Merge pull request #2 from sdsc-ordes/refactor/base-schema

feat: add reference concepts

README.md

@@ -8,29 +8,43 @@ StudyCollection {
 
 }
 Study {
-    datetime start_date  
-    datetime completion_date  
-    uriorcurie id  
-    string name  
-    string description  
+    datetime start_date
+    datetime completion_date
+    uriorcurie id
+    string name
+    string description
 }
 Experiment {
 
 }
 Record {
-    uriorcurie location  
-    DataFormat format  
+    uriorcurie location
+    DataFormat format
+}
+ReferenceGenome {
+    string name
+    integer taxon_id
+    uriorcurie location
+    uriorcurie source_uri
+}
+ReferenceSequence {
+    string name
+    string sequence_md5
+    uriorcurie location
+    uriorcurie source_uri
 }
 Sample {
-    integer taxon_id  
-    string collector  
+    integer taxon_id
+    string collector
 }
 
 StudyCollection ||--}o Study : "entries"
 Study ||--|o Experiment : "has_experiment"
 Experiment ||--|o Sample : "has_sample"
 Experiment ||--|o Record : "has_record"
 Record ||--|o Sample : "has_sample"
+Record ||--|o ReferenceGenome : "has_reference"
+ReferenceGenome ||--|o ReferenceSequence : "has_sequence"
 ```
 
 ## Website

src/smoc_schema/schema/smoc_schema.yaml

@@ -77,6 +77,7 @@ classes:
       - location
       - format
       - has_sample
+      - has_reference
 
   ReferenceGenome:
     description: >-
@@ -178,6 +179,9 @@ slots:
   has_sequence:
     description: Denotes that a sequence beolongs to a collection (e.g. a reference genome).
     range: ReferenceSequence
+  has_reference:
+    description: Specifies the reference coordinate system used by an omics dataset.
+    range: ReferenceGenome
 
 enums:
   OmicsType: