From 304c35e25c33ee6af576c9122e897b0972602481 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Fri, 26 May 2023 13:00:28 +0300
Subject: Move probeset metadata used for a given experiment to it's own dump

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-probeset-metadata.scm | 107 ++++++++++++++++++++++++++++++++++++
 examples/dump-probeset.scm          |  22 --------
 2 files changed, 107 insertions(+), 22 deletions(-)
 create mode 100755 examples/dump-probeset-metadata.scm

(limited to 'examples')

diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm
new file mode 100755
index 0000000..ae9931c
--- /dev/null
+++ b/examples/dump-probeset-metadata.scm
@@ -0,0 +1,107 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+(define-dump dump-probeset-metadata
+  (tables (ProbeSetXRef
+           (left-join ProbeSet "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
+           (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")))
+  (schema-triples
+   (gn:probesetData rdfs:range gn:probeset)
+   (gn:hasProbeset rdfs:range rdfs:Literal))
+  (triples
+      (string->identifier
+       "probesetData"
+       (field ("CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id))"
+               ProbeSetName)))
+    (set rdf:type 'gn:probesetData)
+    (set gn:hasProbeset
+         (ontology
+          'probeset:
+          (regexp-substitute/global
+           #f "[^A-Za-z0-9:]"
+           (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
+                   name))
+           'pre "_" 'post)))
+    (set gn:probesetOfDataset
+         (ontology
+          'probeset:
+          (regexp-substitute/global #f "[^A-Za-z0-9:]"
+                                    (field ProbeSetFreeze Name)
+                                    'pre "_" 'post)))
+    (set gn:mean
+         (annotate-field
+          (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
+          '^^xsd:double))
+    (set gn:se
+         (annotate-field
+          (field ("IFNULL(ProbeSetXRef.se, '')" se))
+          '^^xsd:double))
+    (set gn:locus (field ProbeSetXRef Locus))
+    (set gn:LRS
+         (annotate-field
+          (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
+          '^^xsd:double))
+    (set gn:pValue
+         (annotate-field
+          (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
+          '^^xsd:double))
+    (set gn:additive
+         (annotate-field
+          (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
+          '^^xsd:double))
+    (set gn:h2
+         (annotate-field
+          (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
+          '^^xsd:float))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-probeset-metadata.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (prefix "probeset:" "<http://genenetwork.org/probeset/>")
+       (newline)
+       (dump-probeset-metadata db))
+     #:encoding "utf8")))
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index e659120..4fa030f 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -22,8 +22,6 @@
 
 (define-dump dump-probeset
   (tables (ProbeSet
-           (left-join ProbeSetXRef "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
-           (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id")
            (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
   (schema-triples
    (gn:name rdfs:range rdfs:Literal))
@@ -31,26 +29,6 @@
             'probeset:
             (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
                     name)))
-    (set gn:probesetOfDataset
-         (ontology
-          'probeset:
-          (regexp-substitute/global
-           #f "[^A-Za-z0-9:]"
-           (field ("IFNULL(ProbeSetFreeze.Name, '')" DatasetName))
-           'pre "_" 'post)))
-    (set gn:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
-                                 '^^xsd:double))
-    (set gn:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se))
-                               '^^xsd:double))
-    (set gn:LRS (annotate-field (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS))
-                                '^^xsd:double))
-    (set gn:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
-                                   '^^xsd:double))
-    (set gn:additive (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
-                                     '^^xsd:double))
-    (set gn:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
-                               '^^xsd:float))
-    (set gn:locus (field ProbeSetXRef Locus))
     (set gn:chipOf (string->identifier "platform" (field GeneChip Name)))
     (set gn:name (field ProbeSet Name))
     (set gn:symbol (field ProbeSet Symbol))
-- 
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