Update phenotypes.

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

2 files changed, 39 insertions, 32 deletions

diff --git a/examples/ontology.scm b/examples/ontology.scm
index a834045..2e03c53 100755
--- a/examples/ontology.scm
+++ b/examples/ontology.scm
@@ -232,6 +232,6 @@
       (triple 'gnt:submitter 'rdfs:domain 'gnc:phenotype)
       (triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN")
       (triple 'gnt:submitter 'skos:definition "A person who submitted this resource to GN")
-      (triple 'gnt:has_phenotype_trait 'a 'owl:ObjectProperty)
-      (triple 'gnt:has_phenotype_trait 'rdfs:domain 'gnc:set)
-      (triple 'gnt:has_phenotype_trait 'skos:definition "This is the unique trait id assigned from GeneNetwork for a a phenotype.   It's a combination of the set name and the phenotype's post pub abbreviation."))))
+      (triple 'gnt:has_phenotype_data 'a 'owl:ObjectProperty)
+      (triple 'gnt:has_phenotype_data 'rdfs:domain 'gnc:set)
+      (triple 'gnt:has_phenotype_data 'skos:definition "This resource has phenotype data."))))
diff --git a/examples/phenotype.scm b/examples/phenotype.scm
index 3e69607..b243ccd 100755
--- a/examples/phenotype.scm
+++ b/examples/phenotype.scm
@@ -17,6 +17,38 @@
   (if (string-blank? str) #f str))
 
 
+(define-transformer gn:set->gn:dataset
+  (tables (Species
+           (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
+           (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id"))
+          "WHERE PublishFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, PublishFreeze.ShortName")
+  (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
+    (multiset gnt:has_phenotype_data
+              (map (cut string->identifier "dataset" <> #:separator "_")
+                   (string-split
+                    (field ("GROUP_CONCAT(PublishFreeze.Name SEPARATOR ',')"
+                            dataset_name))
+                    #\,)))))
+
+(define-transformer gn:dataset->gn:trait
+  (tables (PublishXRef
+           (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
+           (inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")
+           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
+           (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
+          "WHERE InbredSet.public > 0")
+  (triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")
+    (set gnt:has_phenotype_trait
+         (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
+               (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
+               (post-desc (blank-p (field Phenotype Post_publication_description)))
+               (pre-desc (blank-p (field Phenotype Post_publication_description))))
+           (string->identifier
+            "trait"
+            (format #f "~a_~a" (field PublishFreeze Name)
+                    (or post-abbrev pre-abbrev post-desc pre-desc))
+            #:separator "_")))))
+
 (define-transformer gnc:phenotype->gn:phenotype
   (tables (Phenotype))
   (triples "gnc:phenotype"
@@ -61,24 +93,6 @@
             (or post-abbrev pre-abbrev post-desc pre-desc)
             #:separator "_")))))
 
-(define-transformer gnc:set->gn:trait
-  (tables (PublishXRef
-           (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
-           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
-           (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
-          "WHERE InbredSet.public > 0")
-  (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
-    (set gnt:has_phenotype_trait
-         (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
-               (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
-               (post-desc (blank-p (field Phenotype Post_publication_description)))
-               (pre-desc (blank-p (field Phenotype Post_publication_description))))
-           (string->identifier
-            "trait"
-            (format #f "~a_~a" (field InbredSet Name InbredSetName)
-                    (or post-abbrev pre-abbrev post-desc pre-desc))
-            #:separator "_")))))
-
 (define-transformer gn:trait->gn:phenotype
   (tables (PublishXRef
            (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
@@ -91,17 +105,14 @@
                  (pre-desc (blank-p (field Phenotype Post_publication_description))))
              (string->identifier
               "trait"
-              (format #f "~a_~a" (field InbredSet Name InbredSetName)
+              (format #f "~a_~a" (field PublishFreeze Name)
                       (or post-abbrev pre-abbrev post-desc pre-desc))
               #:separator "_"))
     (set rdf:type 'gnc:phenotype_trait)
     (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))
     (set owl:equivalentClass
-         (string->identifier
-          "trait"
-          (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
-                  Phenotype))
-          #:separator "_"))
+         (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
+                  Phenotype)))
     (set dct:references
          (let ((pmid (field
                       ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
@@ -172,11 +183,7 @@
       ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
       ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
    (inputs
-    (list
-     gnc:phenotype->gn:phenotype
-     gn:phenotype->metadata
-     gnc:set->gn:trait
-     gn:trait->gn:phenotype))
+    (list gn:set->gn:dataset gn:dataset->gn:trait gnc:phenotype->gn:phenotype gn:phenotype->metadata gn:trait->gn:phenotype))
    (outputs
     `(#:documentation ,documentation
       #:rdf ,output))))