Remove "dump-" prefix

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

1 files changed, 226 insertions, 0 deletions

diff --git a/examples/species-metadata.scm b/examples/species-metadata.scm
new file mode 100755
index 0000000..f3794b8
--- /dev/null
+++ b/examples/species-metadata.scm
@@ -0,0 +1,226 @@
+#! /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 (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 species
+  (tables (Species))
+  (schema-triples
+   (gnc:species a skos:Concept)
+   (gnc:species skos:description "This is a set of controlled terms that are used to describe a given species")
+   (gnc:species skos:broader gnc:family)
+   (gnt:binomialName a owl:ObjectProperty)
+   (gnt:binomialName rdfs:domain gnc:species)
+   (gnt:family a owl:ObjectProperty)
+   (gnt:family rdfs:domain gnc:species)
+   (gnt:family skos:definition "This resource belongs to this family")
+   (gnt:organism a owl:ObjectProperty)
+   (gnt:organism rdfs:domain gnc:species)
+   (gnt:shortName a owl:ObjectProperty)
+   (gnt:shortName rdfs:domain gnc:species))
+  (triples
+      (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                          #:separator ""
+                          #:proc string-capitalize-first)
+    (set rdf:type 'gnc:species)
+    (set skos:label (field Species SpeciesName))
+    (set skos:altLabel (field Species Name))
+    (set rdfs:label (field Species MenuName))
+    (set gnt:binomialName (field Species FullName))
+    (set gnt:family (field Species Family))
+    (set gnt:organism (ontology 'taxon: (field Species TaxonomyId)))))
+
+#!
+
+The ProbeData table contains StrainID.
+
+MariaDB [db_webqtl]> select * from ProbeData limit 2;
++--------+----------+---------+
+| Id     | StrainId | value   |
++--------+----------+---------+
+| 503636 |       42 | 11.6906 |
+| 503636 |       43 | 11.4205 |
++--------+----------+---------+
+
+Likewise
+
+MariaDB [db_webqtl]> select * from ProbeSetData wher limit 2;
++----+----------+-------+
+| Id | StrainId | value |
++----+----------+-------+
+|  1 |        1 | 5.742 |
+|  1 |        2 | 5.006 |
++----+----------+-------+
+
+To get at the strain use
+
+MariaDB [db_webqtl]> select * from Strain where Id=1 limit 15;
++----+--------+--------+-----------+--------+-------+
+| Id | Name   | Name2  | SpeciesId | Symbol | Alias |
++----+--------+--------+-----------+--------+-------+
+|  1 | B6D2F1 | B6D2F1 |         1 | NULL   | NULL  |
++----+--------+--------+-----------+--------+-------+
+
+A typical query may look like
+
+SELECT Strain.Name, Strain.Id FROM Strain, Species
+WHERE Strain.Name IN f{create_in_clause(self.samplelist)}
+AND Strain.SpeciesId=Species.Id
+AND Species.name = %s, (self.group.species,)
+
+At this point it is not very clear how Name, Name2, Symbol and Alias are used.
+
+!#
+
+(define-transformer strain
+  (tables (Strain
+           (left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
+  (schema-triples
+   (gnc:strain skos:broader gnc:species)
+   (gnt:belongsToSpecies rdfs:domain gnc:strain)
+   (gnt:belongsToSpecies skos:definition "This resource belongs to this species")
+   (gnt:belongsToSpecies a owl:ObjectProperty)
+   (gnt:belongsToSpecies skos:definition "This resource belongs to this species")
+   (gnt:alias rdfs:domain gnc:strain)
+   (gnt:alias a owl:ObjectProperty)
+   (gnt:symbol rdfs:domain gnc:strain)
+   (gnt:symbol a owl:ObjectProperty))
+  (triples (string->identifier
+            ""
+            (regexp-substitute/global
+             #f "[^A-Za-z0-9:]"
+             (field Strain Name)
+             'pre "_" 'post)
+            #:separator ""
+            #:proc string-capitalize-first)
+    (set rdf:type 'gnc:strain)
+    (set gnt:belongsToSpecies
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))
+    ;; Name, and maybe a second name
+    (set rdfs:label (sanitize-rdf-string (field Strain Name)))
+    (set rdfs:label (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2))))
+    (set gnt:alias (sanitize-rdf-string (field ("IF ((Strain.Alias != Strain.Name), Strain.Alias, '')" Alias))))
+    (set gnt:symbol (field ("IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '')" Symbol)))))
+
+(define-transformer mapping-method
+  (tables (MappingMethod))
+  (schema-triples
+   (gnc:mappingMethod a skos:Concept)
+   (gnc:mappingMethod skos:definition "Terms that decribe mapping/normalization methods used in GeneNetwork"))
+  (triples
+      (string->identifier "mappingMethod" (field MappingMethod Name))
+    (set rdf:type 'gnc:mappingMethod)
+    (set rdfs:label (field MappingMethod Name))))
+
+
+(define-transformer inbred-set
+  (tables (InbredSet
+           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
+           (left-join MappingMethod
+                      "ON InbredSet.MappingMethodId=MappingMethod.Id")))
+  (schema-triples
+   (gnc:set skos:broader gnc:species)
+   (gnc:set skos:definition "A set of terms used to describe an set, which can be inbredSet, outbredSet etc etc.")
+   (gnt:geneticType a owl:ObjectProperty)
+   (gnt:geneticType rdfs:domain gnc:set)
+   (gnt:code a owl:ObjectProperty)
+   (gnt:code rdfs:domain gnc:set)
+   ;; Already defined as an owl prop in species
+   (gnt:family rdfs:domain gnc:set)
+   (gnt:phenotype a owl:ObjectProperty)
+   (gnt:phenotype rdfs:domain gnc:set)
+   (gnt:genotype a owl:ObjectProperty)
+   (gnt:genotype rdfs:domain gnt:inbredSet)
+   (gnt:mappingMethod a owl:ObjectProperty)
+   (gnt:mappingMethod rdfs:domain gnc:set))
+  (triples (string->identifier
+            "set" (field InbredSet Name)
+            #:separator ""
+            #:proc string-capitalize-first)
+    (set rdf:type 'gnc:set)
+    (set rdfs:label (field InbredSet FullName))
+    (set skos:altLabel (field InbredSet Name))
+    (set gnt:geneticType (field InbredSet GeneticType))
+    (set gnt:family (field InbredSet Family))
+    (set gnt:mappingMethod (field MappingMethod Name))
+    (set gnt:code (field InbredSet InbredSetCode))
+    (set gnt:belongsToSpecies
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))
+    (set gnt:genotype
+         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
+    (set gnt:phenotype
+         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))
+    (multiset gnt:hasTissue
+              (map
+               (lambda (x)
+                 (string->identifier "tissue"
+                                     x))
+               (string-split-substring
+                (field ("(SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name)"
+                        molecularTrait))
+                "||")))))
+
+(define-transformer avg-method
+  ;; The Name and Normalization fields seem to be the same. Dump only
+  ;; the Name field.
+  (tables (AvgMethod))
+  (schema-triples
+   (gnc:avgMethod rdf:type owl:Class))
+  (triples (string->identifier "avgmethod" (field AvgMethod Name))
+    (set rdf:type 'gnc:avgMethod)
+    (set rdfs:label (field AvgMethod Normalization))))
+
+
+
+(with-documentation
+ (name "Species Metadata")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+  '(("gn:" "<http://genenetwork.org/id/>")
+    ("gnc:" "<http://genenetwork.org/category/>")
+    ("owl:" "<http://www.w3.org/2002/07/owl#>")
+    ("gnt:" "<http://genenetwork.org/term/>")
+    ("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#>")
+    ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
+ (inputs
+  (list
+   inbred-set
+   species
+   strain
+   mapping-method
+   avg-method))
+ (outputs
+  '(#:documentation "./docs/species-metadata.md"
+    #:rdf "/export/data/genenetwork-virtuoso/species-metadata.ttl")))