Merge branch 'main' into 1130-emsl_data_object_prefix

microbiomedata · Dec 12, 2023 · 4298471 · 4298471
2 parents 3e4d71f + d531f76
commit 4298471
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -119,6 +119,10 @@ how to deploy a test version of the schema documentation. This requires some bas
  - Anyone who is involved in writing migrations or otherwise checking data from MongoDB against the schema should be comfortable running make `make-rdf`.
  - The main [Makefile](Makefile) should in general not be edited. Instead, edits should be made to [project.Makefile](project.Makefile) (advanced contributors only)
 
+### Recording Decisions
+
+- Use the [NMDC ADR Log](https://github.com/microbiomedata/NMDC_documentation/tree/main/decisions)
+
 ### Making Releases
 
 TODO: Add to this section later

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -9,7 +9,7 @@ theme:
 plugins:
   - search
   - mermaid2
-  - redirects: # reference: https://github.com/mkdocs/mkdocs-redirects
+  - redirects:  # reference: https://github.com/mkdocs/mkdocs-redirects
       redirect_maps:
         'home.md': 'index.md'  # redirects "/home" to "/"
 markdown_extensions:
@@ -25,6 +25,7 @@ nav:
   - NMDC Metadata Standards Documentation: Metadata_Documentation_Overview.md
   - NMDC Schema Validation: schema-validation.md
   - NMDC Schema: index.md
+  - NMDC Style and Collaboration Guide: nmdc-schema-style-and-collaboration-guide.md
   - Schema element deprecation guide: schema_element_deprecation_guide.md
 
 site_url: https://microbiomedata.github.io/nmdc-schema

diff --git a/src/data/invalid/ChromatographySeparationProcess-undefined-solution-component.yaml b/src/data/invalid/ChromatographySeparationProcess-undefined-solution-component.yaml
@@ -9,18 +9,18 @@ ordered_mobile_phases:
   - volume:
       has_numeric_value: 700
       has_unit: mL
-    has_constituents:
-      - name: MeOH
+    has_solution_components:
+      - compound: MeOH
   - volume:
       has_numeric_value: 700
       has_unit: mL
-    has_constituents:
-      - name: chloridic acid
+    has_solution_components:
+      - compound: chloridic acid
         concentration:
           has_numeric_value: 10
           has_unit: mM
   - volume:
       has_numeric_value: 1000
       has_unit: mL
-    has_constituents:
-      - name: water
+    has_solution_components:
+      - compound: water
diff --git a/src/data/invalid/Extraction-metabolomics-concentration-without-compound.yaml b/src/data/invalid/Extraction-metabolomics-concentration-without-compound.yaml
@@ -3,8 +3,8 @@ has_input:
   - "nmdc:ome-6"
 has_output:
   - "nmdc:ome-8"
-extractant: # range: Fluid... multivalued? (no) -> has_solution_component
-  has_constituents:
+extractant: # range: Solution... multivalued? (no) -> has_solution_component
+  has_solution_components:
     - concentration:
         has_numeric_value: 5
         has_unit: "%"
diff --git a/src/data/valid/ChromatographicSeparationProcess-SPE.yaml b/src/data/valid/ChromatographicSeparationProcess-SPE.yaml
@@ -9,18 +9,18 @@ ordered_mobile_phases:
   - volume:
       has_numeric_value: 700
       has_unit: mL
-    has_constituents:
-      - name: methanol
+    has_solution_components:
+      - compound: methanol
   - volume:
       has_numeric_value: 700
       has_unit: mL
-    has_constituents:
-      - name: chloridic acid
+    has_solution_components:
+      - compound: chloridic acid
         concentration:
           has_numeric_value: 10
           has_unit: mM 
   - volume:
       has_numeric_value: 1000
       has_unit: mL  
-    has_constituents:
-      - name: water
+    has_solution_components:
+      - compound: water
diff --git a/src/data/valid/ChromatographicSeparationProcess-compilation_example.yaml b/src/data/valid/ChromatographicSeparationProcess-compilation_example.yaml
@@ -6,12 +6,12 @@ has_output:
   - nmdc:procsm-11-05g48p91
 stationary_phase: "CN"
 ordered_mobile_phases:
-  - has_constituents:
-      - name: methanol
+  - has_solution_components:
+      - compound: methanol
         concentration:
           has_unit: mM
           has_numeric_value: 10
-      - name: chloridic acid
+      - compound: chloridic acid
         concentration:
           has_unit: mM
           has_numeric_value: 15

diff --git a/src/data/valid/Extraction-metabolomics.yaml b/src/data/valid/Extraction-metabolomics.yaml
@@ -3,10 +3,10 @@ has_input:
   - "nmdc:ome-6"
 has_output:
   - "nmdc:ome-8"
-extractant: # range: Fluid... multivalued? (no) -> has_solution_component
-  has_constituents:
-    - name: deionized water
-    - name: methanol
+extractant: # range: Solution... multivalued? (no) -> has_solution_component
+  has_solution_components:
+    - compound: deionized water
+    - compound: methanol
       concentration:
         has_numeric_value: 5
         has_unit: "%"
diff --git a/src/data/valid/Extraction-proteomics.yaml b/src/data/valid/Extraction-proteomics.yaml
@@ -3,11 +3,11 @@ has_input:
   - "nmdc:fasp-37"
 has_output:
   - "nmdc:ome-39"
-extractant: # range: Fluid... multivalued? (no) -> has_solution_component
-  has_constituents:
-    - name: deionized water
-    - name: ammonium bicarbonate
-    - name: trypsin
+extractant: # range: Solution... multivalued? (no) -> has_solution_component
+  has_solution_components:
+    - compound: deionized water
+    - compound: ammonium bicarbonate
+    - compound: trypsin
       concentration:
         has_numeric_value: 0.05
         has_unit: "μg/μL"
diff --git a/src/data/valid/Fluid-minimal.yaml → src/data/valid/Solution-minimal.yaml b/src/data/valid/Fluid-minimal.yaml → src/data/valid/Solution-minimal.yaml
@@ -1,5 +1,5 @@
-has_constituents:
-  - name: methanol
+has_solution_components:
+  - compound: methanol
     concentration:
       has_unit: mM
       has_numeric_value: 10

diff --git a/...data/valid/Fluid-multiple_components.yaml → ...a/valid/Solution-multiple_components.yaml b/...data/valid/Fluid-multiple_components.yaml → ...a/valid/Solution-multiple_components.yaml
@@ -1,13 +1,13 @@
-has_constituents:
-  - name: methanol
+has_solution_components:
+  - compound: methanol
     concentration:
       has_unit: mM
       has_numeric_value: 10
-  - name: chloridic acid
+  - compound: chloridic acid
     concentration:
       has_unit: mM
       has_numeric_value: 15
-  - name: trypsin
+  - compound: trypsin
     concentration:
       has_unit: mM
       has_numeric_value: 20

diff --git a/...ata/valid/ConstituentOfFluid-minimal.yaml → ...data/valid/SolutionComponent-minimal.yaml b/...ata/valid/ConstituentOfFluid-minimal.yaml → ...data/valid/SolutionComponent-minimal.yaml
@@ -1,4 +1,4 @@
-name: methanol
+compound: methanol
 concentration:
   has_unit: mM
   has_numeric_value: 10
diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml
@@ -240,35 +240,26 @@ classes:
       volume:
         description: The volume of the solvent/solute being used, not the input.
 
-  ConstituentOfFluid:
-    description: One constituent of a fluid. For Fluids that consist of one single constituent,
-      the constituent must be a fluid. Fluids with more than one constituent may also contain
-      non-fluid constituents, such as solids in a colloid or a solution
+  SolutionComponent:
+    description: One constituent of a solution
     slots:
-      - name
+      - compound
       - concentration
-    slot_usage:
-      name:
-        domain: ConstituentOfFluid
-        range: ConstituentEnum
-        description: The name of the constituent
-        required: true
 
-  Fluid:
-    description: Material that may continuously move and deform (flow) under an applied shear stress, or external force
+  Solution:
+    description: A mixture that is homogeneous, made up of two or more scattered molecular aggregates, one playing the role of solute and the other playing the role of solvent.
     aliases:
-      - gas
-      - liquid
-      - fluid mixture
-      - solution
+      - mixture
       - solvent
     comments:
-      - The fluid class may be instantiated with a single constituent as long as that constituent is fluid
+      - We acknowledge that users of the nmdc-schema may instantiate Solution with only a single component which goes against the letter of the description.
+      - The solution class may be used to instantiate a single component in the has_solution_components slot
+    notes:
+      - TODO review the description, possibly more descriptive modeling to allow solvent to be used
+      - TODO consider making a "Fluid" class
     slots:
-      - has_constituents
+      - has_solution_components
       - volume
-    exact_mappings:
-      - wikidata:Q102205
 
   Protocol:
     slots:
@@ -2284,7 +2275,7 @@ enums:
   #      Water:
   #      trypsin in ammonium bicarbonate:
 
-  ConstituentEnum:
+  CompoundEnum:
     permissible_values:
       ammonium bicarbonate:
       deionized water:
@@ -2426,7 +2417,7 @@ slots:
     title: zinc
     examples:
       - value: 2.5 mg/kg
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
@@ -2443,7 +2434,7 @@ slots:
       - value: 24.7 mg/kg
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
 
   ammonium_nitrogen:
@@ -2460,7 +2451,7 @@ slots:
       - value: 2.3 mg/kg
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
 
   nitrate_nitrogen:
@@ -2479,7 +2470,7 @@ slots:
       - value: 0.29 mg/kg
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
 
   nitrite_nitrogen:
@@ -2496,7 +2487,7 @@ slots:
       - value: 1.2 mg/kg
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
 
   lbc_thirty:
@@ -2517,7 +2508,7 @@ slots:
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
       - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
 
   lbceq:
@@ -2536,7 +2527,7 @@ slots:
       - value: 1575 mg/kg
     see_also:
       - https://www.ornl.gov/content/bio-scales-0
-    #    is_a: attribute
+#    is_a: attribute
     range: QuantityValue
 
   env_package:
@@ -2552,7 +2543,7 @@ slots:
       subtables and can be reported
     in_subset:
       - mixs extension
-    #    is_a: attribute
+#    is_a: attribute
     range: TextValue
   #      pattern: '[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon
   #        resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc
@@ -2836,7 +2827,7 @@ slots:
 
   ## GOLD PATHS
   gold_path_field:
-    #    is_a: attribute
+#    is_a: attribute
     range: string
     abstract: true
     description: >-
@@ -2906,7 +2897,7 @@ slots:
   principal_investigator:
     aliases:
       - PI
-    #    is_a: attribute
+#    is_a: attribute
     range: PersonValue
     description: Principal Investigator who led the study and/or generated the dataset.
 
@@ -3103,33 +3094,33 @@ slots:
     description: A type of container. i.e. test tube, falcon tube, etc.
   extractant:
     domain: Extraction
-    range: Fluid
+    range: Solution
     description: "The active component(s) primarily responsible for transfer of a solute from one phase to the other."
   concentration:
-    domain: ConstituentOfFluid
+    domain: SolutionComponent
     range: QuantityValue
     description: The concentration of a substance used in a process
   input_volume: # see also `volume`
     domain: PlannedProcess
     range: QuantityValue
     description: The volume of the input sample.
-  has_constituents:
-    description: Relationship from a Fluid to one or more constituent of that fluid
-    range: ConstituentOfFluid
-    domain: Fluid
+  has_solution_components:
+    description: Relationship from a Solution to one or more constituent solution components
+    range: SolutionComponent
+    domain: Solution
     multivalued: true
     inlined_as_list: true
     required: true
     minimum_cardinality: 1
     #list example
   compound:
-    domain: ConstituentOfFluid
-    range: ConstituentEnum
+    domain: SolutionComponent
+    range: CompoundEnum
     description: A substance that consists of more than one atom or ion. Includes solvents and solutes. Can be combined into solutions.
     required: true
   ordered_mobile_phases:
     domain: ChromatographicSeparationProcess
-    range: Fluid
+    range: Solution
     description: The solution(s) that moves through a chromatography column.
     multivalued: true
     list_elements_ordered: true