GeoLocationNameValue with examples

src/data/invalid/GeoLocationNameValue-no_country_or_sea.yaml

@@ -0,0 +1,4 @@
+has_raw_value: "USA: Maryland: Bethesda"
+subnational_1_or_ocean_region: Maryland
+locality: Bethesda
+type: nmdc:GeoLocationNameValue

src/data/invalid/GeoLocationNameValue-no_raw_value.yaml

@@ -0,0 +1,4 @@
+country_or_sea: USA
+subnational_1_or_ocean_region: Maryland
+locality: Bethesda
+type: nmdc:GeoLocationNameValue

src/data/valid/GeoLocationNameValue-1.yaml

@@ -0,0 +1,5 @@
+has_raw_value: "USA: Maryland: Bethesda"
+country_or_sea: USA
+subnational_1_or_ocean_region: Maryland
+locality: Bethesda
+type: nmdc:GeoLocationNameValue

src/data/valid/GeoLocationNameValue-2.yaml

@@ -0,0 +1,5 @@
+has_raw_value: "USA: Bethesda, Maryland"
+country_or_sea: USA
+subnational_1_or_ocean_region: Maryland
+locality: Bethesda
+type: nmdc:GeoLocationNameValue

src/data/valid/GeoLocationNameValue-3.yaml

@@ -0,0 +1,4 @@
+has_raw_value: "Atlantic Ocean: Charlie Gibbs Fracture Zone"
+country_or_sea: Atlantic Ocean
+subnational_1_or_ocean_region: Charlie Gibbs Fracture Zone
+type: nmdc:GeoLocationNameValue

src/schema/attribute_values.yaml

@@ -15,11 +15,31 @@ classes:
     class_uri: 'nmdc:AttributeValue'
     description: >-
       The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic
-      value and the structured value
+        value and the structured value.
     slots:
       - has_raw_value
       - type
 
+  GeoLocationNameValue:
+    class_uri: nmdc:GeoLocationNameValue
+    description: >-
+      A structured address-like record of where something is located, came from, or took place
+    comments:
+      - When an instance of this class is populated via an ETL pipeline, the raw value from the source should go into this class's has_raw_value slot.
+        The ETL pipeline can parse that raw value and insert the results into this class's other slots.
+      - "This class is more useful that string-only representations when data may be ingested from multiple sources, some of which may use a style like 'Nation: State, Locality' and other might use 'Nation: Locality, State'."
+      - country_or_sea is required. Instances of this class should have either a subnational_1_or_ocean_region or a locality. Preferably both.
+    is_a: AttributeValue
+    narrow_mappings:
+      - mixs:0000010
+    slots:
+      - country_or_sea
+      - subnational_1_or_ocean_region
+      - locality
+    slot_usage:
+      has_raw_value:
+        required: true
+
   QuantityValue:
     class_uri: nmdc:QuantityValue
     is_a: AttributeValue

src/schema/basic_slots.yaml

@@ -22,6 +22,56 @@ default_range: string
 
 slots:
 
+  country_or_sea:
+    range: string
+    description: A maximally coarse-grained, geo-political description of where something is, came from, took place, etc.
+    comments:
+      - MIxS states that country or sea names should be chosen from the INSDC country list aka the geo_loc_name-qualifier-vocabulary
+      - https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/
+      - https://www.cia.gov/the-world-factbook/ and http://unstats.un.org/unsd/methods/m49/m49.htm
+    todos:
+      - "ValueError: https://www.cia.gov/the-world-factbook/ and http://unstats.un.org/unsd/methods/m49/m49.htm is not a valid URI or CURIE"
+      - when populating see_also
+    examples:
+      - value: "Canada"
+      - value: "Atlantic Ocean"
+      - value: "USA"
+    narrow_mappings:
+      - mixs:0000010
+    rank: 1
+    required: true
+
+  subnational_1_or_ocean_region:
+    range: string
+    description: A geo-political description of a region that is a direct, unambiguous subdivision of a paired country_or_sea value,
+      OR an unambiguous region or feature within an ocean or "sea".
+    comments:
+      - "INSDC's guidance could be taken to imply that Vancouver or Cote d’Azur are appropriate values for this slot, but NMDC would place those in the locality slot."
+    aliases:
+      - state
+    examples:
+      - value: "British Columbia"
+      - value: "Charlie Gibbs Fracture Zone"
+      - value: "Maryland"
+    narrow_mappings:
+      - mixs:0000010
+    rank: 2
+    recommended: true
+
+  locality:
+    range: string
+    description: A geo-political description of a region or feature that is within or overlaps with a paired subnational_1_or_ocean_region value.
+    aliases:
+      - state
+    examples:
+      - value: "Vancouver"
+      - value: "Cote d’Azur"
+      - value: "Bethesda"
+    narrow_mappings:
+      - mixs:0000010
+    rank: 3
+    recommended: true
+
   qc_comment:
     range: string
     description: >-
@@ -598,27 +648,27 @@ enums:
 
       Virus Summary:
         description: Tab separated file listing the viruses found by geNomad.
-        see_also: 
+        see_also:
           - https://portal.nersc.gov/genomad/
         annotations:
           file_name_pattern: '^_virus_summary\.tsv?$'
 
       Plasmid Summary:
         description: Tab separated file listing the plasmids found be geNomad.
-        see_also: 
+        see_also:
           - https://portal.nersc.gov/genomad/
         annotations:
           file_name_pattern: '^_plasmid_summary\.tsv?$'
-        
+
       GeNomad Aggregated Classification:
         description: >-
           Tab separated file which combines the results from neural network-based classification
           and marker-based classification for virus and plasmid detection with geNomad.
-        see_also: 
+        see_also:
           - https://portal.nersc.gov/genomad/
         annotations:
-          file_name_pattern: '^_aggregated_classification\.tsv?$'  
-        
+          file_name_pattern: '^_aggregated_classification\.tsv?$'
+
       Reference Calibration File:
         description: A file that contains data used to calibrate a natural organic matter or metabalomics analysis.
 
@@ -1090,12 +1140,12 @@ enums:
         title: Metagenome
       metatranscriptome:
         aliases:
-          - metaT  
+          - metaT
         title: Metatranscriptome
       amplicon_sequencing_assay:
         meaning: OBI:0002767
         title: Amplicon
-        
+
   MassSpectrometryEnum:
     permissible_values:
       metaproteome:
@@ -1106,13 +1156,13 @@ enums:
         aliases:
           - metaB
         title: Metabolome
-      lipidome: 
+      lipidome:
         title: Lipidome
       nom:
         aliases:
           - natural organic matter
         title: Natural Organic Matter
-        
+
   ExtractionTargetEnum:
     permissible_values:
       DNA: { }