Rename {genotype,molecular-traits}.scm.

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

1 files changed, 0 insertions, 123 deletions

diff --git a/examples/molecular-traits.scm b/examples/molecular-traits.scm
deleted file mode 100755
index 77bba08..0000000
--- a/examples/molecular-traits.scm
+++ /dev/null
@@ -1,123 +0,0 @@
-#! /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))))