Merge pull request #2117 from microbiomedata/2116-update-description-…

…of-metatranscriptomeactivity-to-make-it-specific-to-the-expression-activity

Modeling of workflow execution activities for metatranscriptomes

src/data/invalid/Database-metatranscriptome_workflow-invalidDatabase.yaml

@@ -0,0 +1,60 @@
+#invalid because using metagenome_assembly_set for a metatranscriptome assembly record
+read_qc_analysis_activity_set:
+  - id: nmdc:wfrqc-11-23984.1
+    git_url: https://github.com/microbiomedata/metaT_ReadsQC
+    version: v0.0.1
+    started_at_time: '2023-08-05T14:48:51+00:00'
+    ended_at_time: '2021-08-05T14:48:51+00:00'
+    type: ReadQcAnalysis
+    execution_resource: LANL-B-div
+    was_informed_by:  nmdc:omprc-11-547rwq95
+    has_input:
+     - nmdc:dobj-11-547rwq96
+    has_output:
+     - nmdc:dobj-11-547rwq97
+     - nmdc:dobj-11-547rwq98
+metagenome_assembly_set:
+  - id: nmdc:wfmtas-11-23986.1
+    git_url: https://github.com/microbiomedata/metaT_Assembly/releases
+    version: v0.0.1
+    started_at_time: '2024-07-06T14:48:51+00:00'
+    ended_at_time: '2024-07-06T14:48:51+00:00'
+    type: MetatranscriptomeAssembly
+    execution_resource: LANL-B-div
+    was_informed_by:  nmdc:omprc-11-547rwq95
+    has_input:
+     - nmdc:dobj-11-547rwq97
+    has_output:
+     - nmdc:dobj-11-547rwq72
+     - nmdc:dobj-11-547rwq73
+metatranscriptome_annotation_set:
+  - id: nmdc:wfmtan-11-23987.1
+    git_url: https://github.com/microbiomedata/mg_annotation
+    version: v1.1.1
+    started_at_time: '2024-07-07T14:48:51+00:00'
+    ended_at_time: '2024-07-07T14:48:51+00:00'
+    type: MetatranscriptomeAnnotationActivity
+    was_informed_by: nmdc:omprc-11-547rwq95
+    execution_resource: LANL-B-div
+    has_input:
+     - nmdc:dobj-11-547rwq72
+    has_output:
+     - nmdc:dobj-11-547rwq75
+     - nmdc:dobj-11-547rwq77
+metatranscriptome_expression_set:
+  - id: nmdc:wfmtex-11-23989.1
+    git_url: https://github.com/microbiomedata/metaT_ReadCounts
+    version: v0.0.1
+    started_at_time: '2024-07-08T14:48:51+00:00'
+    ended_at_time: '2024-07-08T14:48:51+00:00'
+    type: MetatranscriptomeExpressionAnalysis
+    was_informed_by:  nmdc:omprc-11-547rwq95
+    execution_resource: LANL-B-div
+    has_input:
+     - nmdc:dobj-11-547rwq75
+     - nmdc:dobj-11-547rwq77
+     - nmdc:dobj-11-547rwq73
+    has_output:
+     - nmdc:dobj-11-547rwq82
+     - nmdc:dobj-11-547rwq83
+     - nmdc:dobj-11-547rwq84

src/data/valid/Database-metatranscriptome_workflow.yaml

@@ -0,0 +1,59 @@
+read_qc_analysis_activity_set:
+  - id: nmdc:wfrqc-11-23984.1
+    git_url: https://github.com/microbiomedata/metaT_ReadsQC
+    version: v0.0.1
+    started_at_time: '2023-08-05T14:48:51+00:00'
+    ended_at_time: '2021-08-05T14:48:51+00:00'
+    type: ReadQcAnalysis
+    execution_resource: LANL-B-div
+    was_informed_by:  nmdc:omprc-11-547rwq95
+    has_input:
+     - nmdc:dobj-11-547rwq96
+    has_output:
+     - nmdc:dobj-11-547rwq97
+     - nmdc:dobj-11-547rwq98
+metatranscriptome_assembly_set:
+  - id: nmdc:wfmtas-11-23986.1
+    git_url: https://github.com/microbiomedata/metaT_Assembly/releases
+    version: v0.0.1
+    started_at_time: '2024-07-06T14:48:51+00:00'
+    ended_at_time: '2024-07-06T14:48:51+00:00'
+    type: MetatranscriptomeAssembly
+    execution_resource: LANL-B-div
+    was_informed_by:  nmdc:omprc-11-547rwq95
+    has_input:
+     - nmdc:dobj-11-547rwq97
+    has_output:
+     - nmdc:dobj-11-547rwq72
+     - nmdc:dobj-11-547rwq73
+metatranscriptome_annotation_set:
+  - id: nmdc:wfmtan-11-23987.1
+    git_url: https://github.com/microbiomedata/mg_annotation
+    version: v1.1.1
+    started_at_time: '2024-07-07T14:48:51+00:00'
+    ended_at_time: '2024-07-07T14:48:51+00:00'
+    type: MetatranscriptomeAnnotationActivity
+    was_informed_by: nmdc:omprc-11-547rwq95
+    execution_resource: LANL-B-div
+    has_input:
+     - nmdc:dobj-11-547rwq72
+    has_output:
+     - nmdc:dobj-11-547rwq75
+     - nmdc:dobj-11-547rwq77
+metatranscriptome_expression_analysis_set:
+  - id: nmdc:wfmtex-11-23989.1
+    git_url: https://github.com/microbiomedata/metaT_ReadCounts
+    version: v0.0.1
+    started_at_time: '2024-07-08T14:48:51+00:00'
+    ended_at_time: '2024-07-08T14:48:51+00:00'
+    type: MetatranscriptomeExpressionAnalysis
+    was_informed_by:  nmdc:omprc-11-547rwq95
+    execution_resource: LANL-B-div
+    has_input:
+     - nmdc:dobj-11-547rwq75
+     - nmdc:dobj-11-547rwq77
+     - nmdc:dobj-11-547rwq73
+    has_output:
+     - nmdc:dobj-11-547rwq82
+     - nmdc:dobj-11-547rwq83
+     - nmdc:dobj-11-547rwq84

src/schema/nmdc.yaml

@@ -181,7 +181,9 @@ classes:
       - metagenome_assembly_set
       - metagenome_sequencing_activity_set
       - metaproteomics_analysis_activity_set
-      - metatranscriptome_activity_set
+      - metatranscriptome_annotation_set
+      - metatranscriptome_assembly_set
+      - metatranscriptome_expression_analysis_set
       - nom_analysis_activity_set
       - omics_processing_set
       - planned_process_set
@@ -2395,8 +2397,12 @@ enums:
         description: A failure has occurred in library preparation, a lab process.
       MetagenomeAssembly:
         description: A failure has occurred in metagenome assembly, a workflow process.
-      MetatranscriptomeActivity:
-        description: A failure has occurred in metatranscriptome analysis, a workflow process.
+      MetatranscriptomeExpressionAnalysis:
+        description: A failure has occurred in metatranscriptome expression analysis, a workflow process.
+      MetatranscriptomeAnnotation:
+        description: A failure has occurred in metatranscriptome annotation analysis, a workflow process.
+      MetatranscriptomeAssembly:
+        description: A failure has occurred in metatranscriptome assembly analysis, a workflow process.
       MagsAnalysisActivity:
         description: A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).
       ReadQcAnalysisActivity:
@@ -2910,12 +2916,12 @@ slots:
     description:
       This property links a database object to the set of metagenome sequencing
       activities.
-  metatranscriptome_activity_set:
+  metatranscriptome_expression_analysis_set:
     domain: Database # not inherited by mixin users
     mixins: object_set
-    range: MetatranscriptomeActivity
+    range: MetatranscriptomeExpressionAnalysis
     description:
-      This property links a database object to the set of metatranscriptome
+      This property links a database object to the set of metatranscriptome expression
       analysis activities.
   read_qc_analysis_activity_set:
     domain: Database # not inherited by mixin users
@@ -2965,6 +2971,17 @@ slots:
     mixins: object_set
     range: LibraryPreparation
     description: This property links a database object to the set of DNA extractions within it.
+  metatranscriptome_assembly_set:
+    domain: Database # not inherited by mixin users
+    mixins: object_set
+    range: MetatranscriptomeAssembly
+    description: This property links a database object to the set of metatranscriptome assemblies within it.
+  metatranscriptome_annotation_set:
+    domain: Database # not inherited by mixin users
+    mixins: object_set
+    range: MetatranscriptomeAnnotationActivity
+    description: This property links a database object to the set of metatranscriptome annotations within it.
+
 
   omics_type:
     domain: OmicsProcessing

src/schema/workflow_execution_activity.yaml

@@ -215,10 +215,10 @@ classes:
           syntax: "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$"
           interpolated: true
 
-  MetatranscriptomeActivity:
+  MetatranscriptomeExpressionAnalysis:
     is_a: WorkflowExecutionActivity
     description: >-
-      A metatranscriptome activity that e.g. pools assembly and annotation activity.
+      A workflow process that provides expression values and read counts for gene features predicted on the contigs.
     in_subset:
       - workflow subset
     slots:
@@ -227,7 +227,7 @@ classes:
       id:
         required: true
         structured_pattern:
-          syntax: "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}$"
+          syntax: "{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$"
           interpolated: true