Remove monkey data.

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

2 files changed, 18 insertions, 15 deletions

diff --git a/examples/classification.scm b/examples/classification.scm
index 759b5a7..ee59e8f 100755
--- a/examples/classification.scm
+++ b/examples/classification.scm
@@ -15,7 +15,8 @@
 
 ;; Classification Scheme
 (define-transformer gnc:species->gn:species
-  (tables (Species))
+  (tables (Species)
+          "WHERE Name != 'monkey'")
   (schema-triples
    (gnc:resource_classification_scheme a skos:ConceptScheme)
    (gnc:resource_classification_scheme skos:prefLabel "GeneNetwork Resource Classification Scheme")
@@ -46,7 +47,7 @@
 
 (define-transformer gnc:set->gn:set
   (tables (InbredSet)
-          "WHERE public > 0")
+          "WHERE public > 0 AND FullName NOT LIKE '%monkey%'")
   (schema-triples
    (gnc:set a xkos:ClassificationLevel)
    (gnc:set skos:inScheme gnc:resource_classification_scheme)
@@ -60,7 +61,8 @@
           "set" (field InbredSet Name InbredSetName) #:separator "_"))))
 
 (define-transformer gnc:species->metadata
-  (tables (Species))
+  (tables (Species)
+          "WHERE Name != 'monkey'")
   (schema-triples
    (gnt:has_uniprot_taxon_id a owl:ObjectProperty)
    (gnt:has_uniprot_taxon_id rdfs:label "has uniprot taxonomic id")
@@ -92,7 +94,7 @@
 (define-transformer gnc:species->gn:set
   (tables (InbredSet
            (left-join Species "ON InbredSet.SpeciesId=Species.Id"))
-          "WHERE public > 0")
+          "WHERE public > 0 AND Species.Name != 'monkey'")
   (schema-triples
    (gnt:has_strain a owl:ObjectProperty)
    (gnt:has_strain rdfs:range gnc:set)
@@ -105,7 +107,7 @@
 
 (define-transformer gn:family->gn:species/metadata
   (tables (Species)
-          "GROUP BY FAMILY")
+          "WHERE Name != 'monkey' GROUP BY FAMILY")
   (schema-triples
    (gnc:taxonomic_family a xkos:ClassificationLevel)
    (gnc:taxonomic_family skos:inScheme gnc:resource_classification_scheme)
@@ -124,7 +126,8 @@
                          '^^xsd:integer))))
 
 (define-transformer gn:family->gn:species
-  (tables (Species))
+  (tables (Species)
+          "WHERE Name != 'monkey'")
   (schema-triples
    (gnt:has_family_order_id a owl:DatatypeProperty))
   (triples (string->identifier "family" (field Species Family) #:separator "_")
@@ -137,7 +140,7 @@
            (left-join Species "ON InbredSet.SpeciesId=Species.Id")
            (left-join MappingMethod
                       "ON InbredSet.MappingMethodId=MappingMethod.Id"))
-          "WHERE public > 0")
+          "WHERE public > 0 AND Species.Name != 'monkey'")
   (schema-triples
    (gnt:genetic_type a owl:DatatypeProperty)
    (gnt:genetic_type rdfs:label "has genetic type")
@@ -175,7 +178,7 @@
 
 (define-transformer gn:set->gn:population
   (tables (InbredSet)
-          "WHERE Family IS NOT NULL")
+          "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%'")
   (schema-triples
    (gnt:has_reference_population rdfs:domain gnc:set)
    (gnt:has_reference_population a owl:ObjectProperty)
@@ -187,7 +190,7 @@
 
 (define-transformer gn:population->metadata
   (tables (InbredSet)
-          "WHERE Family IS NOT NULL GROUP BY Family")
+          "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%' GROUP BY Family")
   (schema-triples
    (gnc:reference_population a skos:Concept)
    (gnc:reference_population skos:inScheme gnc:population_category)
@@ -203,21 +206,21 @@
 
 (define-transformer gn:population->gn:set
   (tables (InbredSet)
-          "WHERE Family IS NOT NULL")
+          "WHERE Family IS NOT NULL AND FullName NOT LIKE '%monkey%'")
   (triples (string->identifier "population" (field InbredSet Family) #:separator "_")
     (set gnt:has_strain
          (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))))
 
 (define-transformer gnc:population_category->gn:population
   (tables (InbredSet)
-          "WHERE public > 0 GROUP BY Family")
+          "WHERE public > 0 AND FullName NOT LIKE '%monkey%' GROUP BY Family")
   (triples "gnc:population_category"
     (set gnt:has_reference_population
          (string->identifier "population" (field InbredSet Family) #:separator "_"))))
 
 (define-transformer gnc:taxonomic_family->gn:family
   (tables (Species)
-          "GROUP BY Family")
+          "WHERE Name != 'monkey' GROUP BY Family")
   (schema-triples
    (gnt:assigned_species rdfs:domain gnc:set)
    (gnt:assigned_species a owl:ObjectProperty)
diff --git a/examples/molecular-traits.scm b/examples/molecular-traits.scm
index 0393a0d..2f95ca3 100755
--- a/examples/molecular-traits.scm
+++ b/examples/molecular-traits.scm
@@ -35,7 +35,7 @@
            (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 GROUP BY Species.Name, Tissue.Short_Name")
+          "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, Tissue.Short_Name")
   (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
     (multiset gnt:has_probeset_data
               (map (cut string->identifier "dataset" <> #:separator "_")
@@ -50,7 +50,7 @@
            (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")
+          "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)
@@ -73,7 +73,7 @@
            (inner-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
            (inner-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
            (left-join GeneChip "ON GeneChip.Id =  InfoFiles.GeneChipId"))
-          "WHERE ProbeSetFreeze.public > 0")
+          "WHERE ProbeSetFreeze.public > 0 AND Species.Name != 'monkey'")
   (schema-triples
    (gnt:has_case_info a owl:ObjectProperty)
    (gnt:has_case_info rdfs:comment "Information about the cases used in this platform")