nmdc-schema 11.12.0rc1__py3-none-any.whl → 11.12.1__py3-none-any.whl

nmdc_schema/nmdc_materialized_patterns.yaml

@@ -13,7 +13,7 @@ notes:
 - not importing any MIxS terms where the relationship between the name (SCN) and the
   id isn't 1:1
 id: https://w3id.org/nmdc/nmdc
-version: 11.12.0rc1
+version: 11.12.1
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   BFO:
@@ -325,39 +325,6 @@ emit_prefixes:
 default_prefix: nmdc
 default_range: string
 types:
-  external_identifier:
-    name: external_identifier
-    description: A CURIE representing an external identifier
-    from_schema: https://w3id.org/nmdc/nmdc
-    see_also:
-    - https://microbiomedata.github.io/nmdc-schema/identifiers/
-    typeof: uriorcurie
-    uri: xsd:anyURI
-    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
-  bytes:
-    name: bytes
-    description: An integer value that corresponds to a size in bytes
-    from_schema: https://w3id.org/nmdc/nmdc
-    see_also:
-    - UO:0000233
-    base: int
-    uri: xsd:long
-  decimal_degree:
-    name: decimal_degree
-    description: A decimal degree expresses latitude or longitude as decimal fractions.
-    from_schema: https://w3id.org/nmdc/nmdc
-    see_also:
-    - https://en.wikipedia.org/wiki/Decimal_degrees
-    base: float
-    uri: xsd:decimal
-  language_code:
-    name: language_code
-    description: A language code conforming to ISO_639-1
-    from_schema: https://w3id.org/nmdc/nmdc
-    see_also:
-    - https://en.wikipedia.org/wiki/ISO_639-1
-    base: str
-    uri: xsd:language
   string:
     name: string
     description: A character string
@@ -588,6 +555,39 @@ types:
     base: str
     uri: xsd:string
     repr: str
+  external_identifier:
+    name: external_identifier
+    description: A CURIE representing an external identifier
+    from_schema: https://w3id.org/nmdc/nmdc
+    see_also:
+    - https://microbiomedata.github.io/nmdc-schema/identifiers/
+    typeof: uriorcurie
+    uri: xsd:anyURI
+    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
+  bytes:
+    name: bytes
+    description: An integer value that corresponds to a size in bytes
+    from_schema: https://w3id.org/nmdc/nmdc
+    see_also:
+    - UO:0000233
+    base: int
+    uri: xsd:long
+  decimal_degree:
+    name: decimal_degree
+    description: A decimal degree expresses latitude or longitude as decimal fractions.
+    from_schema: https://w3id.org/nmdc/nmdc
+    see_also:
+    - https://en.wikipedia.org/wiki/Decimal_degrees
+    base: float
+    uri: xsd:decimal
+  language_code:
+    name: language_code
+    description: A language code conforming to ISO_639-1
+    from_schema: https://w3id.org/nmdc/nmdc
+    see_also:
+    - https://en.wikipedia.org/wiki/ISO_639-1
+    base: str
+    uri: xsd:language
 enums:
   CalibrationTargetEnum:
     name: CalibrationTargetEnum
@@ -1504,6 +1504,10 @@ enums:
         text: atm
         description: The Unified Code for Units of Measure (UCUM) representation of
           atmosphere.
+      V:
+        text: V
+        description: The Unified Code for Units of Measure (UCUM) representation of
+          volt.
       mV:
         text: mV
         description: The Unified Code for Units of Measure (UCUM) representation of
@@ -5544,6 +5548,74 @@ enums:
       NomAnalysis:
         text: NomAnalysis
         description: A failure has occurred in analyzing NOM data.
+  ProtocolForEnum:
+    name: ProtocolForEnum
+    description: The permitted values for describing the type of planned process that
+      a protocol describes.
+    comments:
+    - These are the non-abstract class descendants of PlannedProcess.
+    from_schema: https://w3id.org/nmdc/nmdc
+    permissible_values:
+      AnnotatingWorkflow:
+        text: AnnotatingWorkflow
+      ChemicalConversionProcess:
+        text: ChemicalConversionProcess
+      ChromatographicSeparationProcess:
+        text: ChromatographicSeparationProcess
+      CollectingBiosamplesFromSite:
+        text: CollectingBiosamplesFromSite
+      DataEmitterProcess:
+        text: DataEmitterProcess
+      DataGeneration:
+        text: DataGeneration
+      DissolvingProcess:
+        text: DissolvingProcess
+      Extraction:
+        text: Extraction
+      FiltrationProcess:
+        text: FiltrationProcess
+      LibraryPreparation:
+        text: LibraryPreparation
+      MagsAnalysis:
+        text: MagsAnalysis
+      MassSpectrometry:
+        text: MassSpectrometry
+      MaterialProcessing:
+        text: MaterialProcessing
+      MetabolomicsAnalysis:
+        text: MetabolomicsAnalysis
+      MetagenomeAnnotation:
+        text: MetagenomeAnnotation
+      MetagenomeAssembly:
+        text: MetagenomeAssembly
+      MetaproteomicsAnalysis:
+        text: MetaproteomicsAnalysis
+      MetatranscriptomeAnnotation:
+        text: MetatranscriptomeAnnotation
+      MetatranscriptomeAssembly:
+        text: MetatranscriptomeAssembly
+      MetatranscriptomeExpressionAnalysis:
+        text: MetatranscriptomeExpressionAnalysis
+      MixingProcess:
+        text: MixingProcess
+      NomAnalysis:
+        text: NomAnalysis
+      NucleotideSequencing:
+        text: NucleotideSequencing
+      PlannedProcess:
+        text: PlannedProcess
+      Pooling:
+        text: Pooling
+      ReadBasedTaxonomyAnalysis:
+        text: ReadBasedTaxonomyAnalysis
+      ReadQcAnalysis:
+        text: ReadQcAnalysis
+      StorageProcess:
+        text: StorageProcess
+      SubSamplingProcess:
+        text: SubSamplingProcess
+      WorkflowExecution:
+        text: WorkflowExecution
   SampleTypeEnum:
     name: SampleTypeEnum
     from_schema: https://w3id.org/nmdc/nmdc
@@ -6423,7 +6495,7 @@ slots:
     - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
       one pH unit
     examples:
-    - value: 543 mg/kg
+    - value: 543 [ppm]
     from_schema: https://w3id.org/nmdc/nmdc
     see_also:
     - https://www.ornl.gov/content/bio-scales-0
@@ -6453,7 +6525,7 @@ slots:
     - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
       one pH unit
     examples:
-    - value: 1575 mg/kg
+    - value: 1575 [ppm]
     from_schema: https://w3id.org/nmdc/nmdc
     see_also:
     - https://www.ornl.gov/content/bio-scales-0
@@ -6537,7 +6609,7 @@ slots:
     annotations:
       storage_units:
         tag: storage_units
-        value: '%|mmol/L|umol/L'
+        value: '%|mmol/L|umol/L|mg/L|g/L'
     description: When solutions A (containing substance X) and B are combined together,
       this slot captures the concentration of X in the combination
     from_schema: https://w3id.org/nmdc/nmdc
@@ -6922,8 +6994,7 @@ slots:
     mappings:
     - qud:unit
     - schema:unitCode
-    range: UnitEnum
-    required: true
+    range: string
   type:
     name: type
     description: the class_uri of the class that has been instantiated
@@ -7020,6 +7091,56 @@ slots:
     range: string
     multivalued: true
     pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\/\/(?!.*[Dd][Oo][Ii]\.[Oo][Rr][Gg]).*$
+  has_attribute_label:
+    name: has_attribute_label
+    description: Human-readable label for the property (e.g., MIxS label, ENVO term
+      label).
+    comments:
+    - This provides a human-friendly name for the asserted property. For example,
+      "bicarbonate ion concentration" or "total phosphorus". The label helps with
+      readability and data discovery.
+    from_schema: https://w3id.org/nmdc/nmdc
+    range: string
+  has_attribute_id:
+    name: has_attribute_id
+    description: CURIE or IRI for the property (MIxS slot, NMDC slot, ENVO/OBI term,
+      etc.).
+    comments:
+    - This provides a resolvable identifier for the property being asserted. Examples
+      include MIXS:0000117 for total phosphorus, or ENVO:01001357 for bicarbonate
+      ion concentration.
+    - Prefer using standard ontology terms (ENVO, PATO, OBI, etc.) or MIxS identifiers
+      when available to enhance interoperability.
+    from_schema: https://w3id.org/nmdc/nmdc
+    range: uriorcurie
+  has_quantity_kind_id:
+    name: has_quantity_kind_id
+    description: Optional CURIE or IRI for the physical quantity kind (e.g., qudt:QuantityKind).
+    comments:
+    - This slot enables precise semantic description of what physical quantity is
+      being measured, independent of the specific units used. For example, qudt:MassConcentration
+      or qudt:Temperature.
+    - Using quantity kind identifiers from QUDT or similar vocabularies improves data
+      integration and enables automated unit conversion.
+    from_schema: https://w3id.org/nmdc/nmdc
+    range: uriorcurie
+  has_value_term_id:
+    name: has_value_term_id
+    description: CURIE or IRI for categorical values (ENVO, PATO, METPO, etc.).
+    comments:
+    - Use this slot when the value of the property is a controlled vocabulary term
+      rather than a numeric or free-text value. For example, ENVO:00002297 for "desert
+      ecosystem" or PATO:0001199 for "dry".
+    from_schema: https://w3id.org/nmdc/nmdc
+    range: uriorcurie
+  has_datetime_value:
+    name: has_datetime_value
+    description: Date-time value for the property in ISO-8601 format.
+    comments:
+    - Use this slot for temporal properties. The value should follow ISO-8601 format
+      (e.g., "2025-06-12T14:30:00Z").
+    from_schema: https://w3id.org/nmdc/nmdc
+    range: string
   processing_institution_workflow_metadata:
     name: processing_institution_workflow_metadata
     description: Information about how workflow results were generated when the processing
@@ -7923,7 +8044,7 @@ slots:
       mixture
     title: absolute air humidity
     examples:
-    - value: 9 gram per gram
+    - value: 9 g/g
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - absolute air humidity
@@ -8112,7 +8233,7 @@ slots:
     description: Temperature of the air at the time of sampling
     title: air temperature
     examples:
-    - value: 20 degree Celsius
+    - value: 20 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - air temperature
@@ -8214,7 +8335,7 @@ slots:
       equivalence point of carbonate or bicarbonate
     title: alkalinity
     examples:
-    - value: 50 milligram per liter
+    - value: 50 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - alkalinity
@@ -8261,7 +8382,7 @@ slots:
     description: Concentration of alkyl diethers
     title: alkyl diethers
     examples:
-    - value: 0.005 mole per liter
+    - value: 0.005 mol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - alkyl diethers
@@ -8286,7 +8407,7 @@ slots:
       sampled position in the air
     title: altitude
     examples:
-    - value: 100 meter
+    - value: 100 m
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - altitude
@@ -8312,7 +8433,7 @@ slots:
     description: Measurement of aminopeptidase activity
     title: aminopeptidase activity
     examples:
-    - value: 0.269 mole per liter per hour
+    - value: 0.269 mol/L/h
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - aminopeptidase activity
@@ -8338,7 +8459,7 @@ slots:
     description: Concentration of ammonium in the sample
     title: ammonium
     examples:
-    - value: 1.5 milligram per liter
+    - value: 1.5 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - ammonium
@@ -8415,7 +8536,7 @@ slots:
       equivalent value derived by such methods as regional indexes or Isohyetal maps.
     title: mean annual precipitation
     examples:
-    - value: ''
+    - value: 225 mm
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - mean annual precipitation
@@ -8441,7 +8562,7 @@ slots:
     description: Mean annual temperature
     title: mean annual temperature
     examples:
-    - value: 12.5 degree Celsius
+    - value: 12.5 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - mean annual temperature
@@ -8624,7 +8745,7 @@ slots:
       hour over a 24 hour period on the sampling day
     title: average dew point
     examples:
-    - value: 25.5 degree Celsius
+    - value: 25.5 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - average dew point
@@ -8672,7 +8793,7 @@ slots:
       over a 24 hour period on the sampling day
     title: average temperature
     examples:
-    - value: 12.5 degree Celsius
+    - value: 12.5 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - average temperature
@@ -8698,7 +8819,7 @@ slots:
     description: Bacterial production in the water column measured by isotope uptake
     title: bacterial production
     examples:
-    - value: 5 milligram per cubic meter per day
+    - value: 5 mg/m3/d
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - bacterial production
@@ -8724,7 +8845,7 @@ slots:
     description: Measurement of bacterial respiration in the water column
     title: bacterial respiration
     examples:
-    - value: 300 micromole oxygen per liter per hour
+    - value: 300 umol/L/h
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - bacterial respiration
@@ -8750,7 +8871,7 @@ slots:
     description: Measurement of bacterial carbon production
     title: bacterial carbon production
     examples:
-    - value: 2.53 microgram per liter per hour
+    - value: 50 ng/h
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - bacterial carbon production
@@ -8777,7 +8898,7 @@ slots:
       above that surface
     title: barometric pressure
     examples:
-    - value: 5 millibar
+    - value: 1013 mbar
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - barometric pressure
@@ -9054,7 +9175,7 @@ slots:
     description: Concentration of bishomohopanol
     title: bishomohopanol
     examples:
-    - value: 14 microgram per liter
+    - value: 14 ug/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - bishomohopanol
@@ -9132,7 +9253,7 @@ slots:
     description: Concentration of bromide
     title: bromide
     examples:
-    - value: 0.05 parts per million
+    - value: 0.05 [ppm]
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - bromide
@@ -9219,7 +9340,7 @@ slots:
     description: The age of the built structure since construction
     title: built structure age
     examples:
-    - value: '15'
+    - value: 15 a
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - built structure age
@@ -9289,7 +9410,7 @@ slots:
     description: Concentration of calcium in the sample
     title: calcium
     examples:
-    - value: 0.2 micromole per liter
+    - value: 0.2 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - calcium
@@ -9315,7 +9436,7 @@ slots:
     description: Carbon dioxide (gas) amount or concentration at the time of sampling
     title: carbon dioxide
     examples:
-    - value: 410 parts per million
+    - value: 410 [ppm]
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - carbon dioxide
@@ -9341,7 +9462,7 @@ slots:
     description: Carbon monoxide (gas) amount or concentration at the time of sampling
     title: carbon monoxide
     examples:
-    - value: 0.1 parts per million
+    - value: 0.1 [ppm]
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - carbon monoxide
@@ -9390,7 +9511,7 @@ slots:
     description: The area of the ceiling space within the room
     title: ceiling area
     examples:
-    - value: 25 square meter
+    - value: 25 m2
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - ceiling area
@@ -9720,7 +9841,7 @@ slots:
     description: Concentration of chloride in the sample
     title: chloride
     examples:
-    - value: 5000 milligram per liter
+    - value: 5000 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - chloride
@@ -9746,7 +9867,7 @@ slots:
     description: Concentration of chlorophyll
     title: chlorophyll
     examples:
-    - value: 5 milligram per cubic meter
+    - value: 5 mg/m3
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - chlorophyll
@@ -9817,7 +9938,7 @@ slots:
     description: Electrical conductivity of water
     title: conductivity
     examples:
-    - value: 10 milliSiemens per centimeter
+    - value: 10 uS/cm
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - conductivity
@@ -9992,7 +10113,7 @@ slots:
       mass density)
     title: density
     examples:
-    - value: 1000 kilogram per cubic meter
+    - value: 1000 kg/m3
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - density
@@ -10035,7 +10156,7 @@ slots:
       can be reported as an interval for subsurface samples.
     title: depth
     examples:
-    - value: 10 meter
+    - value: 10 m
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - depth
@@ -10062,7 +10183,7 @@ slots:
       at constant barometric pressure, for water vapor to condense into water.
     title: dew point
     examples:
-    - value: 22 degree Celsius
+    - value: 22 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dew point
@@ -10115,7 +10236,7 @@ slots:
       portion of the sample
     title: dissolved carbon dioxide
     examples:
-    - value: 5 milligram per liter
+    - value: 5 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved carbon dioxide
@@ -10141,7 +10262,7 @@ slots:
     description: Concentration of dissolved hydrogen
     title: dissolved hydrogen
     examples:
-    - value: 0.3 micromole per liter
+    - value: 0.3 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved hydrogen
@@ -10163,12 +10284,12 @@ slots:
         value: '1'
       storage_units:
         tag: storage_units
-        value: '[ppm]|mg/L|ug/L'
+        value: '[ppm]|mg/L|ug/L|umol/kg'
     description: Dissolved inorganic carbon concentration in the sample, typically
       measured after filtering the sample using a 0.45 micrometer filter
     title: dissolved inorganic carbon
     examples:
-    - value: 2059 micromole per kilogram
+    - value: 2059 umol/kg
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved inorganic carbon
@@ -10194,7 +10315,7 @@ slots:
     description: Concentration of dissolved inorganic nitrogen
     title: dissolved inorganic nitrogen
     examples:
-    - value: 761 micromole per liter
+    - value: 761 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved inorganic nitrogen
@@ -10216,11 +10337,11 @@ slots:
         value: '1'
       storage_units:
         tag: storage_units
-        value: '[ppm]|mg/L|ug/L'
+        value: '[ppm]|mg/L|ug/L|umol/L'
     description: Concentration of dissolved inorganic phosphorus in the sample
     title: dissolved inorganic phosphorus
     examples:
-    - value: 56.5 micromole per liter
+    - value: 56.5 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved inorganic phosphorus
@@ -10273,7 +10394,7 @@ slots:
       of the sample, or aqueous phase of the fluid
     title: dissolved organic carbon
     examples:
-    - value: 197 micromole per liter
+    - value: 197 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved organic carbon
@@ -10300,7 +10421,7 @@ slots:
       nitrogen - NH4 - NO3 - NO2
     title: dissolved organic nitrogen
     examples:
-    - value: 0.05 micromole per liter
+    - value: 0.05 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved organic nitrogen
@@ -10326,7 +10447,7 @@ slots:
     description: Concentration of dissolved oxygen
     title: dissolved oxygen
     examples:
-    - value: 175 micromole per kilogram
+    - value: 175 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - dissolved oxygen
@@ -10499,7 +10620,7 @@ slots:
     description: The size of the door
     title: door area or size
     examples:
-    - value: 2.5 square meter
+    - value: 2.5 m2
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - door area or size
@@ -10608,7 +10729,7 @@ slots:
       column
     title: downward PAR
     examples:
-    - value: 28.71 microEinstein per square meter per second
+    - value: 28.71 umol/m2/s
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - downward PAR
@@ -11394,11 +11515,11 @@ slots:
         value: '1'
       storage_units:
         tag: storage_units
-        value: mg/m3
+        value: mg/m3|V
     description: Raw or converted fluorescence of water
     title: fluorescence
     examples:
-    - value: 2.5 volts
+    - value: 2.5 V
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - fluorescence
@@ -11639,7 +11760,7 @@ slots:
     description: Measurement of glucosidase activity
     title: glucosidase activity
     examples:
-    - value: 5 mol per liter per hour
+    - value: 5 mol/L/h
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - glucosidase activity
@@ -12177,7 +12298,7 @@ slots:
       and study, e.g. Could be seconds for amoebae or centuries for trees
     title: host age
     examples:
-    - value: 10 days
+    - value: 10 d
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host age
@@ -12272,7 +12393,7 @@ slots:
     description: Core body temperature of the host when sample was collected
     title: host body temperature
     examples:
-    - value: 15 degree Celsius
+    - value: 15 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host body temperature
@@ -12384,7 +12505,7 @@ slots:
     description: Measurement of dry mass
     title: host dry mass
     examples:
-    - value: 500 gram
+    - value: 500 g
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host dry mass
@@ -12474,7 +12595,7 @@ slots:
     description: The height of subject
     title: host height
     examples:
-    - value: 0.1 meter
+    - value: 0.1 m
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host height
@@ -12523,7 +12644,7 @@ slots:
     description: The length of subject
     title: host length
     examples:
-    - value: 1 meter
+    - value: 1 m
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host length
@@ -12744,7 +12865,7 @@ slots:
     description: Total mass of the host at collection, the unit depends on host
     title: host total mass
     examples:
-    - value: 2500 gram
+    - value: 2500 g
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host total mass
@@ -12770,7 +12891,7 @@ slots:
     description: Measurement of wet mass
     title: host wet mass
     examples:
-    - value: 1500 gram
+    - value: 1500 g
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - host wet mass
@@ -12796,7 +12917,7 @@ slots:
     description: Amount of water vapour in the air, at the time of sampling
     title: humidity
     examples:
-    - value: 25 gram per cubic meter
+    - value: 25 g/m3
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - humidity
@@ -13079,7 +13200,7 @@ slots:
     description: Measurement of light intensity
     title: light intensity
     examples:
-    - value: 0.3 lux
+    - value: 0.3 lx
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - light intensity
@@ -13280,7 +13401,7 @@ slots:
     description: Concentration of magnesium in the sample
     title: magnesium
     examples:
-    - value: 52.8 micromole per kilogram
+    - value: 52.8 umol/kg
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - magnesium
@@ -13329,7 +13450,7 @@ slots:
     description: Measurement of mean friction velocity
     title: mean friction velocity
     examples:
-    - value: 0.5 meter per second
+    - value: 0.5 m/s
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - mean friction velocity
@@ -13355,7 +13476,7 @@ slots:
     description: Measurement of mean peak friction velocity
     title: mean peak friction velocity
     examples:
-    - value: 1 meter per second
+    - value: 1 m/s
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - mean peak friction velocity
@@ -13424,7 +13545,7 @@ slots:
     description: Methane (gas) amount or concentration at the time of sampling
     title: methane
     examples:
-    - value: 1800 parts per billion
+    - value: 1800 [ppb]
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - methane
@@ -13520,9 +13641,11 @@ slots:
       occurrence:
         tag: occurrence
         value: m
-    description: Any other measurement performed or parameter collected, that is not
-      listed here
+    description: Structured miscellaneous property assertions for this Biosample.
+      Use when a value cannot cleanly fit an existing, policy-governed slot.
     title: miscellaneous parameter
+    todos:
+    - This slot should not be available in the submission portal.
     examples:
     - value: Bicarbonate ion concentration;2075 micromole per kilogram
     from_schema: https://w3id.org/nmdc/nmdc
@@ -13531,7 +13654,7 @@ slots:
     is_a: core field
     string_serialization: '{text};{float} {unit}'
     slot_uri: MIXS:0000752
-    range: TextValue
+    range: PropertyAssertion
     multivalued: true
     inlined_as_list: true
   n_alkanes:
@@ -13577,7 +13700,7 @@ slots:
     description: Concentration of nitrate in the sample
     title: nitrate
     examples:
-    - value: 65 micromole per liter
+    - value: 65 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - nitrate
@@ -13603,7 +13726,7 @@ slots:
     description: Concentration of nitrite in the sample
     title: nitrite
     examples:
-    - value: 0.5 micromole per liter
+    - value: 0.5 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - nitrite
@@ -13629,7 +13752,7 @@ slots:
     description: Concentration of nitrogen (total)
     title: nitrogen
     examples:
-    - value: 4.2 micromole per liter
+    - value: 4.2 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - nitrogen
@@ -13855,11 +13978,11 @@ slots:
         value: '1'
       storage_units:
         tag: storage_units
-        value: umol/L|%
+        value: umol/L|%|mg/L
     description: Concentration of organic carbon
     title: organic carbon
     examples:
-    - value: 1.5 microgram per liter
+    - value: 0.015 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - organic carbon
@@ -13916,7 +14039,7 @@ slots:
     description: Concentration of organic matter
     title: organic matter
     examples:
-    - value: 1.75 milligram per cubic meter
+    - value: 200 ug/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - organic matter
@@ -13942,7 +14065,7 @@ slots:
     description: Concentration of organic nitrogen
     title: organic nitrogen
     examples:
-    - value: 4 micromole per liter
+    - value: 4 ug/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - organic nitrogen
@@ -14071,7 +14194,7 @@ slots:
     description: Oxygen (gas) amount or concentration at the time of sampling
     title: oxygen
     examples:
-    - value: 600 parts per million
+    - value: 600 [ppm]
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - oxygen
@@ -14097,7 +14220,7 @@ slots:
     description: Concentration of particulate organic carbon
     title: particulate organic carbon
     examples:
-    - value: 1.92 micromole per liter
+    - value: 0.02 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - particulate organic carbon
@@ -14123,7 +14246,7 @@ slots:
     description: Concentration of particulate organic nitrogen
     title: particulate organic nitrogen
     examples:
-    - value: 0.3 micromole per liter
+    - value: 0.3 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - particulate organic nitrogen
@@ -14297,7 +14420,7 @@ slots:
     description: Concentration of petroleum hydrocarbon
     title: petroleum hydrocarbon
     examples:
-    - value: 0.05 micromole per liter
+    - value: 0.05 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - petroleum hydrocarbon
@@ -14415,7 +14538,7 @@ slots:
     description: Concentration of phosphate
     title: phosphate
     examples:
-    - value: 0.7 micromole per liter
+    - value: 0.7 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - phosphate
@@ -14466,7 +14589,7 @@ slots:
     description: Measurement of photon flux
     title: photon flux
     examples:
-    - value: 3.926 micromole photons per second per square meter
+    - value: 3.926 umol/m2/s
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - photon flux
@@ -14656,7 +14779,7 @@ slots:
     description: Concentration of potassium in the sample
     title: potassium
     examples:
-    - value: 463 milligram per liter
+    - value: 463 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - potassium
@@ -14755,7 +14878,7 @@ slots:
     description: Pressure to which the sample is subject to, in atmospheres
     title: pressure
     examples:
-    - value: 50 atmosphere
+    - value: 50 atm
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - pressure
@@ -14824,7 +14947,7 @@ slots:
       uptake
     title: primary production
     examples:
-    - value: 100 milligram per cubic meter per day
+    - value: 100 mg/m3/d
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - primary production
@@ -15041,7 +15164,7 @@ slots:
       oxidation or reduction potential
     title: redox potential
     examples:
-    - value: 300 millivolt
+    - value: 300 mV
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - redox potential
@@ -15784,7 +15907,7 @@ slots:
       seawater.
     title: salinity
     examples:
-    - value: 25 practical salinity unit
+    - value: 70 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - salinity
@@ -16036,7 +16159,7 @@ slots:
       If "other" is specified, please propose entry in "additional info" field
     title: sample measured depth
     examples:
-    - value: 1534 meter;MSL
+    - value: 1534 m
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - sample measured depth
@@ -16130,7 +16253,7 @@ slots:
       sample collected.
     title: amount or size of sample collected
     examples:
-    - value: 5 liter
+    - value: 5 L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - amount or size of sample collected
@@ -16223,7 +16346,7 @@ slots:
     description: Temperature at which sample was stored, e.g. -80 degree Celsius
     title: sample storage temperature
     examples:
-    - value: -80 degree Celsius
+    - value: -80 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - sample storage temperature
@@ -16389,7 +16512,7 @@ slots:
       Sample Size (MIXS:0000001).'
     title: sample volume or weight for DNA extraction
     examples:
-    - value: 1500 milliliter
+    - value: 1500 mL
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - sample volume or weight for DNA extraction
@@ -16533,7 +16656,7 @@ slots:
       equivalent value derived by such methods as regional indexes or Isohyetal maps.
     title: mean seasonal precipitation
     examples:
-    - value: ''
+    - value: 10 mm
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - mean seasonal precipitation
@@ -16559,7 +16682,7 @@ slots:
     description: Mean seasonal temperature
     title: mean seasonal temperature
     examples:
-    - value: 18 degree Celsius
+    - value: 18 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - mean seasonal temperature
@@ -16833,7 +16956,7 @@ slots:
     description: Concentration of silicate
     title: silicate
     examples:
-    - value: 0.05 micromole per liter
+    - value: 0.05 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - silicate
@@ -16878,7 +17001,7 @@ slots:
       Materials larger than the size threshold are excluded from the sample
     title: size-fraction lower threshold
     examples:
-    - value: 0.2 micrometer
+    - value: 0.2 um
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - size-fraction lower threshold
@@ -16905,7 +17028,7 @@ slots:
       smaller than the size threshold are excluded from the sample
     title: size-fraction upper threshold
     examples:
-    - value: 20 micrometer
+    - value: 20 um
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - size-fraction upper threshold
@@ -16934,7 +17057,7 @@ slots:
       influence soil temperature and evapotranspiration.
     title: slope aspect
     examples:
-    - value: ''
+    - value: 35 deg
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - slope aspect
@@ -17014,7 +17137,7 @@ slots:
     description: Sodium concentration in the sample
     title: sodium
     examples:
-    - value: 10.5 milligram per liter
+    - value: 10.5 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - sodium
@@ -17156,7 +17279,7 @@ slots:
       during a specific time interval
     title: solar irradiance
     examples:
-    - value: 1.36 kilowatts per square meter per day
+    - value: 1.36 kW/m2/d
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - solar irradiance
@@ -17234,7 +17357,7 @@ slots:
     description: Concentration of soluble reactive phosphorus
     title: soluble reactive phosphorus
     examples:
-    - value: 0.1 milligram per liter
+    - value: 0.1 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - soluble reactive phosphorus
@@ -17515,7 +17638,7 @@ slots:
     description: Concentration of sulfate in the sample
     title: sulfate
     examples:
-    - value: 5 micromole per liter
+    - value: 5 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - sulfate
@@ -17567,7 +17690,7 @@ slots:
     description: Concentration of sulfide in the sample
     title: sulfide
     examples:
-    - value: 2 micromole per liter
+    - value: 2 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - sulfide
@@ -17659,7 +17782,7 @@ slots:
     description: Water held on a surface
     title: surface moisture
     examples:
-    - value: 0.01 gram per square meter
+    - value: 0.01 g/m2
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - surface moisture
@@ -17705,7 +17828,7 @@ slots:
     description: Temperature of the surface at the time of sampling
     title: surface temperature
     examples:
-    - value: 15 degree Celsius
+    - value: 15 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - surface temperature
@@ -17731,7 +17854,7 @@ slots:
     description: Concentration of suspended particulate matter
     title: suspended particulate matter
     examples:
-    - value: 0.5 milligram per liter
+    - value: 0.5 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - suspended particulate matter
@@ -17847,7 +17970,7 @@ slots:
     description: Temperature of the sample at the time of sampling.
     title: temperature
     examples:
-    - value: 25 degree Celsius
+    - value: 25 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - temperature
@@ -17873,7 +17996,7 @@ slots:
     description: The recorded temperature value at sampling time outside
     title: temperature outside house
     examples:
-    - value: 5 degree Celsius
+    - value: 5 Cel
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - temperature outside house
@@ -18034,7 +18157,7 @@ slots:
     description: Measurement of total depth of water column
     title: total depth of water column
     examples:
-    - value: 500 meter
+    - value: 500 m
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total depth of water column
@@ -18061,7 +18184,7 @@ slots:
       by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'
     title: total dissolved nitrogen
     examples:
-    - value: 40 microgram per liter
+    - value: 40 ug/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total dissolved nitrogen
@@ -18087,7 +18210,7 @@ slots:
     description: Total inorganic nitrogen content
     title: total inorganic nitrogen
     examples:
-    - value: 40 microgram per liter
+    - value: 40 ug/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total inorganic nitrogen
@@ -18141,7 +18264,7 @@ slots:
       without filtering, reported as nitrogen'
     title: total nitrogen concentration
     examples:
-    - value: 50 micromole per liter
+    - value: 50 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total nitrogen concentration
@@ -18188,7 +18311,7 @@ slots:
     description: Total nitrogen content of the sample
     title: total nitrogen content
     examples:
-    - value: ''
+    - value: 5 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total nitrogen content
@@ -18236,7 +18359,7 @@ slots:
       otherwise: total organic carbon content'
     title: total organic carbon
     examples:
-    - value: ''
+    - value: 5 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total organic carbon
@@ -18262,7 +18385,7 @@ slots:
     description: Total particulate carbon content
     title: total particulate carbon
     examples:
-    - value: 35 micromole per liter
+    - value: 35 umol/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total particulate carbon
@@ -18289,7 +18412,7 @@ slots:
       phosphorus = total dissolved phosphorus + particulate phosphorus'
     title: total phosphorus
     examples:
-    - value: 0.03 milligram per liter
+    - value: 0.03 mg/L
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - total phosphorus
@@ -18428,7 +18551,7 @@ slots:
       individual particles
     title: turbidity
     examples:
-    - value: 0.3 nephelometric turbidity units
+    - value: 0.3 [NTU]
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - turbidity
@@ -18528,7 +18651,7 @@ slots:
     description: Ventilation rate of the system in the sampled premises
     title: ventilation rate
     examples:
-    - value: 750 cubic meter per minute
+    - value: 750 m3/min
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - ventilation rate
@@ -18967,7 +19090,7 @@ slots:
     description: Measurement of magnitude and direction of flow within a fluid
     title: water current
     examples:
-    - value: 10 cubic meter per second
+    - value: 10 m3/s
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - water current
@@ -19213,7 +19336,7 @@ slots:
     description: Speed of wind measured at the time of sampling
     title: wind speed
     examples:
-    - value: 21 kilometer per hour
+    - value: 21 km/h
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - wind speed
@@ -19752,6 +19875,11 @@ slots:
     - For example, low read count from a sequencer, malformed fastq files, etc.
     from_schema: https://w3id.org/nmdc/nmdc
     range: FailureWhatEnum
+  protocol_for:
+    name: protocol_for
+    description: The type of planned process that the protocol describes.
+    from_schema: https://w3id.org/nmdc/nmdc
+    range: ProtocolForEnum
   emsl_store_temp:
     name: emsl_store_temp
     description: The temperature at which the sample should be stored upon delivery
@@ -22057,8 +22185,6 @@ classes:
         - Aspect is the orientation of slope, measured clockwise in degrees from 0
           to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing,
           and 270 is west-facing.
-        examples:
-        - value: '35'
       slope_gradient:
         name: slope_gradient
         todos:
@@ -22094,10 +22220,6 @@ classes:
         - Required when aluminum saturation is provided.
         examples:
         - value: https://doi.org/10.1371/journal.pone.0176357
-      annual_precpt:
-        name: annual_precpt
-        examples:
-        - value: 8.94 inch
       cur_vegetation:
         name: cur_vegetation
         description: Vegetation classification from one or more standard classification
@@ -22158,9 +22280,6 @@ classes:
         comments:
         - Seasons are defined as spring (March, April, May), summer (June, July, August),
           autumn (September, October, November) and winter (December, January, February).
-        examples:
-        - value: 0.4 inch
-        - value: 10.16 mm
       water_cont_soil_meth:
         name: water_cont_soil_meth
         todos:
@@ -22216,10 +22335,6 @@ classes:
         examples:
         - value: https://doi.org/10.2134/agronmonogr9.2.c32
         - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
-      tot_nitro_content:
-        name: tot_nitro_content
-        examples:
-        - value: 5 mg N/ L
       tot_org_c_meth:
         name: tot_org_c_meth
         examples:
@@ -22228,8 +22343,6 @@ classes:
         name: tot_org_carb
         todos:
         - check description. How are they different?
-        examples:
-        - value: 5 mg N/ L
       salinity_meth:
         name: salinity_meth
         examples:
@@ -22619,6 +22732,8 @@ classes:
       has_unit:
         name: has_unit
         description: The unit of the quantity
+        range: UnitEnum
+        required: true
       has_numeric_value:
         name: has_numeric_value
         description: The number part of the quantity
@@ -22731,6 +22846,72 @@ classes:
         name: longitude
         required: true
     class_uri: nmdc:GeolocationValue
+  PropertyAssertion:
+    name: PropertyAssertion
+    description: A structured record of data that doesn't fit nicely within the constraints
+      of other NMDC AttributeValues. Uses primitive ranges only.
+    comments:
+    - This class enables flexible metadata capture for properties that don't align
+      with existing, policy-governed slots in NMDC schema.
+    - 'Interoperability note: This approach is aligned with the BERtron schema''s
+      ''properties'' slot pattern (see https://github.com/ber-data/bertron-schema),
+      which uses any_of to support both TextValue and QuantityValue ranges. NMDC''s
+      PropertyAssertion provides a more granular approach by using primitive types
+      with optional semantic annotations, enabling better validation while maintaining
+      flexibility for diverse metadata types.'
+    - PropertyAssertion supports both categorical values (via has_value_term_id) and
+      numeric values (via has_numeric_value with optional min/max ranges), along with
+      temporal (has_datetime_value) and boolean (has_boolean_value) data types.
+    examples:
+    - description: Data provided from submission that doesn't conform to required
+        abs_air_humidity units
+      object:
+        type: nmdc:PropertyAssertion
+        has_raw_value: 50 kPa
+        has_attribute_id: MIXS:0000122
+        has_attribute_label: absolute air humidity
+        has_numeric_value: 50
+        has_unit: kPa
+    - description: Data provided from submission that doesn't conform to required
+        UCUM unit
+      object:
+        type: nmdc:PropertyAssertion
+        has_raw_value: 5.5 mL/L
+        has_attribute_id: MIXS:0000119
+        has_attribute_label: dissolved oxygen
+        has_numeric_value: 5.5
+        has_unit: mL/L
+    - description: Unit provided is invalid for UCUM and standard
+      object:
+        type: nmdc:PropertyAssertion
+        has_raw_value: 250 W/m2
+        has_attribute_id: MIXS:0000112
+        has_attribute_label: solar irradiance
+        has_numeric_value: 250
+        has_unit: W/m2
+    from_schema: https://w3id.org/nmdc/nmdc
+    is_a: AttributeValue
+    slots:
+    - has_attribute_label
+    - has_attribute_id
+    - has_quantity_kind_id
+    - has_value_term_id
+    - has_boolean_value
+    - has_datetime_value
+    - has_numeric_value
+    - has_minimum_numeric_value
+    - has_maximum_numeric_value
+    - has_unit
+    slot_usage:
+      has_raw_value:
+        name: has_raw_value
+        description: Original contributor string representation (unparsed)
+        required: true
+      has_unit:
+        name: has_unit
+        description: UCUM unit code (required only when numeric value is present)
+        required: false
+    class_uri: nmdc:PropertyAssertion
   NamedThing:
     name: NamedThing
     description: a databased entity or concept/class
@@ -22835,7 +23016,8 @@ classes:
   Instrument:
     name: Instrument
     description: A material entity that is designed to perform a function in a scientific
-      investigation, but is not a reagent.
+      investigation, but is not a reagent. This class models the make and model of
+      the instrument, not the specific instance of the instrument.
     from_schema: https://w3id.org/nmdc/nmdc
     aliases:
     - device
@@ -22853,6 +23035,13 @@ classes:
           syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'
           interpolated: true
     class_uri: nmdc:Instrument
+    unique_keys:
+      main:
+        unique_key_name: main
+        unique_key_slots:
+        - vendor
+        - model
+        description: A unique instrument is defined by its vendor and model.
   PlannedProcess:
     name: PlannedProcess
     title: Planned Process
@@ -22878,6 +23067,8 @@ classes:
     - name
     - type
     - description
+    - protocol_for
+    - analysis_type
     class_uri: nmdc:Protocol
   CreditAssociation:
     name: CreditAssociation