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/genotype.scm | 124 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)
 create mode 100755 examples/genotype.scm

(limited to 'examples/genotype.scm')

diff --git a/examples/genotype.scm b/examples/genotype.scm
new file mode 100755
index 0000000..63b85a7
--- /dev/null
+++ b/examples/genotype.scm
@@ -0,0 +1,124 @@
+#! /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 (remap-species-identifiers str)
+  "This procedure remaps identifiers to standard binominal. Obviously this should
+   be sorted by correcting the database!"
+  (match str
+    ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
+    ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
+    ["Macaca mulatta" "Macaca nemestrina"]
+    ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
+    [str str]))
+
+(define-transformer genotypes
+  (tables (Geno
+           (left-join Species "USING (SpeciesId)")))
+  (schema-triples
+   (gnc:genotype a skos:Concept)
+   (gnc:genotype
+    skos:description
+    "This is a set of controlled terms that are used to describe a given genotype")
+   (gnt:chr a owl:ObjectProperty)
+   (gnt:chr skos:description "This resource is located on a given chromosome")
+   (gnt:chr rdfs:domain gnc:genotype)
+   (gnt:mb a owl:ObjectProperty)
+   (gnt:mb skos:definition "The size of this resource in Mb")
+   (gnt:mb rdfs:domain gnc:genotype)
+   (gnt:mbMm8 a owl:ObjectProperty)
+   (gnt:mbMm8 skos:definition "TODO")
+   (gnt:mbMm8 rdfs:domain gnc:genotype)
+   (gnt:mb2016 a owl:ObjectProperty)
+   (gnt:mb2016 skos:definition "TODO")
+   (gnt:mb2016 rdfs:domain gnc:genotype)
+   (gnt:hasSequence a owl:ObjectProperty)
+   (gnt:hasSequence skos:definition "This resource has a given sequence")
+   (gnt:hasSequence rdfs:domain gnc:genotype)
+   (gnt:hasSource a owl:ObjectProperty)
+   (gnt:hasSource rdfs:domain gnc:genotype)
+   (gnt:hasSource skos:definition "This resource was obtained from this given source")
+   (gnt:hasAltSourceName a owl:ObjectProperty)
+   (gnt:hasAltSourceName rdfs:domain gnc:genotype)
+   (gnt:hasAltSourceName
+    skos:definition
+    "The alternative name this resource was obtained from")
+   (gnt:chrNum a owl:ObjectProperty)
+   (gnt:chrNum rdfs:domain gnc:genotype)
+   (gnt:chrNum skos:definition "The chromosome number for this resource")
+   (gnt:chrNum skos:definition "The chromosome number for this resource"))
+  (triples
+      (string->identifier
+       ""
+       (regexp-substitute/global
+        #f "[^A-Za-z0-9:]"
+        (field Geno Name)
+        'pre "_" 'post)
+       #:separator ""
+       #:proc string-capitalize-first)
+    (set rdf:type 'gnc:genotype)
+    (set skos:prefLabel (sanitize-rdf-string (field Geno Name)))
+    (set gnt:chr (field Geno Chr))
+    (set gnt:mb (annotate-field
+                 (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
+    (set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8))
+                                   '^^xsd:double))
+    (set gnt:mb2016
+         (annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016))
+                         '^^xsd:double))
+    (set gnt:hasSequence (field Geno Sequence))
+    (set gnt:hasSource (field Geno Source))
+    ;; Only dump Source2 if it differs from Source
+    (set gnt:hasAltSourceName
+         (field ("IF((Source2 = Source), NULL, Source2)"
+                 Source2)))
+    (set gnt:belongsToSpecies
+         (string->identifier
+          "" (remap-species-identifiers (field Species Fullname))
+          #:separator ""
+          #:proc string-capitalize-first))
+    (set gnt:chrNum
+         (annotate-field
+          (field Geno chr_num)
+          '^^xsd:int))
+    (set rdfs:comments (field Geno Comments))))
+
+
+
+(with-documentation
+ (name "Genotype Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+  '(("dct:" "<http://purl.org/dc/terms/>")
+    ("gn:" "<http://genenetwork.org/id/>")
+    ("gnc:" "<http://genenetwork.org/category/>")
+    ("gnt:" "<http://genenetwork.org/term/>")
+    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+    ("owl:" "<http://www.w3.org/2002/07/owl#>")
+    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
+ (inputs
+  (list genotypes))
+ (outputs
+  '(#:documentation "./docs/genotype.md"
+    #:rdf "/export/data/genenetwork-virtuoso/genotype.ttl")))
-- 
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