Add slot to WorkflowExecution and DataObject classes to point to newer versions of associated WorkflowExecution

src/data/invalid/MagsAnalysis_invalid-newer-version.yaml

@@ -0,0 +1,29 @@
+id: nmdc:wfmag-11-547rwq94.1
+ended_at_time: '2021-09-15T10:13:20+00:00'
+execution_resource: NERSC-Perlmutter
+processing_institution: NMDC
+git_url: git_url1
+name: MAG analysis for project ABCD
+started_at_time: '2021-08-05T14:48:51+00:00'
+type: nmdc:MagsAnalysis
+was_informed_by:
+  - "nmdc:omprc-11-547rwq95"
+has_input:
+  - "nmdc:dobj-11-547rwq96"
+has_output:
+  - "nmdc:dobj-11-547rwq97"
+  - "nmdc:dobj-11-547rwq98"
+mags_list:
+  - bin_name: bins.10
+    bin_quality: LQ
+    members_id:
+      - nmdc:wfmgas-13-56028x05.1_7_c1
+      - nmdc:wfmgas-13-56028x05.1_9_c1
+    type: nmdc:MagBin
+    eukaryotic_evaluation:
+      type: nmdc:EukEval
+      completeness: 14.71
+      contamination: 8.82
+      ncbi_lineage_tax_ids: "1-131567-2759-2611352-33682-191814-2603949"
+      ncbi_lineage: "root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae"
+superseded_by: nmdc:wfmb-11-547rwq94.2

src/data/valid/MagsAnalysis.yaml

@@ -25,4 +25,5 @@ mags_list:
       completeness: 14.71
       contamination: 8.82
       ncbi_lineage_tax_ids: "1-131567-2759-2611352-33682-191814-2603949"
-      ncbi_lineage: "root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae" 
+      ncbi_lineage: "root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae"
+superseded_by: nmdc:wfmag-11-547rwq94.2

src/schema/basic_classes.yaml

@@ -368,6 +368,7 @@ classes:
       - url
       - was_generated_by
       - in_manifest
+      - superseded_by
     slot_usage:
       name:
         required: true
@@ -387,6 +388,7 @@ classes:
         required: true
       data_category:
         required: true
+
   DataEmitterProcess:
     class_uri: nmdc:DataEmitterProcess
     is_a: PlannedProcess
@@ -462,6 +464,7 @@ classes:
       - version
       - was_informed_by
       - processing_institution_workflow_metadata
+      - superseded_by
     rules:
       - title: qc_status_pass_has_output_required
         description: >-
@@ -687,6 +690,13 @@ slots:
     description: >-
       The type of planned process that the protocol describes.
 
+  superseded_by:
+    range: WorkflowExecution
+    description: >-
+      Links a DataObject or WorkflowExecution record to a newer WorkflowExecution that 
+      supersedes it, marking this record as outdated. The linked WorkflowExecution or
+      resultant DataObjects should be used in favor of this record.
+
 enums:
   CreditEnum:
     permissible_values:

src/schema/workflow_execution_activity.yaml

@@ -61,6 +61,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: NucleotideSequencing
+      superseded_by:
+        range: MetagenomeAssembly
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   MetatranscriptomeAssembly:
     class_uri: nmdc:MetatranscriptomeAssembly
@@ -105,6 +110,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: NucleotideSequencing
+      superseded_by:
+        range: MetatranscriptomeAssembly
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   MetatranscriptomeAnnotation:
     class_uri: nmdc:MetatranscriptomeAnnotation
@@ -137,6 +147,11 @@ classes:
         structured_pattern:
           syntax: "^gold:Ga[0-9]+$"
           interpolated: true
+      superseded_by:
+        range: MetatranscriptomeAnnotation
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   MetatranscriptomeExpressionAnalysis:
     is_a: WorkflowExecution
@@ -157,6 +172,12 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: NucleotideSequencing
+      superseded_by:
+        range: MetatranscriptomeExpressionAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
+
     class_uri: nmdc:MetatranscriptomeExpressionAnalysis
 
 
@@ -186,6 +207,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: NucleotideSequencing
+      superseded_by:
+        range: MagsAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   ReadQcAnalysis:
     class_uri: nmdc:ReadQcAnalysis
@@ -210,6 +236,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: NucleotideSequencing
+      superseded_by:
+        range: ReadQcAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   ReadBasedTaxonomyAnalysis:
     class_uri: nmdc:ReadBasedTaxonomyAnalysis
@@ -227,6 +258,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: NucleotideSequencing
+      superseded_by:
+        range: ReadBasedTaxonomyAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   MetabolomicsAnalysis:
     class_uri: nmdc:MetabolomicsAnalysis
@@ -246,6 +282,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: MassSpectrometry
+      superseded_by:
+        range: MetabolomicsAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   MetaproteomicsAnalysis:
     class_uri: nmdc:MetaproteomicsAnalysis
@@ -263,6 +304,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: MassSpectrometry
+      superseded_by:
+        range: MetaproteomicsAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
   NomAnalysis:
     class_uri: nmdc:NomAnalysis
@@ -280,6 +326,11 @@ classes:
           syntax: "{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$"
           interpolated: true
         range: MassSpectrometry
+      superseded_by:
+        range: NomAnalysis
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$"
+          interpolated: true
 
 slots: