From 63c1af8d4e855979bec53e716dd046df44c956bc Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 27 Jan 2026 16:42:43 +0300
Subject: Rename tissue.scm -> molecular-traits.scm.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/molecular-traits.scm | 63 +++++++++++++++++++++++++++++++++++++++++++
 examples/tissue.scm           | 56 --------------------------------------
 2 files changed, 63 insertions(+), 56 deletions(-)
 create mode 100755 examples/molecular-traits.scm
 delete mode 100755 examples/tissue.scm

(limited to 'examples')

diff --git a/examples/molecular-traits.scm b/examples/molecular-traits.scm
new file mode 100755
index 0000000..737c0b0
--- /dev/null
+++ b/examples/molecular-traits.scm
@@ -0,0 +1,63 @@
+#! /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 tissue
+  ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
+  ;; and BIRN_lex_Name are mostly NULL.
+  (tables (Tissue))
+  (schema-triples
+   (gnc:tissue a owl:Class)
+   (gnc:tissue rdfs:subClassOf obo:UBERON_0000479) ; Anatomical Entity
+   (gnc:tissue rdfs:label "Tissue (GN)")
+   (gnt:has_tissue rdf:type owl:ObjectProperty)
+   (gnt:has_tissue rdfs:domain gnc:molecular_traits)
+   (gnt:has_tissue rdfs:range gnc:tissue)
+   (gnt:has_tissue rdfs:label "has tissue"))
+  (triples (string->identifier "tissue" (field Tissue Short_Name)
+                               #:separator "_")
+    (set rdf:type 'gnc:tissue)
+    (set rdfs:label (field Tissue Name))))
+
+
+
+(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 "Tissue Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+      ("obo:" "<http://purl.obolibrary.org/obo/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
+   (inputs
+    (list tissue))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
+;; http://purl.obolibrary.org/obo/UBERON_0000479
diff --git a/examples/tissue.scm b/examples/tissue.scm
deleted file mode 100755
index 82cc226..0000000
--- a/examples/tissue.scm
+++ /dev/null
@@ -1,56 +0,0 @@
-#! /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 tissue
-  ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID
-  ;; and BIRN_lex_Name are mostly NULL.
-  (tables (Tissue))
-  (schema-triples
-   (gnc:tissue a skos:Concept))
-  ;; Hopefully the Short_Name field is distinct and can be used as an
-  ;; identifier.
-  (triples (string->identifier "tissue" (field Tissue Short_Name)
-                               #:separator "_")
-    (set rdf:type 'gnc:tissue)
-    (set rdfs:label (field Tissue Name))))
-
-
-
-(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 "Tissue Metadata")
-   (connection %connection-settings)
-   (table-metadata? #f)
-   (prefixes
-    '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
-      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
-      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
-      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
-   (inputs
-    (list tissue))
-   (outputs
-    `(#:documentation ,documentation
-      #:rdf ,output))))
-- 
cgit 1.4.1