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

nmdc_schema/nmdc_materialized_patterns.json

@@ -6,7 +6,7 @@
     "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": {
@@ -417,47 +417,6 @@
   "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_\\-\\/\\.,]*$"
-    },
-    "bytes": {
-      "name": "bytes",
-      "description": "An integer value that corresponds to a size in bytes",
-      "from_schema": "https://w3id.org/nmdc/nmdc",
-      "see_also": [
-        "UO:0000233"
-      ],
-      "base": "int",
-      "uri": "xsd:long"
-    },
-    "decimal_degree": {
-      "name": "decimal_degree",
-      "description": "A decimal degree expresses latitude or longitude as decimal fractions.",
-      "from_schema": "https://w3id.org/nmdc/nmdc",
-      "see_also": [
-        "https://en.wikipedia.org/wiki/Decimal_degrees"
-      ],
-      "base": "float",
-      "uri": "xsd:decimal"
-    },
-    "language_code": {
-      "name": "language_code",
-      "description": "A language code conforming to ISO_639-1",
-      "from_schema": "https://w3id.org/nmdc/nmdc",
-      "see_also": [
-        "https://en.wikipedia.org/wiki/ISO_639-1"
-      ],
-      "base": "str",
-      "uri": "xsd:language"
-    },
     "string": {
       "name": "string",
       "description": "A character string",
@@ -708,6 +667,47 @@
       "base": "str",
       "uri": "xsd:string",
       "repr": "str"
+    },
+    "external_identifier": {
+      "name": "external_identifier",
+      "description": "A CURIE representing an external identifier",
+      "from_schema": "https://w3id.org/nmdc/nmdc",
+      "see_also": [
+        "https://microbiomedata.github.io/nmdc-schema/identifiers/"
+      ],
+      "typeof": "uriorcurie",
+      "uri": "xsd:anyURI",
+      "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$"
+    },
+    "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": {
@@ -1814,6 +1814,10 @@
           "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 millivolt."
@@ -7498,6 +7502,106 @@
         }
       }
     },
+    "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",
@@ -8593,7 +8697,7 @@
       ],
       "examples": [
         {
-          "value": "543 mg/kg"
+          "value": "543 [ppm]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -8634,7 +8738,7 @@
       ],
       "examples": [
         {
-          "value": "1575 mg/kg"
+          "value": "1575 [ppm]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -8743,7 +8847,7 @@
       "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",
@@ -9204,8 +9308,7 @@
         "qud:unit",
         "schema:unitCode"
       ],
-      "range": "UnitEnum",
-      "required": true
+      "range": "string"
     },
     "type": {
       "name": "type",
@@ -9331,6 +9434,53 @@
       "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 is done by an external organziation (e.g., JGI) such as software tool name and version or pipeline name and version.",
@@ -10446,7 +10596,7 @@
       "title": "absolute air humidity",
       "examples": [
         {
-          "value": "9 gram per gram"
+          "value": "9 g/g"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -10694,7 +10844,7 @@
       "title": "air temperature",
       "examples": [
         {
-          "value": "20 degree Celsius"
+          "value": "20 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -10829,7 +10979,7 @@
       "title": "alkalinity",
       "examples": [
         {
-          "value": "50 milligram per liter"
+          "value": "50 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -10894,7 +11044,7 @@
       "title": "alkyl diethers",
       "examples": [
         {
-          "value": "0.005 mole per liter"
+          "value": "0.005 mol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -10922,7 +11072,7 @@
       "title": "altitude",
       "examples": [
         {
-          "value": "100 meter"
+          "value": "100 m"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -10958,7 +11108,7 @@
       "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",
@@ -10994,7 +11144,7 @@
       "title": "ammonium",
       "examples": [
         {
-          "value": "1.5 milligram per liter"
+          "value": "1.5 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11095,7 +11245,7 @@
       "title": "mean annual precipitation",
       "examples": [
         {
-          "value": ""
+          "value": "225 mm"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11131,7 +11281,7 @@
       "title": "mean annual temperature",
       "examples": [
         {
-          "value": "12.5 degree Celsius"
+          "value": "12.5 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11361,7 +11511,7 @@
       "title": "average dew point",
       "examples": [
         {
-          "value": "25.5 degree Celsius"
+          "value": "25.5 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11425,7 +11575,7 @@
       "title": "average temperature",
       "examples": [
         {
-          "value": "12.5 degree Celsius"
+          "value": "12.5 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11461,7 +11611,7 @@
       "title": "bacterial production",
       "examples": [
         {
-          "value": "5 milligram per cubic meter per day"
+          "value": "5 mg/m3/d"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11497,7 +11647,7 @@
       "title": "bacterial respiration",
       "examples": [
         {
-          "value": "300 micromole oxygen per liter per hour"
+          "value": "300 umol/L/h"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11533,7 +11683,7 @@
       "title": "bacterial carbon production",
       "examples": [
         {
-          "value": "2.53 microgram per liter per hour"
+          "value": "50 ng/h"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11569,7 +11719,7 @@
       "title": "barometric pressure",
       "examples": [
         {
-          "value": "5 millibar"
+          "value": "1013 mbar"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -11939,7 +12089,7 @@
       "title": "bishomohopanol",
       "examples": [
         {
-          "value": "14 microgram per liter"
+          "value": "14 ug/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12047,7 +12197,7 @@
       "title": "bromide",
       "examples": [
         {
-          "value": "0.05 parts per million"
+          "value": "0.05 [ppm]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12167,7 +12317,7 @@
       "title": "built structure age",
       "examples": [
         {
-          "value": "15"
+          "value": "15 a"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12261,7 +12411,7 @@
       "title": "calcium",
       "examples": [
         {
-          "value": "0.2 micromole per liter"
+          "value": "0.2 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12297,7 +12447,7 @@
       "title": "carbon dioxide",
       "examples": [
         {
-          "value": "410 parts per million"
+          "value": "410 [ppm]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12333,7 +12483,7 @@
       "title": "carbon monoxide",
       "examples": [
         {
-          "value": "0.1 parts per million"
+          "value": "0.1 [ppm]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12401,7 +12551,7 @@
       "title": "ceiling area",
       "examples": [
         {
-          "value": "25 square meter"
+          "value": "25 m2"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12830,7 +12980,7 @@
       "title": "chloride",
       "examples": [
         {
-          "value": "5000 milligram per liter"
+          "value": "5000 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12866,7 +13016,7 @@
       "title": "chlorophyll",
       "examples": [
         {
-          "value": "5 milligram per cubic meter"
+          "value": "5 mg/m3"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -12956,7 +13106,7 @@
       "title": "conductivity",
       "examples": [
         {
-          "value": "10 milliSiemens per centimeter"
+          "value": "10 uS/cm"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13192,7 +13342,7 @@
       "title": "density",
       "examples": [
         {
-          "value": "1000 kilogram per cubic meter"
+          "value": "1000 kg/m3"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13248,7 +13398,7 @@
       "title": "depth",
       "examples": [
         {
-          "value": "10 meter"
+          "value": "10 m"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13284,7 +13434,7 @@
       "title": "dew point",
       "examples": [
         {
-          "value": "22 degree Celsius"
+          "value": "22 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13354,7 +13504,7 @@
       "title": "dissolved carbon dioxide",
       "examples": [
         {
-          "value": "5 milligram per liter"
+          "value": "5 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13390,7 +13540,7 @@
       "title": "dissolved hydrogen",
       "examples": [
         {
-          "value": "0.3 micromole per liter"
+          "value": "0.3 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13419,14 +13569,14 @@
         },
         "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",
@@ -13462,7 +13612,7 @@
       "title": "dissolved inorganic nitrogen",
       "examples": [
         {
-          "value": "761 micromole per liter"
+          "value": "761 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13491,14 +13641,14 @@
         },
         "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",
@@ -13570,7 +13720,7 @@
       "title": "dissolved organic carbon",
       "examples": [
         {
-          "value": "197 micromole per liter"
+          "value": "197 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13606,7 +13756,7 @@
       "title": "dissolved organic nitrogen",
       "examples": [
         {
-          "value": "0.05 micromole per liter"
+          "value": "0.05 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13642,7 +13792,7 @@
       "title": "dissolved oxygen",
       "examples": [
         {
-          "value": "175 micromole per kilogram"
+          "value": "175 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13882,7 +14032,7 @@
       "title": "door area or size",
       "examples": [
         {
-          "value": "2.5 square meter"
+          "value": "2.5 m2"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -14031,7 +14181,7 @@
       "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",
@@ -15046,14 +15196,14 @@
         },
         "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",
@@ -15365,7 +15515,7 @@
       "title": "glucosidase activity",
       "examples": [
         {
-          "value": "5 mol per liter per hour"
+          "value": "5 mol/L/h"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16073,7 +16223,7 @@
       "title": "host age",
       "examples": [
         {
-          "value": "10 days"
+          "value": "10 d"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16196,7 +16346,7 @@
       "title": "host body temperature",
       "examples": [
         {
-          "value": "15 degree Celsius"
+          "value": "15 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16345,7 +16495,7 @@
       "title": "host dry mass",
       "examples": [
         {
-          "value": "500 gram"
+          "value": "500 g"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16468,7 +16618,7 @@
       "title": "host height",
       "examples": [
         {
-          "value": "0.1 meter"
+          "value": "0.1 m"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16534,7 +16684,7 @@
       "title": "host length",
       "examples": [
         {
-          "value": "1 meter"
+          "value": "1 m"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16827,7 +16977,7 @@
       "title": "host total mass",
       "examples": [
         {
-          "value": "2500 gram"
+          "value": "2500 g"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16863,7 +17013,7 @@
       "title": "host wet mass",
       "examples": [
         {
-          "value": "1500 gram"
+          "value": "1500 g"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -16899,7 +17049,7 @@
       "title": "humidity",
       "examples": [
         {
-          "value": "25 gram per cubic meter"
+          "value": "25 g/m3"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17276,7 +17426,7 @@
       "title": "light intensity",
       "examples": [
         {
-          "value": "0.3 lux"
+          "value": "0.3 lx"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17546,7 +17696,7 @@
       "title": "magnesium",
       "examples": [
         {
-          "value": "52.8 micromole per kilogram"
+          "value": "52.8 umol/kg"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17614,7 +17764,7 @@
       "title": "mean friction velocity",
       "examples": [
         {
-          "value": "0.5 meter per second"
+          "value": "0.5 m/s"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17650,7 +17800,7 @@
       "title": "mean peak friction velocity",
       "examples": [
         {
-          "value": "1 meter per second"
+          "value": "1 m/s"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17744,7 +17894,7 @@
       "title": "methane",
       "examples": [
         {
-          "value": "1800 parts per billion"
+          "value": "1800 [ppb]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17867,8 +18017,11 @@
           "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"
@@ -17881,7 +18034,7 @@
       "is_a": "core field",
       "string_serialization": "{text};{float} {unit}",
       "slot_uri": "MIXS:0000752",
-      "range": "TextValue",
+      "range": "PropertyAssertion",
       "multivalued": true,
       "inlined_as_list": true
     },
@@ -17943,7 +18096,7 @@
       "title": "nitrate",
       "examples": [
         {
-          "value": "65 micromole per liter"
+          "value": "65 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17979,7 +18132,7 @@
       "title": "nitrite",
       "examples": [
         {
-          "value": "0.5 micromole per liter"
+          "value": "0.5 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18015,7 +18168,7 @@
       "title": "nitrogen",
       "examples": [
         {
-          "value": "4.2 micromole per liter"
+          "value": "4.2 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18315,14 +18468,14 @@
         },
         "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",
@@ -18391,7 +18544,7 @@
       "title": "organic matter",
       "examples": [
         {
-          "value": "1.75 milligram per cubic meter"
+          "value": "200 ug/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18427,7 +18580,7 @@
       "title": "organic nitrogen",
       "examples": [
         {
-          "value": "4 micromole per liter"
+          "value": "4 ug/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18598,7 +18751,7 @@
       "title": "oxygen",
       "examples": [
         {
-          "value": "600 parts per million"
+          "value": "600 [ppm]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18634,7 +18787,7 @@
       "title": "particulate organic carbon",
       "examples": [
         {
-          "value": "1.92 micromole per liter"
+          "value": "0.02 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18670,7 +18823,7 @@
       "title": "particulate organic nitrogen",
       "examples": [
         {
-          "value": "0.3 micromole per liter"
+          "value": "0.3 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -18887,7 +19040,7 @@
       "title": "petroleum hydrocarbon",
       "examples": [
         {
-          "value": "0.05 micromole per liter"
+          "value": "0.05 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -19044,7 +19197,7 @@
       "title": "phosphate",
       "examples": [
         {
-          "value": "0.7 micromole per liter"
+          "value": "0.7 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -19114,7 +19267,7 @@
       "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",
@@ -19360,7 +19513,7 @@
       "title": "potassium",
       "examples": [
         {
-          "value": "463 milligram per liter"
+          "value": "463 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -19490,7 +19643,7 @@
       "title": "pressure",
       "examples": [
         {
-          "value": "50 atmosphere"
+          "value": "50 atm"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -19584,7 +19737,7 @@
       "title": "primary production",
       "examples": [
         {
-          "value": "100 milligram per cubic meter per day"
+          "value": "100 mg/m3/d"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -19866,7 +20019,7 @@
       "title": "redox potential",
       "examples": [
         {
-          "value": "300 millivolt"
+          "value": "300 mV"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -20859,7 +21012,7 @@
       "title": "salinity",
       "examples": [
         {
-          "value": "25 practical salinity unit"
+          "value": "70 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -21178,7 +21331,7 @@
       "title": "sample measured depth",
       "examples": [
         {
-          "value": "1534 meter;MSL"
+          "value": "1534 m"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -21296,7 +21449,7 @@
       "title": "amount or size of sample collected",
       "examples": [
         {
-          "value": "5 liter"
+          "value": "5 L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -21420,7 +21573,7 @@
       "title": "sample storage temperature",
       "examples": [
         {
-          "value": "-80 degree Celsius"
+          "value": "-80 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -21629,7 +21782,7 @@
       "title": "sample volume or weight for DNA extraction",
       "examples": [
         {
-          "value": "1500 milliliter"
+          "value": "1500 mL"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -21814,7 +21967,7 @@
       "title": "mean seasonal precipitation",
       "examples": [
         {
-          "value": ""
+          "value": "10 mm"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -21850,7 +22003,7 @@
       "title": "mean seasonal temperature",
       "examples": [
         {
-          "value": "18 degree Celsius"
+          "value": "18 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -22222,7 +22375,7 @@
       "title": "silicate",
       "examples": [
         {
-          "value": "0.05 micromole per liter"
+          "value": "0.05 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -22283,7 +22436,7 @@
       "title": "size-fraction lower threshold",
       "examples": [
         {
-          "value": "0.2 micrometer"
+          "value": "0.2 um"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -22319,7 +22472,7 @@
       "title": "size-fraction upper threshold",
       "examples": [
         {
-          "value": "20 micrometer"
+          "value": "20 um"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -22355,7 +22508,7 @@
       "title": "slope aspect",
       "examples": [
         {
-          "value": ""
+          "value": "35 deg"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -22463,7 +22616,7 @@
       "title": "sodium",
       "examples": [
         {
-          "value": "10.5 milligram per liter"
+          "value": "10.5 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -22646,7 +22799,7 @@
       "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",
@@ -22750,7 +22903,7 @@
       "title": "soluble reactive phosphorus",
       "examples": [
         {
-          "value": "0.1 milligram per liter"
+          "value": "0.1 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23103,7 +23256,7 @@
       "title": "sulfate",
       "examples": [
         {
-          "value": "5 micromole per liter"
+          "value": "5 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23175,7 +23328,7 @@
       "title": "sulfide",
       "examples": [
         {
-          "value": "2 micromole per liter"
+          "value": "2 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23303,7 +23456,7 @@
       "title": "surface moisture",
       "examples": [
         {
-          "value": "0.01 gram per square meter"
+          "value": "0.01 g/m2"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23367,7 +23520,7 @@
       "title": "surface temperature",
       "examples": [
         {
-          "value": "15 degree Celsius"
+          "value": "15 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23403,7 +23556,7 @@
       "title": "suspended particulate matter",
       "examples": [
         {
-          "value": "0.5 milligram per liter"
+          "value": "0.5 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23555,7 +23708,7 @@
       "title": "temperature",
       "examples": [
         {
-          "value": "25 degree Celsius"
+          "value": "25 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23591,7 +23744,7 @@
       "title": "temperature outside house",
       "examples": [
         {
-          "value": "5 degree Celsius"
+          "value": "5 Cel"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23813,7 +23966,7 @@
       "title": "total depth of water column",
       "examples": [
         {
-          "value": "500 meter"
+          "value": "500 m"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23849,7 +24002,7 @@
       "title": "total dissolved nitrogen",
       "examples": [
         {
-          "value": "40 microgram per liter"
+          "value": "40 ug/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23885,7 +24038,7 @@
       "title": "total inorganic nitrogen",
       "examples": [
         {
-          "value": "40 microgram per liter"
+          "value": "40 ug/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -23957,7 +24110,7 @@
       "title": "total nitrogen concentration",
       "examples": [
         {
-          "value": "50 micromole per liter"
+          "value": "50 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -24022,7 +24175,7 @@
       "title": "total nitrogen content",
       "examples": [
         {
-          "value": ""
+          "value": "5 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -24087,7 +24240,7 @@
       "title": "total organic carbon",
       "examples": [
         {
-          "value": ""
+          "value": "5 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -24123,7 +24276,7 @@
       "title": "total particulate carbon",
       "examples": [
         {
-          "value": "35 micromole per liter"
+          "value": "35 umol/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -24159,7 +24312,7 @@
       "title": "total phosphorus",
       "examples": [
         {
-          "value": "0.03 milligram per liter"
+          "value": "0.03 mg/L"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -24351,7 +24504,7 @@
       "title": "turbidity",
       "examples": [
         {
-          "value": "0.3 nephelometric turbidity units"
+          "value": "0.3 [NTU]"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -24487,7 +24640,7 @@
       "title": "ventilation rate",
       "examples": [
         {
-          "value": "750 cubic meter per minute"
+          "value": "750 m3/min"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -25086,7 +25239,7 @@
       "title": "water current",
       "examples": [
         {
-          "value": "10 cubic meter per second"
+          "value": "10 m3/s"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -25412,7 +25565,7 @@
       "title": "wind speed",
       "examples": [
         {
-          "value": "21 kilometer per hour"
+          "value": "21 km/h"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -26080,6 +26233,12 @@
       "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 to EMSL",
@@ -28799,11 +28958,6 @@
           "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.",
           "comments": [
             "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": {
@@ -28856,14 +29010,6 @@
             }
           ]
         },
-        "annual_precpt": {
-          "name": "annual_precpt",
-          "examples": [
-            {
-              "value": "8.94 inch"
-            }
-          ]
-        },
         "cur_vegetation": {
           "name": "cur_vegetation",
           "description": "Vegetation classification from one or more standard classification systems, or agricultural crop",
@@ -28948,14 +29094,6 @@
           ],
           "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": {
@@ -29048,14 +29186,6 @@
             }
           ]
         },
-        "tot_nitro_content": {
-          "name": "tot_nitro_content",
-          "examples": [
-            {
-              "value": "5 mg N/ L"
-            }
-          ]
-        },
         "tot_org_c_meth": {
           "name": "tot_org_c_meth",
           "examples": [
@@ -29068,11 +29198,6 @@
           "name": "tot_org_carb",
           "todos": [
             "check description. How are they different?"
-          ],
-          "examples": [
-            {
-              "value": "5 mg N/ L"
-            }
           ]
         },
         "salinity_meth": {
@@ -29545,7 +29670,9 @@
         },
         "has_unit": {
           "name": "has_unit",
-          "description": "The unit of the quantity"
+          "description": "The unit of the quantity",
+          "range": "UnitEnum",
+          "required": true
         },
         "has_numeric_value": {
           "name": "has_numeric_value",
@@ -29692,6 +29819,77 @@
       },
       "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",
@@ -29793,7 +29991,7 @@
     },
     "Instrument": {
       "name": "Instrument",
-      "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.",
+      "description": "A material entity that is designed to perform a function in a scientific 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"
@@ -29816,7 +30014,17 @@
           }
         }
       },
-      "class_uri": "nmdc:Instrument"
+      "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",
@@ -29844,7 +30052,9 @@
         "url",
         "name",
         "type",
-        "description"
+        "description",
+        "protocol_for",
+        "analysis_type"
       ],
       "class_uri": "nmdc:Protocol"
     },