Merge pull request #2249 from microbiomedata/2154-berkeley-breakdown-…

…analytecategoryenum-into-types-allowable-for-nucleotidesequencing-and-massspectrometry Remodeling of range for analyte_cateogry
microbiomedata · Dec 17, 2024 · 4b01a37 · 4b01a37
2 parents cb94e96 + 88724e0
commit 4b01a37
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Showing 4 changed files with 52 additions and 7 deletions.
diff --git a/src/data/invalid/MassSpectrometry-working.yaml b/src/data/invalid/MassSpectrometry-working.yaml
@@ -0,0 +1,11 @@
+id: nmdc:dgms-99-oW43DzG1
+type: nmdc:MassSpectrometry
+has_input:
+  - nmdc:procsm-11-9gjxns61
+has_output:
+  - nmdc:dobj-00-9n9n9n
+has_mass_spectrometry_configuration: nmdc:mscon-99-oW43DzG0
+eluent_introduction_category: direct_infusion_syringe
+analyte_category: metagenome
+associated_studies:
+  - nmdc:sty-00-555xxx
diff --git a/src/data/invalid/NucleotideSequencing-working.yaml b/src/data/invalid/NucleotideSequencing-working.yaml
@@ -0,0 +1,19 @@
+#test to check readding prefix 'omprc' as a valid id pattern
+id: nmdc:omprc-99-zUCd5N
+type: nmdc:NucleotideSequencing
+analyte_category: metaproteome
+alternative_identifiers:
+  - gold:Gp0108335
+name: Thawing permafrost microbial communities from the Arctic, studying carbon
+  transformations - Permafrost 712P3D
+has_input:
+  - nmdc:bsm-00-red
+add_date: 30-OCT-14 12.00.00.000000000 AM
+mod_date: 22-MAY-20 06.13.12.927000000 PM
+has_output:
+  - nmdc:dobj-00-9n9n9n
+ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying
+  carbon transformations - Permafrost 712P3D
+processing_institution: JGI
+associated_studies:
+  - nmdc:sty-00-xxx
diff --git a/src/schema/basic_slots.yaml b/src/schema/basic_slots.yaml
@@ -413,7 +413,7 @@ slots:
     description: >
       The type of analyte(s) that were measured in the data generation process and analyzed
         in the Workflow Chain
-    range: AnalyteCategoryEnum
+
 
   type:
     required: true
@@ -1081,27 +1081,38 @@ enums:
   #      submitted: { }
   #      superseded: { }
   #      withdrawn: { }
-
-  AnalyteCategoryEnum:
+  
+  NucleotideSequencingEnum:
     permissible_values:
       metagenome:
         aliases:
           - metaG
+        title: Metagenome
       metatranscriptome:
         aliases:
-          - metaT
+          - metaT  
+        title: Metatranscriptome
+      amplicon_sequencing_assay:
+        meaning: OBI:0002767
+        title: Amplicon
+
+  MassSpectrometryEnum:
+    permissible_values:
       metaproteome:
         aliases:
           - metaP
+        title: Metaproteome
       metabolome:
         aliases:
           - metaB
-      lipidome: { }
+        title: Metabolome
+      lipidome: 
+        title: Lipidome
       nom:
         aliases:
           - natural organic matter
-      amplicon_sequencing_assay:
-        meaning: OBI:0002767 
+        title: Natural Organic Matter
+
   ExtractionTargetEnum:
     permissible_values:
       DNA: { }

diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml
@@ -148,6 +148,8 @@ classes:
         structured_pattern:
           syntax: "{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$"
           interpolated: true
+      analyte_category:
+        range: NucleotideSequencingEnum
 
   MassSpectrometry:
     class_uri: nmdc:MassSpectrometry
@@ -173,6 +175,8 @@ classes:
         structured_pattern:
           syntax: "{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$"
           interpolated: true
+      analyte_category: 
+        range: MassSpectrometryEnum
     rules:
       - title: generates_calibration_required_if_gc
         description: >-