,4 +249,22 @@
       (triple 'gnt:has_marker_count 'rdf:type 'owl:ObjectProperty)
       (triple 'gnt:has_marker_count 'rdfs:label "this resources has N number of dna markers/SNPs.")
       (triple 'gnt:has_marker_count 'rdfs:domain 'xsd:integer)
-      (triple 'gnt:has_marker_count 'rdfs:range 'dcat:Dataset))))
+      (triple 'gnt:has_marker_count 'rdfs:range 'dcat:Dataset)
+      (triple 'gnt:chr 'a 'qb:MeasureProperty)
+      (triple 'gnt:chr 'a 'rdf:Property)
+      (triple 'gnt:chr 'rdfs:label "Chromosome")
+      (triple 'gnt:chr 'rdfs:domain 'gnc:marker)
+      (triple 'gnt:chr 'rdfs:range 'rdfs:Literal)
+      (triple 'gnt:chr 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
+      (triple 'gnt:mb 'rdfs:label "Megabase")
+      (triple 'gnt:mb 'rdfs:domain 'gnc:marker)
+      (triple 'gnt:mb 'rdfs:range 'rdfs:Literal)
+      (triple 'gnt:mb 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
+      (triple 'gnt:sequence 'rdfs:label "Sequence")
+      (triple 'gnt:sequence 'rdfs:domain 'gnc:marker)
+      (triple 'gnt:sequence 'rdfs:range 'rdfs:Literal)
+      (triple 'gnt:sequence 'rdfs:subPropertyOf 'sdmx-measure:obsValue)
+      (triple 'gnt:source 'rdfs:label "Source")
+      (triple 'gnt:source 'rdfs:domain 'gnc:marker)
+      (triple 'gnt:source 'rdfs:range 'rdfs:Literal)
+      (triple 'gnt:source 'rdfs:subPropertyOf 'sdmx-measure:obsValue))))
-- 
cgit 1.4.1