Rename {genotype,molecular-traits}.scm.

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

1 files changed, 123 insertions, 0 deletions

diff --git a/examples/molecular-traits-datasets.scm b/examples/molecular-traits-datasets.scm
new file mode 100755
index 0000000..77bba08
--- /dev/null
+++ b/examples/molecular-traits-datasets.scm
@@ -0,0 +1,123 @@
+#! /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 gn:molecular-trait->gn:dataset
+  (tables (Tissue))
+  (schema-triples
+   (gnc:molecular_trait a owl:Class)
+   (gnc:molecular_trait a skos:Concept)
+   (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479)
+   (gnc:molecular_trait rdfs:label "Molecular Trait.   This describes a melecular trait of a given species.  We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups."))
+  (triples (string->identifier "trait" (field Tissue Short_Name) #:separator "_")
+    (set rdf:type 'gnc:molecular_trait)
+    (set skos:prefLabel (field Tissue Name))
+    (set skos:altLabel (field Tissue Short_Name))))
+
+(define-transformer gnc:molecular_trait->gn:molecular_trait
+  (tables (Tissue))
+  (triples "gnc:molecular_trait"
+    (set skos:member (string->identifier "trait" (field Tissue Short_Name) #:separator "_"))))
+
+(define-transformer gn:set->gn:dataset
+  (tables (Species
+           (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
+           (inner-join ProbeFreeze "ON ProbeFreeze.InbredSetId = InbredSet.Id")
+           (inner-join ProbeSetFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
+           (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
+          "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, Tissue.Short_Name")
+  (schema-triples
+   (gnt:has_probeset_data rdf:type owl:ObjectProperty)
+   (gnt:has_probeset_data rdfs:label "this resources has this probeset data.")
+   (gnt:has_probeset_data rdfs:comment "Associates a resource with this probeset data.")
+   (gnt:has_probeset_data rdfs:domain gnc:set)
+   (gnt:has_probeset_data rdfs:range gnc:molecular_trait)
+   (gnt:has_probeset_data rdfs:subPropertyOf dct:relation))
+  (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
+    (multiset gnt:has_probeset_data
+              (map (cut string->identifier "dataset" <> #:separator "_")
+                   (string-split
+                    (field ("GROUP_CONCAT(ProbeSetFreeze.Name SEPARATOR ',')"
+                            dataset_name))
+                    #\,)))))
+
+(define-transformer gn:dataset->metadata
+  (tables (ProbeSetFreeze
+           (inner-join ProbeFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
+           (inner-join InbredSet "ON InbredSet.Id = ProbeFreeze.InbredSetId")
+           (inner-join Species "ON InbredSet.SpeciesId = Species.Id")
+           (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id")
+           (inner-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
+           (inner-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
+           (inner-join Datasets "ON InfoFiles.DatasetId = Datasets.DatasetId")
+           (left-join GeneChip "ON GeneChip.Id =  InfoFiles.GeneChipId"))
+          "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'")
+  (schema-triples
+   (gnt:has_molecular_trait rdf:type owl:ObjectProperty)
+   (gnt:has_molecular_trait rdfs:domain gnc:set)
+   (gnt:has_molecular_trait rdfs:range gnc:molecular_trait)
+   (gnt:has_molecular_trait rdfs:label "has molecular trait")
+   (gnt:uses_genechip a owl:ObjectProperty)
+   (gnt:uses_genechip rdfs:domain dcat:Dataset)
+   (gnt:uses_genechip skos:definition "The Platform this resource uses..")
+   (gnt:uses_normalization_method rdfs:comment "The normalization method used for the molecular traits in this dataset")
+   (gnt:uses_normalization_method rdfs:domain dcat:Dataset)
+   (gnt:uses_normalization_method rdfs:label "Averaging method used for the molecular traits in this dataset.")
+   (gnt:uses_normalization_method rdfs:range gnc:avg_method))
+  (triples (string->identifier "dataset" (field ProbeSetFreeze Name) #:separator "_")
+    (set dct:created (annotate-field (field ProbeSetFreeze CreateTime) '^^xsd:datetime))
+    (set gnt:uses_normalization_method
+         (string->identifier "avg_method" (field AvgMethod Name AvgMethodName) #:separator "_"))
+    (set gnt:has_molecular_trait
+         (string->identifier "trait" (field Tissue Short_Name) #:separator "_"))
+    (set gnt:uses_genechip
+         (string->identifier "platform" (field GeneChip Name) #:separator "_"))))
+
+
+(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 "Molecular Trait Datasets")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("dcat:" "<http://www.w3.org/ns/dcat#>")
+      ("gn:" "<http://rdf.genenetwork.org/v1/id/>")
+      ("obo:" "<http://purl.obolibrary.org/obo/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+      ("dct:" "<http://purl.org/dc/terms/>")
+      ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
+      ("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
+     gn:dataset->metadata
+     gn:molecular-trait->gn:dataset
+     gn:set->gn:dataset
+     gnc:molecular_trait->gn:molecular_trait))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))