Update cds-model.yml

model-desc/cds-model.yml

@@ -8,6 +8,7 @@ Nodes:
       - program_full_description
       - program_external_url
       - program_sort_order
+      - institution
   study:
     Props:
       - study_name
@@ -36,24 +37,28 @@ Nodes:
       - data_access_level
       - cds_primary_bucket
       - cds_secondary_bucket
-      - cds_tertiary_bucket      
+      - cds_tertiary_bucket
       - number_of_participants
       - number_of_samples
       - study_data_types
       - file_types_and_format
       - size_of_data_being_uploaded
       - acl
+      - study_access
+      - authz
   participant:
     Props:
+      - study_participant_id
       - participant_id
       - race
       - gender
       - ethnicity
       #  - vital_status
       - dbGaP_subject_id
-      
+
   diagnosis: # may have multiple dxs for multiple timepoints?
     Props:
+      - study_diagnosis_id
       - diagnosis_id
       - disease_type
       - vital_status
@@ -78,9 +83,6 @@ Nodes:
       - treatment_outcome
       - days_to_treatment
       - therapeutic_agents
-  specimen:
-    Props:
-      - specimen_id
   sample: # aka subspecimen (CMB)
     Props:
       - sample_id
@@ -90,8 +92,7 @@ Nodes:
       - sample_age_at_collection
       - derived_from_specimen
       - biosample_accession
-      - experimental_strategy_and_data_subtypes
-
+
   file:
     Props:
       - file_id
@@ -102,9 +103,11 @@ Nodes:
       - md5sum
       - file_url_in_cds
       - experimental_strategy_and_data_subtypes
+      #- file_access
 
   genomic_info:
     Props:
+      - genomic_info_id
       - library_id
       - bases
       - number_of_reads
@@ -120,11 +123,6 @@ Nodes:
       - platform
       - instrument_model
       - sequence_alignment_software
-
-  methylation:
-    Props:
-      - reporter_label
-      - methylation_platform
 Relationships:
   of_program:
     Props: null
@@ -146,51 +144,17 @@ Relationships:
     Ends:
       - Src: diagnosis
         Dst: participant
-      - Src: specimen
-        Dst: participant
       - Src: sample
         Dst: participant
-  of_specimen:
+  of_sample:
     Props: null
     Mul: many_to_one
-    Ends:
-      - Src: sample
-        Dst: specimen
-  from_sample:
-    Props: null
-    Mul: many_to_many
     Ends:
       - Src: file
         Dst: sample
-  from_genomic_info:
-    Props: null
-    Mul: many_to_many
-    Ends:
-      - Src: file
-        Dst: genomic_info
-  in_genomic_info:
-    Props: null
-    Mul: many_to_many
-    Ends:
-      - Src: sample
-        Dst: genomic_info
   of_file:
     Props: null
     Mul: one_to_one
     Ends:
       - Src: genomic_info
         Dst: file
-      - Src: methylation
-        Dst: file
-  from_methylation:
-    Props: null
-    Mul: many_to_many
-    Ends:
-      - Src: file
-        Dst: methylation
-  in_methylation:
-    Props: null
-    Mul: many_to_many
-    Ends:
-      - Src: sample
-        Dst: methylation