Rename tissue.scm -> molecular-traits.scm.

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

1 files changed, 63 insertions, 0 deletions

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