Add probesetXRef metadata.

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

1 files changed, 93 insertions, 0 deletions

diff --git a/examples/probesets-experiment-metadata.scm b/examples/probesets-experiment-metadata.scm
new file mode 100755
index 0000000..e019928
--- /dev/null
+++ b/examples/probesets-experiment-metadata.scm
@@ -0,0 +1,93 @@
+#! /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)
+             (web uri))
+
+
+(define-transformer probesetxref->metadata
+  (tables (ProbeSetXRef
+           (inner-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")
+           (inner-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId")))
+  (triples (string->identifier
+            "probeset_data"
+            (uri-encode
+             (format #f "~a_~a" (field ProbeSetFreeze Name ProbeSetFreezeName) (field ProbeSet Name ProbeSetName))) #:separator "_")
+    (set rdf:type 'gnc:molecular_trait_metadata)
+    (set gnt:has_probeset (string->identifier "probeset" (field ProbeSet Name ProbeSetName)))
+    (set dcat:isPartOf (string->identifier "dataset" (field ProbeSetFreeze Name ProbeSetFreezeName)
+                                           #:separator "_"))
+    (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
+                                  '^^xsd:double))
+    (set gnt:SE (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se))
+                                '^^xsd:double))
+    (set gnt:locus (sanitize-rdf-string (field ProbeSetXRef Locus)))
+    (set gnt:lod_score (annotate-field
+                        (field ("IFNULL((ProbeSetXRef.LRS/4.604), '')" lrs))
+                        '^^xsd:double))
+    (set gnt:pvalue (annotate-field
+                        (field ("IFNULL((ProbeSetXRef.pValue), '')" pValue))
+                        '^^xsd:double))
+    (set gnt:additive (annotate-field
+                        (field ("IFNULL((ProbeSetXRef.additive), '')" additive))
+                        '^^xsd:double))
+    (set gnt:h2 (annotate-field
+                 (field ("IFNULL((ProbeSetXRef.h2), '')" h2))
+                 '^^xsd:double))))
+
+
+
+(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)))
+  (call-with-target-database
+   %connection-settings
+   (lambda (db)
+     (with-documentation
+      (name "ProbeSet Experiments Metadata")
+      (connection %connection-settings)
+      (table-metadata? #f)
+      (total-rows (assoc-ref
+                   (sql-find db "SELECT count(*) AS count from ProbeSetXRef")
+                   "count"))
+      (rows-per-chunk 1000000)
+      (prefixes
+       '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+         ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
+         ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
+         ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+         ("kegg:" "<http://bio2rdf.org/ns/kegg#>")
+         ("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+         ("omim:" "<https://www.omim.org/entry/>")
+         ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+         ("uniprot:" "<http://purl.uniprot.org/uniprot/>")
+         ("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+         ("dcat:" "<http://www.w3.org/ns/dcat#>")
+         ("dct:" "<http://purl.org/dc/terms/>")
+         ("owl:" "<http://www.w3.org/2002/07/owl#>")
+         ("homologene:" "<https://bio2rdf.org/homologene:>")
+         ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+         ("qb:" "<http://purl.org/linked-data/cube#>")
+         ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
+         ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
+      (inputs
+       (list probesetxref->metadata))
+      (outputs
+       `(#:documentation ,documentation
+         #:rdf ,output))))))