nmdc-schema 11.15.0__py3-none-any.whl → 11.16.0__py3-none-any.whl

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()@:%_\\+.~#?&\\/=]*)$$",
+                    "pattern": "^(PMID:\\d+|doi:10.\\d{2,9}/.*|https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*))$",
                     "type": [
                         "string",
                         "null"
@@ -5431,7 +5430,8 @@
             "description": "",
             "enum": [
                 "fames",
-                "alkanes"
+                "alkanes",
+                "srfa"
             ],
             "title": "CalibrationStandardEnum",
             "type": "string"
@@ -8744,7 +8744,7 @@
                         }
                     ],
                     "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids",
-                    "pattern": "^^PMID:\\d+$|^doi:10.\\d{2,9}/.*$|^https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)$$"
+                    "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()@:%_\\+.~#?&\\/=]*))$"
                 },
                 "pcr_cond": {
                     "description": "Description of reaction conditions and components of polymerase chain reaction performed during library preparation",
@@ -10040,9 +10040,12 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
-                    "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                    "items": {
+                        "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -12212,9 +12215,12 @@
                 },
                 "uses_calibration": {
                     "description": "calibration information is used by a process",
-                    "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                    "items": {
+                        "pattern": "^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$",
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
@@ -15773,6 +15779,6 @@
     },
     "title": "NMDC",
     "type": "object",
-    "version": "11.15.0"
+    "version": "11.16.0"
 }
 

nmdc_schema/nmdc_materialized_patterns.yaml

@@ -13,7 +13,7 @@ notes:
 - not importing any MIxS terms where the relationship between the name (SCN) and the
   id isn't 1:1
 id: https://w3id.org/nmdc/nmdc
-version: 11.15.0
+version: 11.16.0
 license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   BFO:
@@ -619,6 +619,15 @@ enums:
         text: alkanes
         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
   StrandedOrientationEnum:
     name: StrandedOrientationEnum
     description: This enumeration specifies information about stranded RNA library
@@ -5584,7 +5593,7 @@ slots:
     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()@:%_\+.~#?&\/=]*)$$
+    pattern: ^PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$
     structured_pattern:
       syntax: ^{PMID}|{DOI}|{URL}$
       interpolated: true
@@ -5636,6 +5645,7 @@ slots:
       run is used when analyzing metabolomics data
     from_schema: https://w3id.org/nmdc/nmdc
     range: CalibrationInformation
+    multivalued: true
     pattern: ^(nmdc):calib-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$
     structured_pattern:
       syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'
@@ -7640,7 +7650,7 @@ slots:
     - start
     slot_uri: MIXS:0001009
     pattern: ^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer
-      Addition|Surfactant Addition|Not Applicable|other);(\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\d|3[01])(T([01]\d|2[0-3]):([0-5]\d):([0-5]\d)(\.\d+)?(Z|([+-][01]\d:[0-5]\d))?)?)?)?$$
+      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
@@ -7710,7 +7720,7 @@ slots:
     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))?)?)?)?$$
+    pattern: ^.*;[-+]?[0-9]*\.?[0-9]+ ([^\s-]{1,2}|[^\s-]+.+[^\s-]+);(\d{4})(-(0[1-9]|1[0-2])(-(0[1-9]|[12]\d|3[01])(T([01]\d|2[0-3]):([0-5]\d)(:([0-5]\d))?(\.\d+)?(Z|([+-][01]\d:[0-5]\d))?)?)?)?$
     structured_pattern:
       syntax: ^{agrochemical_name};{amount} {unit};{date_time_stamp}$
       interpolated: true
@@ -7826,9 +7836,9 @@ slots:
     - unusual
     slot_uri: MIXS:0000324
     range: string
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
+    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
   alkalinity:
@@ -9132,9 +9142,9 @@ slots:
     - culture
     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()@:%_\+.~#?&\/=]*)$$
+    pattern: ^(.*|PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*))$
     structured_pattern:
-      syntax: ^{text}|{PMID}|{DOI}|{URL}$
+      syntax: ^({text}|{PMID}|{DOI}|{URL})$
       interpolated: true
   cur_land_use:
     name: cur_land_use
@@ -9188,9 +9198,9 @@ slots:
     - vegetation
     slot_uri: MIXS:0000314
     range: string
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
+    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
   date_last_rain:
@@ -10321,11 +10331,10 @@ slots:
       storage_units:
         tag: storage_units
         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
     keywords:
     - frequency
@@ -10435,9 +10444,9 @@ slots:
     - value: PMID:19497774
     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()@:%_\+.~#?&\/=]*)$$
+    pattern: ^(PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*))$
     structured_pattern:
-      syntax: ^{PMID}|{DOI}|{URL}$
+      syntax: ^({PMID}|{DOI}|{URL})$
       interpolated: true
   geo_loc_name:
     name: geo_loc_name
@@ -10788,9 +10797,9 @@ slots:
     slot_uri: MIXS:0000343
     range: string
     inlined_as_list: true
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
+    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
   height_carper_fiber:
@@ -10846,9 +10855,9 @@ slots:
     - method
     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()@:%_\+.~#?&\/=]*)$$
+    pattern: ^(PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*))$
     structured_pattern:
-      syntax: ^{PMID}|{DOI}|{URL}$
+      syntax: ^({PMID}|{DOI}|{URL})$
       interpolated: true
       partial_match: true
   host_age:
@@ -11064,9 +11073,9 @@ slots:
     - host.
     slot_uri: MIXS:0000871
     range: TextValue
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|.*$
+    pattern: ^(PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)|.*)$
     structured_pattern:
-      syntax: ^{PMID}|{DOI}|{URL}|{text}$
+      syntax: ^({PMID}|{DOI}|{URL}|{text})$
       interpolated: true
       partial_match: true
   host_height:
@@ -11631,9 +11640,9 @@ slots:
     - link
     slot_uri: MIXS:0000340
     range: TextValue
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
+    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
   link_class_info:
@@ -11661,9 +11670,9 @@ slots:
     - link
     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()@:%_\+.~#?&\/=]*)$$
+    pattern: ^(PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*))$
     structured_pattern:
-      syntax: ^{PMID}|{DOI}|{URL}$
+      syntax: ^({PMID}|{DOI}|{URL})$
       interpolated: true
       partial_match: true
   lithology:
@@ -11702,9 +11711,9 @@ slots:
     - method
     slot_uri: MIXS:0000331
     range: string
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
+    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
   magnesium:
@@ -12056,9 +12065,9 @@ slots:
     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()@:%_\+.~#?&\/=]*)$$
+    pattern: ^(PMID:\d+|doi:10.\d{2,9}/.*|https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*))$
     structured_pattern:
-      syntax: ^{PMID}|{DOI}|{URL}$
+      syntax: ^({PMID}|{DOI}|{URL})$
       interpolated: true
       partial_match: true
   nucl_acid_ext:
@@ -12072,9 +12081,9 @@ slots:
     from_schema: https://w3id.org/nmdc/nmdc
     slot_uri: MIXS:0000037
     range: TextValue
-    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
+    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
   number_pets:
@@ -12925,9 +12934,9 @@ slots:
     - use
     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
   previous_land_use:
@@ -12939,7 +12948,7 @@ slots:
     description: Previous land use and dates
     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
     keywords:
     - history
@@ -13521,9 +13530,9 @@ slots:
     - condition
     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
   root_med_carbon:
@@ -14907,9 +14916,6 @@ slots:
     - 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}$
   substructure_type:
     name: substructure_type
     description: The substructure or under building is that largely hidden section
@@ -15305,9 +15311,9 @@ slots:
     - growth
     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
   toluene:
@@ -15495,9 +15501,9 @@ slots:
     - total
     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
   tot_nitro_content:
@@ -15537,9 +15543,9 @@ slots:
     - total
     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
   tot_org_carb:
@@ -20427,11 +20433,10 @@ classes:
         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 ;
         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
       season_precpt:
         name: season_precpt
@@ -21149,13 +21154,13 @@ settings:
     setting_value: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)
   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
     setting_value: '[ACGT]'
   DOI:
     setting_key: DOI
-    setting_value: ^doi:10.\d{2,9}/.*$
+    setting_value: doi:10.\d{2,9}/.*
   duration:
     setting_key: duration
     setting_value: 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)
@@ -21185,7 +21190,7 @@ settings:
     setting_value: .*
   PMID:
     setting_key: PMID
-    setting_value: ^PMID:\d+$
+    setting_value: PMID:\d+
   primer_adapter_codes:
     setting_key: primer_adapter_codes
     setting_value: '[ACGTRYSWKMBDHVNI]'
@@ -21219,12 +21224,15 @@ settings:
   text:
     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
     setting_value: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)