Merge pull request ga4gh-beacon#1 from kellrott/genotype-to-phenotype

Emphasising the association in the class that connects the genotype and the phenotype

src/main/resources/avro/wip/genotypephenotype.avdl

@@ -1,6 +1,6 @@
 @namespace("org.ga4gh")
 /**
-This protocol defines genotype to phenotype relationships 
+This protocol defines genotype to phenotype relationships
 */
 protocol GenotypePhenotype {
 
@@ -11,21 +11,23 @@ import idl "metadata.avdl";
 /**
 An association between a variant or variant set and a phenotype
 */
-record VariantPhenotype {
+record VariantPhenotypeAssociation {
   string id;
 
-  /** 
+  Evidence evidenceSet;
+
+  /**
     The set of variants of the organism that bears the phenotype.
-    If the goal is to associate a single variant, then a singleton VariantSet is used 
+    If the goal is to associate a single variant, then a singleton VariantSet is used
   */
   VariantSet variantSet;
 
-  /** 
+  /**
     The phenotypic component of this association.
     Note that we delegate this to a separate record to allow us the flexibility to composition of phenotype
     associations with records that are not variant sets - for example, diseases.
   */
-  PhenotypeAssociation phenotypeAssociation;
+  Phenotype phenotypeAssociation;
 
 }
 
@@ -34,7 +36,7 @@ An association to a phenotype and related information.
 This record is intended primarily to be used in conjunction with variants, but the record can
 also be composed with other kinds of entities such as diseases
 */
-record PhenotypeAssociation {
+record Phenotype {
 
   /** HPO is recommended */
   OntologyTerm phenotype;
@@ -49,13 +51,12 @@ record PhenotypeAssociation {
   /** A textual description of the phenotype. This is used to complement the structured phenotype description in the phenotype field */
   union { null, string } description = null;
 
-  /** 
+  /**
     the environmental context in which the phenotype arises.
     multiple contexts can be specified - these are assumed to all hold together
   */
   array<EnvironmentContext> environmentalContexts;
 
-  array<Evidence> evidenceSet;
 
 }
 
@@ -75,7 +76,7 @@ record EnvironmentalContext {
 }
 
 /**
-Evidence for the phenotype association. 
+Evidence for the phenotype association.
 */
 record Evidence {