nmdc-schema 11.15.0__tar.gz → 11.15.1__tar.gz

{nmdc_schema-11.15.0 → nmdc_schema-11.15.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_schema
-Version: 11.15.0
+Version: 11.15.1
 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-11.15.0 → nmdc_schema-11.15.1}/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: 2026-01-21T19:39:27
 # 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 = "11.15.1"
 
 # Namespaces
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')

{nmdc_schema-11.15.0 → nmdc_schema-11.15.1}/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": [
@@ -15466,5 +15466,5 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.15.0"
+    "version": "11.15.1"
 }

{nmdc_schema-11.15.0 → nmdc_schema-11.15.1}/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": "11.15.1",
   "license": "https://creativecommons.org/publicdomain/zero/1.0/",
   "prefixes": {
     "BFO": {
@@ -7480,7 +7480,7 @@
       "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()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$",
       "structured_pattern": {
         "syntax": "^{PMID}|{DOI}|{URL}$",
         "interpolated": true
@@ -9957,7 +9957,7 @@
         "start"
       ],
       "slot_uri": "MIXS:0001009",
-      "pattern": "^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d):([0-5]\\d)(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$$",
+      "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 +10042,7 @@
       "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))?)?)?)?$$",
+      "pattern": "^.*;[-+]?[0-9]*\\.?[0-9]+ ([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d)(:([0-5]\\d))?(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$",
       "structured_pattern": {
         "syntax": "^{agrochemical_name};{amount} {unit};{date_time_stamp}$",
         "interpolated": true,
@@ -10183,9 +10183,9 @@
       ],
       "slot_uri": "MIXS:0000324",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -11833,9 +11833,9 @@
       ],
       "slot_uri": "MIXS:0001041",
       "range": "TextValue",
-      "pattern": "^.*|^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(.*|PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{text}|{PMID}|{DOI}|{URL}$",
+        "syntax": "^({text}|{PMID}|{DOI}|{URL})$",
         "interpolated": true
       }
     },
@@ -11890,9 +11890,9 @@
       ],
       "slot_uri": "MIXS:0000314",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -13303,11 +13303,11 @@
           "value": "1/d"
         }
       },
-      "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually",
+      "description": "The number of times the sample location is cleaned per day.",
       "title": "frequency of cleaning",
       "examples": [
         {
-          "value": "Daily"
+          "value": "2 1/d"
         }
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
@@ -13446,9 +13446,9 @@
       ],
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "slot_uri": "MIXS:0000859",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true
       }
     },
@@ -13886,9 +13886,9 @@
       "slot_uri": "MIXS:0000343",
       "range": "string",
       "inlined_as_list": true,
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -13955,9 +13955,9 @@
       ],
       "slot_uri": "MIXS:0000321",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -14221,9 +14221,9 @@
       ],
       "slot_uri": "MIXS:0000871",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$|.*$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)|.*)$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}|{text}$",
+        "syntax": "^({PMID}|{DOI}|{URL}|{text})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -14931,9 +14931,9 @@
       ],
       "slot_uri": "MIXS:0000340",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -14968,9 +14968,9 @@
       ],
       "slot_uri": "MIXS:0000328",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -15020,9 +15020,9 @@
       ],
       "slot_uri": "MIXS:0000331",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -15472,9 +15472,9 @@
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "slot_uri": "MIXS:0000038",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
       "structured_pattern": {
-        "syntax": "^{PMID}|{DOI}|{URL}$",
+        "syntax": "^({PMID}|{DOI}|{URL})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -15491,9 +15491,9 @@
       "from_schema": "https://w3id.org/nmdc/nmdc",
       "slot_uri": "MIXS:0000037",
       "range": "TextValue",
-      "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+      "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -16562,9 +16562,9 @@
       ],
       "slot_uri": "MIXS:0000316",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^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 +16581,7 @@
       "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 +17301,9 @@
       ],
       "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 +19012,7 @@
         "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 +19527,9 @@
       ],
       "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 +19765,9 @@
       ],
       "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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -19824,9 +19820,9 @@
       ],
       "slot_uri": "MIXS:0000337",
       "range": "string",
-      "pattern": "^^PMID:\\d+$|^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})$",
         "interpolated": true,
         "partial_match": true
       }
@@ -25762,15 +25758,17 @@
           "name": "heavy_metals_meth",
           "title": "heavy metals method/ extreme unusual properties",
           "comments": [
-            "Required when heavy metals are provided",
-            "If different methods are used for multiple metals, indicate the metal and method. Separate metals by ;"
+            "Required when heavy metals are provided"
           ],
           "examples": [
             {
               "value": "https://doi.org/10.3390/ijms9040434"
             },
             {
-              "value": "mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8"
+              "value": "doi:10.1007/BF01056090"
+            },
+            {
+              "value": "https://doi.org/10.1007/s00216-006-0322-8"
             }
           ],
           "multivalued": true
@@ -26688,7 +26686,7 @@
     },
     "date_time_stamp": {
       "setting_key": "date_time_stamp",
-      "setting_value": "(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d):([0-5]\\d)(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$"
+      "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 +26694,7 @@
     },
     "DOI": {
       "setting_key": "DOI",
-      "setting_value": "^doi:10.\\d{2,9}/.*$"
+      "setting_value": "doi:10.\\d{2,9}/.*"
     },
     "duration": {
       "setting_key": "duration",
@@ -26736,7 +26734,7 @@
     },
     "PMID": {
       "setting_key": "PMID",
-      "setting_value": "^PMID:\\d+$"
+      "setting_value": "PMID:\\d+"
     },
     "primer_adapter_codes": {
       "setting_key": "primer_adapter_codes",
@@ -26782,13 +26780,17 @@
       "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",

{nmdc_schema-11.15.0 → nmdc_schema-11.15.1}/nmdc_schema/nmdc_materialized_patterns.schema.json

@@ -85,7 +85,7 @@
                 },
                 "add_recov_method": {
                     "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field",
-                    "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))?)?)?)?$$",
+                    "pattern": "^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|Surfactant Addition|Not Applicable|other);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d)(:([0-5]\\d))?(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$",
                     "type": [
                         "string",
                         "null"
@@ -130,7 +130,7 @@
                     "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications",
                     "items": {
                         "$ref": "#/$defs/TextValue",
-                        "pattern": "^.*;[-+]?[0-9]*\\.?[0-9]+ ([^\\s-]{1,2}|[^\\s-]+.+[^\\s-]+);(\\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\\d|3[01])(T([01]\\d|2[0-3]):([0-5]\\d):([0-5]\\d)(\\.\\d+)?(Z|([+-][01]\\d:[0-5]\\d))?)?)?)?$$"
+                        "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))?)?)?)?$"
                     },
                     "type": [
                         "array",
@@ -184,7 +184,7 @@
                 },
                 "al_sat_meth": {
                     "description": "Reference or method used in determining Aluminum saturation",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -982,7 +982,7 @@
                         }
                     ],
                     "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors",
-                    "pattern": "^.*|^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$"
+                    "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()@:%_\\+.~#?&\\/=]*))$"
                 },
                 "cur_land_use": {
                     "description": "Present state of sample site",
@@ -1004,7 +1004,7 @@
                 },
                 "cur_vegetation_meth": {
                     "description": "Reference or method used in vegetation classification",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -1657,7 +1657,7 @@
                             "type": "null"
                         }
                     ],
-                    "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually"
+                    "description": "The number of times the sample location is cleaned per day."
                 },
                 "freq_cook": {
                     "anyOf": [
@@ -1711,7 +1711,7 @@
                 },
                 "genetic_mod": {
                     "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "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()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -1915,7 +1915,7 @@
                 "heavy_metals_meth": {
                     "description": "Reference or method used in determining heavy metals",
                     "items": {
-                        "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                        "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
                         "type": "string"
                     },
                     "type": [
@@ -1947,7 +1947,7 @@
                 },
                 "horizon_meth": {
                     "description": "Reference or method used in determining the horizon",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "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()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -2098,7 +2098,7 @@
                         }
                     ],
                     "description": "Literature reference giving growth conditions of the host",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$|.*$"
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)|.*)$"
                 },
                 "host_height": {
                     "anyOf": [
@@ -2495,7 +2495,7 @@
                         }
                     ],
                     "description": "Link to additional analysis results performed on the sample",
-                    "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()@:%_\\+.~#?&\\/=]*)$$"
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$"
                 },
                 "link_class_info": {
                     "description": "Link to digitized soil maps or other soil classification information",
@@ -2514,7 +2514,7 @@
                         }
                     ],
                     "description": "Link to climate resource",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$"
+                    "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()@:%_\\+.~#?&\\/=]*))$"
                 },
                 "lithology": {
                     "$ref": "#/$defs/LithologyEnum",
@@ -2533,7 +2533,7 @@
                 },
                 "local_class_meth": {
                     "description": "Reference or method used in determining the local soil classification",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -3257,7 +3257,7 @@
                 },
                 "prev_land_use_meth": {
                     "description": "Reference or method used in determining previous land use and dates",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "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()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -3642,7 +3642,7 @@
                         }
                     ],
                     "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$|.*$"
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)|.*)$"
                 },
                 "root_med_carbon": {
                     "anyOf": [
@@ -3742,7 +3742,7 @@
                 },
                 "salinity_meth": {
                     "description": "Reference or method used in determining salinity.",
-                    "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()@:%_\\+.~#?&\\/=]*)$",
                     "type": [
                         "string",
                         "null"
@@ -4412,8 +4412,7 @@
                             "type": "null"
                         }
                     ],
-                    "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)",
-                    "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)$"
+                    "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)"
                 },
                 "substructure_type": {
                     "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level",
@@ -4628,7 +4627,7 @@
                         }
                     ],
                     "description": "Description of plant tissue culture growth media used",
-                    "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()@:%_\\+.~#?&\\/=]*)|.*)$"
                 },
                 "toluene": {
                     "anyOf": [
@@ -4716,7 +4715,7 @@
                 },
                 "tot_nitro_cont_meth": {
                     "description": "Reference or method used in determining the total nitrogen",
-                    "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()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -4736,7 +4735,7 @@
                 },
                 "tot_org_c_meth": {
                     "description": "Reference or method used in determining total organic carbon",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$",
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -8744,7 +8743,7 @@
                         }
                     ],
                     "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$"
+                    "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()@:%_\\+.~#?&\\/=]*))$"
                 },
                 "pcr_cond": {
                     "description": "Description of reaction conditions and components of polymerase chain reaction performed during library preparation",
@@ -15773,6 +15772,6 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.15.0"
+    "version": "11.15.1"
 }