From 51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 21 Aug 2023 14:54:21 +0300
Subject: Remove "dump-" prefix

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/phenotype.scm | 125 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 125 insertions(+)
 create mode 100755 examples/phenotype.scm

(limited to 'examples/phenotype.scm')

diff --git a/examples/phenotype.scm b/examples/phenotype.scm
new file mode 100755
index 0000000..1c68159
--- /dev/null
+++ b/examples/phenotype.scm
@@ -0,0 +1,125 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (rnrs programs)
+             (rnrs io ports)
+             (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-transformer phenotypes
+  (tables (PublishXRef
+           (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
+           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
+           (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
+          "WHERE PublishXRef.InbredSetId IN (SELECT PublishFreeze.InbredSetId FROM PublishFreeze)")
+  (schema-triples
+   (gnc:phenotype a skos:Concept)
+   (gnc:phenotype skos:description "This is a set of controlled terms that are used to describe a given phenotype")
+   (gnt:abbreviation a owl:ObjectProperty)
+   (gnt:abbreviation rdfs:domain gnc:phenotype)
+   (gnt:abbreviation skos:definition "The abbreviation used for this resource")
+   (gnt:traitName a owl:ObjectProperty)
+   (gnt:traitName rdfs:domain gnc:phenotype)
+   (gnt:traitName skos:definition "The trait Name of this resource")
+   (gnt:labCode a owl:ObjectProperty)
+   (gnt:labCode rdfs:domain gnc:phenotype)
+   (gnt:submitter a owl:ObjectProperty)
+   (gnt:submitter rdfs:domain gnc:phenotype)
+   (gnt:submitter skos:definition "A person who submitted this resource to GN")
+   (gnt:mean rdfs:domain gnc:phenotype)
+   (gnt:mean rdfs:range xsd:double)
+   (gnt:LRS rdfs:domain gnc:phenotype)
+   (gnt:LRS rdfs:range xsd:double)
+   (gnt:locus rdfs:domain gnc:phenotype)
+   (gnt:locus rdfs:range rdfs:Literal)
+   (gnt:additive rdfs:domain gnc:phenotype)
+   (gnt:additive rdfs:range xsd:double)
+   (gnt:sequence rdfs:domain gnc:phenotype)
+   (gnt:sequence rdfs:range xsd:integer))
+  (triples (string->identifier
+            "trait"
+            (field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
+                    Phenotype)))
+    (set rdf:type 'gnc:phenotype)
+    (set gnt:belongsToSet
+         (string->identifier
+          "set" (field InbredSet Name)
+          #:separator ""
+          #:proc string-capitalize-first))
+    (set gnt:traitName
+         (let ((trait-id (field PublishXRef Id)))
+           (if (number? trait-id)
+               (number->string trait-id)
+               trait-id)))
+    (set rdfs:label
+         (field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
+                 Phenotype)))
+    ;; All phenotypes have a post-publication description
+    (set dct:description
+         (sanitize-rdf-string
+          (field Phenotype Post_publication_description)))
+    ;; All phenotypes have a post-publication abbreviation
+    (set gnt:abbreviation (field Phenotype Post_publication_abbreviation))
+    (set gnt:labCode (field Phenotype Lab_code))
+    (set gnt:submitter
+         (sanitize-rdf-string (field Phenotype Submitter)))
+    (multiset dct:contributor
+              (string-split
+               (sanitize-rdf-string (field Phenotype Owner))
+               #\,))
+    (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
+                                  '^^xsd:double))
+    (set gnt:locus (field PublishXRef Locus))
+    (set gnt:LRS (annotate-field
+                  (field ("IFNULL(PublishXRef.LRS, '')" lrs))
+                  '^^xsd:double))
+    (set gnt:additive
+         (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive))
+                         '^^xsd:double))
+    (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:integer))
+    (set dct:isReferencedBy
+         (let ((pmid (field
+                      ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
+                       pmid)))
+               (publication-id (field Publication Id)))
+           (if (string-null? pmid)
+               (string->identifier "unpublished"
+                                   (number->string publication-id))
+               (ontology 'pubmed: pmid))))))
+
+
+
+(with-documentation
+ (name "Phenotypes Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+  '(("dct:" "<http://purl.org/dc/terms/>")
+    ("gn:" "<http://genenetwork.org/id/>")
+    ("owl:" "<http://www.w3.org/2002/07/owl#>")
+    ("gnc:" "<http://genenetwork.org/category/>")
+    ("gnt:" "<http://genenetwork.org/terms/>")
+    ("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#>")
+    ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
+ (inputs
+  (list
+   phenotypes))
+ (outputs
+  '(#:documentation "./docs/phenotype.md"
+    #:rdf "/export/data/genenetwork-virtuoso/phenotype.ttl")))
-- 
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