nmdc-schema 11.15.0__tar.gz → 11.16.0__tar.gz

{nmdc_schema-11.15.0 → nmdc_schema-11.16.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.15.0
+Version: 11.16.0
 Summary: Schema resources for the National Microbiome Data Collaborative (NMDC)
 License: MIT
 License-File: LICENSE
@@ -27,6 +27,8 @@ Requires-Dist: jsonasobj2 (>=1,<2)
 Requires-Dist: jsonschema (>=4,<5)
 Requires-Dist: linkml (>=1.9.6,<2.0.0)
 Requires-Dist: linkml-runtime (>=1.9.5,<2.0.0)
+Requires-Dist: pyasn1 (>=0.6.2)
+Requires-Dist: pymdown-extensions (>=10.16.1)
 Requires-Dist: pymongo (>=4.7.2,<5.0.0)
 Requires-Dist: python-dotenv
 Requires-Dist: pyyaml (>=6,<7)

nmdc_schema-11.16.0/nmdc_schema/migrators/migrator_from_11_14_0_to_11_15_1.py

@@ -0,0 +1,12 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class Migrator(MigratorBase):
+    r"""Migrates a database between two schemas."""
+
+    _from_version = "11.14.0"
+    _to_version = "11.15.1"
+
+    def upgrade(self, commit_changes: bool = False) -> None:
+        r"""No upgrade needed."""
+        pass

nmdc_schema-11.16.0/nmdc_schema/migrators/migrator_from_11_15_1_to_11_16_0.py

@@ -0,0 +1,28 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class Migrator(MigratorBase):
+    r"""Migrates a database between two schemas."""
+
+    _from_version = "11.15.1"
+    _to_version = "11.16.0"
+
+    def upgrade(self, commit_changes: bool = False) -> None:
+        r"""Migrates the database from conforming to the original schema, to conforming to the new schema."""
+
+        self.adapter.process_each_document("workflow_execution_set", [self.make_uses_calibration_multivalued])
+
+    def make_uses_calibration_multivalued(self, workflow_execution: dict) -> dict:
+        r"""
+        If a WorkflowExecution record in the workflow_execution_set has a 'uses_calibration' field, convert it to a list containing the original value.
+
+        >>> m = Migrator()
+        >>> m.make_uses_calibration_multivalued({'id': 123})  # no `extraction_target` field
+        {'id': 123}
+        >>> m.make_uses_calibration_multivalued({'id': 123, 'uses_calibration': 'nmdc:calib-13-tester'})  # test: casts it as a list value
+        {'id': 123, 'uses_calibration': ['nmdc:calib-13-tester']}
+        """
+
+        if workflow_execution.get("uses_calibration") is not None:
+            workflow_execution["uses_calibration"] = [workflow_execution["uses_calibration"]]
+        return workflow_execution

{nmdc_schema-11.15.0 → nmdc_schema-11.16.0}/nmdc_schema/nmdc.py

@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-15T00:37:30
+# Generation date: 2026-02-05T23:25:00
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc
@@ -60,7 +60,7 @@ from linkml_runtime.linkml_model.types import Boolean, Decimal, Float, Integer,
 from linkml_runtime.utils.metamodelcore import Bool, Decimal, URIorCURIE
 
 metamodel_version = "1.7.0"
-version = "11.15.0"
+version = "11.16.0"
 
 # Namespaces
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')
@@ -6231,7 +6231,7 @@ class MetabolomicsAnalysis(WorkflowExecution):
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
     metabolomics_analysis_category: Union[str, "MetabolomicsAnalysisCategoryEnum"] = None
     has_metabolite_identifications: Optional[Union[Union[dict, MetaboliteIdentification], list[Union[dict, MetaboliteIdentification]]]] = empty_list()
-    uses_calibration: Optional[Union[str, CalibrationInformationId]] = None
+    uses_calibration: Optional[Union[Union[str, CalibrationInformationId], list[Union[str, CalibrationInformationId]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
     superseded_by: Optional[Union[str, MetabolomicsAnalysisId]] = None
 
@@ -6250,8 +6250,9 @@ class MetabolomicsAnalysis(WorkflowExecution):
             self.has_metabolite_identifications = [self.has_metabolite_identifications] if self.has_metabolite_identifications is not None else []
         self.has_metabolite_identifications = [v if isinstance(v, MetaboliteIdentification) else MetaboliteIdentification(**as_dict(v)) for v in self.has_metabolite_identifications]
 
-        if self.uses_calibration is not None and not isinstance(self.uses_calibration, CalibrationInformationId):
-            self.uses_calibration = CalibrationInformationId(self.uses_calibration)
+        if not isinstance(self.uses_calibration, list):
+            self.uses_calibration = [self.uses_calibration] if self.uses_calibration is not None else []
+        self.uses_calibration = [v if isinstance(v, CalibrationInformationId) else CalibrationInformationId(v) for v in self.uses_calibration]
 
         if not isinstance(self.was_informed_by, list):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
@@ -6281,7 +6282,7 @@ class NomAnalysis(WorkflowExecution):
     started_at_time: str = None
     has_input: Union[Union[str, DataObjectId], list[Union[str, DataObjectId]]] = None
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
-    uses_calibration: Optional[Union[str, CalibrationInformationId]] = None
+    uses_calibration: Optional[Union[Union[str, CalibrationInformationId], list[Union[str, CalibrationInformationId]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
     superseded_by: Optional[Union[str, NomAnalysisId]] = None
 
@@ -6291,8 +6292,9 @@ class NomAnalysis(WorkflowExecution):
         if not isinstance(self.id, NomAnalysisId):
             self.id = NomAnalysisId(self.id)
 
-        if self.uses_calibration is not None and not isinstance(self.uses_calibration, CalibrationInformationId):
-            self.uses_calibration = CalibrationInformationId(self.uses_calibration)
+        if not isinstance(self.uses_calibration, list):
+            self.uses_calibration = [self.uses_calibration] if self.uses_calibration is not None else []
+        self.uses_calibration = [v if isinstance(v, CalibrationInformationId) else CalibrationInformationId(v) for v in self.uses_calibration]
 
         if not isinstance(self.was_informed_by, list):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
@@ -6531,6 +6533,7 @@ class CalibrationStandardEnum(EnumDefinitionImpl):
 
     fames = PermissibleValue(text="fames")
     alkanes = PermissibleValue(text="alkanes")
+    srfa = PermissibleValue(text="srfa")
 
     _defn = EnumDefinition(
         name="CalibrationStandardEnum",
@@ -10450,7 +10453,7 @@ slots.generates_calibration = Slot(uri=NMDC.generates_calibration, name="generat
                    model_uri=NMDC.generates_calibration, domain=None, range=Optional[Union[str, CalibrationInformationId]])
 
 slots.uses_calibration = Slot(uri=NMDC.uses_calibration, name="uses_calibration", curie=NMDC.curie('uses_calibration'),
-                   model_uri=NMDC.uses_calibration, domain=None, range=Optional[Union[str, CalibrationInformationId]])
+                   model_uri=NMDC.uses_calibration, domain=None, range=Optional[Union[Union[str, CalibrationInformationId], list[Union[str, CalibrationInformationId]]]])
 
 slots.calibration_object = Slot(uri=NMDC.calibration_object, name="calibration_object", curie=NMDC.curie('calibration_object'),
                    model_uri=NMDC.calibration_object, domain=None, range=Optional[Union[str, DataObjectId]])

{nmdc_schema-11.15.0 → nmdc_schema-11.16.0}/nmdc_schema/nmdc.schema.json

@@ -1584,7 +1584,7 @@
                             "type": "null"
                         }
                     ],
-                    "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually"
+                    "description": "The number of times the sample location is cleaned per day."
                 },
                 "freq_cook": {
                     "anyOf": [
@@ -5222,7 +5222,8 @@
             "description": "",
             "enum": [
                 "fames",
-                "alkanes"
+                "alkanes",
+                "srfa"
             ],
             "title": "CalibrationStandardEnum",
             "type": "string"
@@ -9787,8 +9788,11 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
+                    "items": {
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -11928,8 +11932,11 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
+                    "items": {
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -15466,5 +15473,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.15.0"
+    "version": "11.16.0"
 }

{nmdc_schema-11.15.0 → nmdc_schema-11.16.0}/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": "11.15.0",
+  "version": "11.16.0",
   "license": "https://creativecommons.org/publicdomain/zero/1.0/",
   "prefixes": {
     "BFO": {
@@ -752,6 +752,18 @@
           "aliases": [
             "Alkanes"
           ]
+        },
+        "srfa": {
+          "text": "srfa",
+          "comments": [
+            "Reference standard Suwannee River Fulvic Acid Standard II (2S101F) from International Humic Substances Society"
+          ],
+          "see_also": [
+            "https://humic-substances.org/source-materials-for-ihss-samples/"
+          ],
+          "aliases": [
+            "Suwannee River fulvic acid"
+          ]
         }
       }
     },
@@ -7480,7 +7492,7 @@
       "slot_uri": "MIXS:0000341",
       "range": "string",
       "multivalued": false,
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$",
       "structured_pattern": {
         "syntax": "^{PMID}|{DOI}|{URL}$",
         "interpolated": true
@@ -7539,6 +7551,7 @@
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "range": "CalibrationInformation",
+      "multivalued": true,
       "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
       "structured_pattern": {
         "syntax": "{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$",
@@ -9957,7 +9970,7 @@
         "start"
       ],
       "slot_uri": "MIXS:0001009",
-      "pattern": "^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d):([0-5]\\d)(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$$",
+      "pattern": "^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d)(:([0-5]\\d))?(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$",
       "structured_pattern": {
         "syntax": "^({add_recov_methods});{date_time_stamp}$",
         "interpolated": true,
@@ -10042,7 +10055,7 @@
       "range": "TextValue",
       "multivalued": true,
       "inlined_as_list": true,
-      "pattern": "^.*;[-+]?[0-9]*\\.?[0-9]+ ([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d):([0-5]\\d)(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$$",
+      "pattern": "^.*;[-+]?[0-9]*\\.?[0-9]+ ([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d)(:([0-5]\\d))?(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$",
       "structured_pattern": {
         "syntax": "^{agrochemical_name};{amount} {unit};{date_time_stamp}$",
         "interpolated": true,
@@ -10183,9 +10196,9 @@
       ],
       "slot_uri": "MIXS:0000324",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -11833,9 +11846,9 @@
       ],
       "slot_uri": "MIXS:0001041",
       "range": "TextValue",
-      "pattern": "^.*|^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(.*|PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{text}|{PMID}|{DOI}|{URL}$",
+        "syntax": "^({text}|{PMID}|{DOI}|{URL})$",
         "interpolated": true
       }
     },
@@ -11890,9 +11903,9 @@
       ],
       "slot_uri": "MIXS:0000314",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -13303,11 +13316,11 @@
           "value": "1/d"
         }
       },
-      "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually",
+      "description": "The number of times the sample location is cleaned per day.",
       "title": "frequency of cleaning",
       "examples": [
         {
-          "value": "Daily"
+          "value": "2 1/d"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13446,9 +13459,9 @@
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "slot_uri": "MIXS:0000859",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true
       }
     },
@@ -13886,9 +13899,9 @@
       "slot_uri": "MIXS:0000343",
       "range": "string",
       "inlined_as_list": true,
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -13955,9 +13968,9 @@
       ],
       "slot_uri": "MIXS:0000321",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -14221,9 +14234,9 @@
       ],
       "slot_uri": "MIXS:0000871",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$|.*$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)|.*)$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}|{text}$",
+        "syntax": "^({PMID}|{DOI}|{URL}|{text})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -14931,9 +14944,9 @@
       ],
       "slot_uri": "MIXS:0000340",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -14968,9 +14981,9 @@
       ],
       "slot_uri": "MIXS:0000328",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -15020,9 +15033,9 @@
       ],
       "slot_uri": "MIXS:0000331",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -15472,9 +15485,9 @@
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "slot_uri": "MIXS:0000038",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -15491,9 +15504,9 @@
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "slot_uri": "MIXS:0000037",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -16562,9 +16575,9 @@
       ],
       "slot_uri": "MIXS:0000316",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -16581,7 +16594,7 @@
       "title": "history/previous land use",
       "examples": [
         {
-          "value": "fallow; 2018-05-11:T14:30Z"
+          "value": "fallow;2018-05-11T14:30Z"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -17301,9 +17314,9 @@
       ],
       "slot_uri": "MIXS:0001061",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$|.*$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)|.*)$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}|{text}$",
+        "syntax": "^({PMID}|{DOI}|{URL}|{text})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -19012,11 +19025,7 @@
         "storage"
       ],
       "slot_uri": "MIXS:0000327",
-      "range": "TextValue",
-      "pattern": "^([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+);P(?:(?:\\d+D|\\d+M(?:\\d+D)?|\\d+Y(?:\\d+M(?:\\d+D)?)?)(?:T(?:\\d+H(?:\\d+M(?:\\d+S)?)?|\\d+M(?:\\d+S)?|\\d+S))?|T(?:\\d+H(?:\\d+M(?:\\d+S)?)?|\\d+M(?:\\d+S)?|\\d+S)|\\d+W)$",
-      "structured_pattern": {
-        "syntax": "^{storage_condition_type};{duration}$"
-      }
+      "range": "TextValue"
     },
     "substructure_type": {
       "name": "substructure_type",
@@ -19531,9 +19540,9 @@
       ],
       "slot_uri": "MIXS:0001070",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$|.*$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)|.*)$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}|{text}$",
+        "syntax": "^({PMID}|{DOI}|{URL}|{text})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -19769,9 +19778,9 @@
       ],
       "slot_uri": "MIXS:0000338",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -19824,9 +19833,9 @@
       ],
       "slot_uri": "MIXS:0000337",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -25762,15 +25771,17 @@
           "name": "heavy_metals_meth",
           "title": "heavy metals method/ extreme unusual properties",
           "comments": [
-            "Required when heavy metals are provided",
-            "If different methods are used for multiple metals, indicate the metal and method. Separate metals by ;"
+            "Required when heavy metals are provided"
           ],
           "examples": [
             {
               "value": "https://doi.org/10.3390/ijms9040434"
             },
             {
-              "value": "mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8"
+              "value": "doi:10.1007/BF01056090"
+            },
+            {
+              "value": "https://doi.org/10.1007/s00216-006-0322-8"
             }
           ],
           "multivalued": true
@@ -26688,7 +26699,7 @@
     },
     "date_time_stamp": {
       "setting_key": "date_time_stamp",
-      "setting_value": "(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d):([0-5]\\d)(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$"
+      "setting_value": "(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d)(:([0-5]\\d))?(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?"
     },
     "dna_bases": {
       "setting_key": "dna_bases",
@@ -26696,7 +26707,7 @@
     },
     "DOI": {
       "setting_key": "DOI",
-      "setting_value": "^doi:10.\\d{2,9}/.*$"
+      "setting_value": "doi:10.\\d{2,9}/.*"
     },
     "duration": {
       "setting_key": "duration",
@@ -26736,7 +26747,7 @@
     },
     "PMID": {
       "setting_key": "PMID",
-      "setting_value": "^PMID:\\d+$"
+      "setting_value": "PMID:\\d+"
     },
     "primer_adapter_codes": {
       "setting_key": "primer_adapter_codes",
@@ -26782,13 +26793,17 @@
       "setting_key": "text",
       "setting_value": ".*"
     },
+    "timestamp": {
+      "setting_key": "timestamp",
+      "setting_value": "(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d)(:([0-5]\\d))?(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?"
+    },
     "unit": {
       "setting_key": "unit",
       "setting_value": "([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+)"
     },
     "URL": {
       "setting_key": "URL",
-      "setting_value": "^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$"
+      "setting_value": "https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)"
     },
     "version": {
       "setting_key": "version",