nmdc-schema 11.15.0__py3-none-any.whl → 11.15.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nmdc_schema/nmdc.py +2 -2
- nmdc_schema/nmdc.schema.json +2 -2
- nmdc_schema/nmdc_materialized_patterns.json +55 -53
- nmdc_schema/nmdc_materialized_patterns.schema.json +22 -23
- nmdc_schema/nmdc_materialized_patterns.yaml +50 -52
- nmdc_schema/nmdc_pydantic.py +53 -73
- {nmdc_schema-11.15.0.dist-info → nmdc_schema-11.15.1.dist-info}/METADATA +3 -1
- {nmdc_schema-11.15.0.dist-info → nmdc_schema-11.15.1.dist-info}/RECORD +11 -11
- {nmdc_schema-11.15.0.dist-info → nmdc_schema-11.15.1.dist-info}/WHEEL +1 -1
- {nmdc_schema-11.15.0.dist-info → nmdc_schema-11.15.1.dist-info}/entry_points.txt +0 -0
- {nmdc_schema-11.15.0.dist-info → nmdc_schema-11.15.1.dist-info}/licenses/LICENSE +0 -0
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@@ -13,7 +13,7 @@ notes:
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- not importing any MIxS terms where the relationship between the name (SCN) and the
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id isn't 1:1
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id: https://w3id.org/nmdc/nmdc
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-
version: 11.15.
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+
version: 11.15.1
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license: https://creativecommons.org/publicdomain/zero/1.0/
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prefixes:
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BFO:
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@@ -5584,7 +5584,7 @@ slots:
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slot_uri: MIXS:0000341
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range: string
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multivalued: false
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-
pattern:
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+
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()@:%_\+.~#?&\/=]*)$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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interpolated: true
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@@ -7640,7 +7640,7 @@ slots:
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- start
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slot_uri: MIXS:0001009
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pattern: ^(Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer
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7643
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-
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))?)?)?)
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7643
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+
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))?)?)?)?$
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structured_pattern:
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syntax: ^({add_recov_methods});{date_time_stamp}$
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interpolated: true
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@@ -7710,7 +7710,7 @@ slots:
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range: TextValue
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multivalued: true
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inlined_as_list: true
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-
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))?)?)?)
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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))?)?)?)?$
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structured_pattern:
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syntax: ^{agrochemical_name};{amount} {unit};{date_time_stamp}$
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interpolated: true
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@@ -7826,9 +7826,9 @@ slots:
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- unusual
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slot_uri: MIXS:0000324
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range: string
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-
pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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-
syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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alkalinity:
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@@ -9132,9 +9132,9 @@ slots:
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- culture
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slot_uri: MIXS:0001041
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range: TextValue
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pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{text}|{PMID}|{DOI}|{URL}$
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syntax: ^({text}|{PMID}|{DOI}|{URL})$
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interpolated: true
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cur_land_use:
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name: cur_land_use
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@@ -9188,9 +9188,9 @@ slots:
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- vegetation
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slot_uri: MIXS:0000314
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range: string
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pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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date_last_rain:
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@@ -10321,11 +10321,10 @@ slots:
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storage_units:
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tag: storage_units
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value: 1/d
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description: The number of times the sample location is cleaned
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cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually
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description: The number of times the sample location is cleaned per day.
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title: frequency of cleaning
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examples:
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- value:
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- value: 2 1/d
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from_schema: https://w3id.org/nmdc/nmdc
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keywords:
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- frequency
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@@ -10435,9 +10434,9 @@ slots:
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- value: PMID:19497774
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from_schema: https://w3id.org/nmdc/nmdc
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slot_uri: MIXS:0000859
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-
pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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geo_loc_name:
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name: geo_loc_name
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@@ -10788,9 +10787,9 @@ slots:
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slot_uri: MIXS:0000343
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range: string
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inlined_as_list: true
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-
pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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height_carper_fiber:
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@@ -10846,9 +10845,9 @@ slots:
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- method
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slot_uri: MIXS:0000321
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range: string
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pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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host_age:
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@@ -11064,9 +11063,9 @@ slots:
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- host.
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slot_uri: MIXS:0000871
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range: TextValue
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pattern:
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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()@:%_\+.~#?&\/=]*)|.*)$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}|{text}$
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syntax: ^({PMID}|{DOI}|{URL}|{text})$
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interpolated: true
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partial_match: true
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host_height:
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@@ -11631,9 +11630,9 @@ slots:
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- link
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slot_uri: MIXS:0000340
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range: TextValue
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pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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link_class_info:
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@@ -11661,9 +11660,9 @@ slots:
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- link
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slot_uri: MIXS:0000328
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range: TextValue
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pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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lithology:
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@@ -11702,9 +11701,9 @@ slots:
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- method
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slot_uri: MIXS:0000331
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range: string
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pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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magnesium:
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@@ -12056,9 +12055,9 @@ slots:
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from_schema: https://w3id.org/nmdc/nmdc
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slot_uri: MIXS:0000038
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range: TextValue
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-
pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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nucl_acid_ext:
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@@ -12072,9 +12071,9 @@ slots:
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from_schema: https://w3id.org/nmdc/nmdc
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slot_uri: MIXS:0000037
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range: TextValue
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-
pattern:
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+
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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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number_pets:
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@@ -12925,9 +12924,9 @@ slots:
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- use
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slot_uri: MIXS:0000316
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range: string
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-
pattern:
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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()@:%_\+.~#?&\/=]*))$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}$
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syntax: ^({PMID}|{DOI}|{URL})$
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interpolated: true
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partial_match: true
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previous_land_use:
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@@ -12939,7 +12938,7 @@ slots:
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description: Previous land use and dates
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title: history/previous land use
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examples:
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-
- value: fallow;
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+
- value: fallow;2018-05-11T14:30Z
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from_schema: https://w3id.org/nmdc/nmdc
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keywords:
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- history
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@@ -13521,9 +13520,9 @@ slots:
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- condition
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slot_uri: MIXS:0001061
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range: TextValue
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-
pattern:
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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()@:%_\+.~#?&\/=]*)|.*)$
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structured_pattern:
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syntax: ^{PMID}|{DOI}|{URL}|{text}$
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syntax: ^({PMID}|{DOI}|{URL}|{text})$
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interpolated: true
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partial_match: true
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root_med_carbon:
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@@ -14907,9 +14906,6 @@ slots:
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- storage
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slot_uri: MIXS:0000327
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range: TextValue
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|
-
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)$
|
|
14911
|
-
structured_pattern:
|
|
14912
|
-
syntax: ^{storage_condition_type};{duration}$
|
|
14913
14909
|
substructure_type:
|
|
14914
14910
|
name: substructure_type
|
|
14915
14911
|
description: The substructure or under building is that largely hidden section
|
|
@@ -15305,9 +15301,9 @@ slots:
|
|
|
15305
15301
|
- growth
|
|
15306
15302
|
slot_uri: MIXS:0001070
|
|
15307
15303
|
range: TextValue
|
|
15308
|
-
pattern:
|
|
15304
|
+
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()@:%_\+.~#?&\/=]*)|.*)$
|
|
15309
15305
|
structured_pattern:
|
|
15310
|
-
syntax: ^{PMID}|{DOI}|{URL}|{text}$
|
|
15306
|
+
syntax: ^({PMID}|{DOI}|{URL}|{text})$
|
|
15311
15307
|
interpolated: true
|
|
15312
15308
|
partial_match: true
|
|
15313
15309
|
toluene:
|
|
@@ -15495,9 +15491,9 @@ slots:
|
|
|
15495
15491
|
- total
|
|
15496
15492
|
slot_uri: MIXS:0000338
|
|
15497
15493
|
range: string
|
|
15498
|
-
pattern:
|
|
15494
|
+
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()@:%_\+.~#?&\/=]*))$
|
|
15499
15495
|
structured_pattern:
|
|
15500
|
-
syntax: ^{PMID}|{DOI}|{URL}$
|
|
15496
|
+
syntax: ^({PMID}|{DOI}|{URL})$
|
|
15501
15497
|
interpolated: true
|
|
15502
15498
|
partial_match: true
|
|
15503
15499
|
tot_nitro_content:
|
|
@@ -15537,9 +15533,9 @@ slots:
|
|
|
15537
15533
|
- total
|
|
15538
15534
|
slot_uri: MIXS:0000337
|
|
15539
15535
|
range: string
|
|
15540
|
-
pattern:
|
|
15536
|
+
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()@:%_\+.~#?&\/=]*))$
|
|
15541
15537
|
structured_pattern:
|
|
15542
|
-
syntax: ^{PMID}|{DOI}|{URL}$
|
|
15538
|
+
syntax: ^({PMID}|{DOI}|{URL})$
|
|
15543
15539
|
interpolated: true
|
|
15544
15540
|
partial_match: true
|
|
15545
15541
|
tot_org_carb:
|
|
@@ -20427,11 +20423,10 @@ classes:
|
|
|
20427
20423
|
title: heavy metals method/ extreme unusual properties
|
|
20428
20424
|
comments:
|
|
20429
20425
|
- Required when heavy metals are provided
|
|
20430
|
-
- If different methods are used for multiple metals, indicate the metal and
|
|
20431
|
-
method. Separate metals by ;
|
|
20432
20426
|
examples:
|
|
20433
20427
|
- value: https://doi.org/10.3390/ijms9040434
|
|
20434
|
-
- value:
|
|
20428
|
+
- value: doi:10.1007/BF01056090
|
|
20429
|
+
- value: https://doi.org/10.1007/s00216-006-0322-8
|
|
20435
20430
|
multivalued: true
|
|
20436
20431
|
season_precpt:
|
|
20437
20432
|
name: season_precpt
|
|
@@ -21149,13 +21144,13 @@ settings:
|
|
|
21149
21144
|
setting_value: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)
|
|
21150
21145
|
date_time_stamp:
|
|
21151
21146
|
setting_key: date_time_stamp
|
|
21152
|
-
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))?)?)?)
|
|
21147
|
+
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))?)?)?)?
|
|
21153
21148
|
dna_bases:
|
|
21154
21149
|
setting_key: dna_bases
|
|
21155
21150
|
setting_value: '[ACGT]'
|
|
21156
21151
|
DOI:
|
|
21157
21152
|
setting_key: DOI
|
|
21158
|
-
setting_value:
|
|
21153
|
+
setting_value: doi:10.\d{2,9}/.*
|
|
21159
21154
|
duration:
|
|
21160
21155
|
setting_key: duration
|
|
21161
21156
|
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 +21180,7 @@ settings:
|
|
|
21185
21180
|
setting_value: .*
|
|
21186
21181
|
PMID:
|
|
21187
21182
|
setting_key: PMID
|
|
21188
|
-
setting_value:
|
|
21183
|
+
setting_value: PMID:\d+
|
|
21189
21184
|
primer_adapter_codes:
|
|
21190
21185
|
setting_key: primer_adapter_codes
|
|
21191
21186
|
setting_value: '[ACGTRYSWKMBDHVNI]'
|
|
@@ -21219,12 +21214,15 @@ settings:
|
|
|
21219
21214
|
text:
|
|
21220
21215
|
setting_key: text
|
|
21221
21216
|
setting_value: .*
|
|
21217
|
+
timestamp:
|
|
21218
|
+
setting_key: timestamp
|
|
21219
|
+
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))?)?)?)?
|
|
21222
21220
|
unit:
|
|
21223
21221
|
setting_key: unit
|
|
21224
21222
|
setting_value: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)
|
|
21225
21223
|
URL:
|
|
21226
21224
|
setting_key: URL
|
|
21227
|
-
setting_value:
|
|
21225
|
+
setting_value: https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)
|
|
21228
21226
|
version:
|
|
21229
21227
|
setting_key: version
|
|
21230
21228
|
setting_value: ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)
|