Class: Soil MIxS Inspired Mixin (SoilMixsInspiredMixin)
Mixin with SoilMixsInspired Terms
URI: nmdc_sub_schema:SoilMixsInspiredMixin
classDiagram
class SoilMixsInspiredMixin
SoilMixsInspiredMixin <|-- SoilInterface
SoilMixsInspiredMixin : collection_date_inc
SoilMixsInspiredMixin : collection_time
SoilMixsInspiredMixin : collection_time_inc
SoilMixsInspiredMixin : experimental_factor_other
SoilMixsInspiredMixin : filter_method
SoilMixsInspiredMixin : isotope_exposure
SoilMixsInspiredMixin : micro_biomass_c_meth
SoilMixsInspiredMixin : micro_biomass_n_meth
SoilMixsInspiredMixin : microbial_biomass_c
SoilMixsInspiredMixin : microbial_biomass_n
SoilMixsInspiredMixin : non_microb_biomass
SoilMixsInspiredMixin : non_microb_biomass_method
SoilMixsInspiredMixin : org_nitro_method
SoilMixsInspiredMixin : other_treatment
SoilMixsInspiredMixin : start_date_inc
SoilMixsInspiredMixin : start_time_inc
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
collection_date_inc | 0..1 recommended String |
Date the incubation was harvested/collected/ended | direct |
collection_time | 0..1 recommended String |
The time of sampling, either as an instance (single point) or interval | direct |
collection_time_inc | 0..1 recommended String |
Time the incubation was harvested/collected/ended | direct |
experimental_factor_other | 0..1 recommended String |
Other details about your sample that you feel can't be accurately represented... | direct |
filter_method | 0..1 recommended String |
Type of filter used or how the sample was filtered | direct |
isotope_exposure | 0..1 recommended String |
List isotope exposure or addition applied to your sample | direct |
micro_biomass_c_meth | 0..1 recommended String |
Reference or method used in determining microbial biomass carbon | direct |
micro_biomass_n_meth | 0..1 String |
Reference or method used in determining microbial biomass nitrogen | direct |
microbial_biomass_c | 0..1 String |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
microbial_biomass_n | 0..1 String |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
non_microb_biomass | 0..1 String |
Amount of biomass; should include the name for the part of biomass measured, ... | direct |
non_microb_biomass_method | 0..1 String |
Reference or method used in determining biomass | direct |
org_nitro_method | 0..1 String |
Method used for obtaining organic nitrogen | direct |
other_treatment | 0..1 recommended String |
Other treatments applied to your samples that are not applicable to the provi... | direct |
start_date_inc | 0..1 recommended String |
Date the incubation was started | direct |
start_time_inc | 0..1 recommended String |
Time the incubation was started | direct |
collection_date_inc | 0..1 recommended String |
Date the incubation was harvested/collected/ended | direct |
collection_time | 0..1 recommended String |
The time of sampling, either as an instance (single point) or interval | direct |
collection_time_inc | 0..1 recommended String |
Time the incubation was harvested/collected/ended | direct |
experimental_factor_other | 0..1 recommended String |
Other details about your sample that you feel can't be accurately represented... | direct |
filter_method | 0..1 recommended String |
Type of filter used or how the sample was filtered | direct |
isotope_exposure | 0..1 recommended String |
List isotope exposure or addition applied to your sample | direct |
micro_biomass_c_meth | 0..1 recommended String |
Reference or method used in determining microbial biomass carbon | direct |
micro_biomass_n_meth | 0..1 String |
Reference or method used in determining microbial biomass nitrogen | direct |
microbial_biomass_c | 0..1 String |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
microbial_biomass_n | 0..1 String |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
non_microb_biomass | 0..1 String |
Amount of biomass; should include the name for the part of biomass measured, ... | direct |
non_microb_biomass_method | 0..1 String |
Reference or method used in determining biomass | direct |
org_nitro_method | 0..1 String |
Method used for obtaining organic nitrogen | direct |
other_treatment | 0..1 recommended String |
Other treatments applied to your samples that are not applicable to the provi... | direct |
start_date_inc | 0..1 recommended String |
Date the incubation was started | direct |
start_time_inc | 0..1 recommended String |
Time the incubation was started | direct |
Mixin Usage
mixed into | description |
---|---|
SoilInterface | soil dh_interface |
Identifier and Mapping Information
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:SoilMixsInspiredMixin |
native | nmdc_sub_schema:SoilMixsInspiredMixin |
LinkML Source
Direct
name: SoilMixsInspiredMixin
description: Mixin with SoilMixsInspired Terms
title: Soil MIxS Inspired Mixin
from_schema: https://example.com/nmdc_submission_schema
mixin: true
slots:
- collection_date_inc
- collection_time
- collection_time_inc
- experimental_factor_other
- filter_method
- isotope_exposure
- micro_biomass_c_meth
- micro_biomass_n_meth
- microbial_biomass_c
- microbial_biomass_n
- non_microb_biomass
- non_microb_biomass_method
- org_nitro_method
- other_treatment
- start_date_inc
- start_time_inc
- collection_date_inc
- collection_time
- collection_time_inc
- experimental_factor_other
- filter_method
- isotope_exposure
- micro_biomass_c_meth
- micro_biomass_n_meth
- microbial_biomass_c
- microbial_biomass_n
- non_microb_biomass
- non_microb_biomass_method
- org_nitro_method
- other_treatment
- start_date_inc
- start_time_inc
slot_usage:
collection_date_inc:
name: collection_date_inc
description: Date the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 2
string_serialization: '{date, arbitrary precision}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
collection_time:
name: collection_time
description: The time of sampling, either as an instance (single point) or interval.
title: collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 1
string_serialization: '{time, seconds optional}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
collection_time_inc:
name: collection_time_inc
description: Time the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 3
string_serialization: '{time, seconds optional}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
experimental_factor_other:
name: experimental_factor_other
description: Other details about your sample that you feel can't be accurately
represented in the available columns.
title: experimental factor- other
comments:
- This slot accepts open-ended text about your sample.
- We recommend using key:value pairs.
- Provided pairs will be considered for inclusion as future slots/terms in this
data collection template.
examples:
- value: 'experimental treatment: value'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000008
- MIXS:0000300
rank: 7
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
filter_method:
name: filter_method
description: Type of filter used or how the sample was filtered
title: filter method
comments:
- describe the filter or provide a catalog number and manufacturer
examples:
- value: C18
- value: Basix PES, 13-100-106 FisherSci
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000765
rank: 6
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
isotope_exposure:
name: isotope_exposure
description: List isotope exposure or addition applied to your sample.
title: isotope exposure/addition
todos:
- Can we make the H218O correctly super and subscripted?
comments:
- This is required when your experimental design includes the use of isotopically
labeled compounds
examples:
- value: 13C glucose
- value: H218O
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000751
rank: 16
string_serialization: '{termLabel} {[termID]}; {timestamp}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
micro_biomass_c_meth:
name: micro_biomass_c_meth
description: Reference or method used in determining microbial biomass carbon
title: microbial biomass carbon method
todos:
- How should we separate values? | or ;? lets be consistent
comments:
- required if "microbial_biomass_c" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 1004
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
micro_biomass_n_meth:
name: micro_biomass_n_meth
description: Reference or method used in determining microbial biomass nitrogen
title: microbial biomass nitrogen method
comments:
- required if "microbial_biomass_n" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 1004
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
microbial_biomass_c:
name: microbial_biomass_c
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass carbon
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug C/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 1004
string_serialization: '{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
microbial_biomass_n:
name: microbial_biomass_n
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass nitrogen
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug N/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 1004
string_serialization: '{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
non_microb_biomass:
name: non_microb_biomass
description: Amount of biomass; should include the name for the part of biomass
measured, e.g.insect, plant, total. Can include multiple measurements separated
by ;
title: non-microbial biomass
examples:
- value: insect 0.23 ug; plant 1g
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000174
- MIXS:0000650
rank: 8
string_serialization: '{text};{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
non_microb_biomass_method:
name: non_microb_biomass_method
description: Reference or method used in determining biomass
title: non-microbial biomass method
comments:
- required if "non-microbial biomass" is provided
examples:
- value: https://doi.org/10.1038/s41467-021-26181-3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 9
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
org_nitro_method:
name: org_nitro_method
description: Method used for obtaining organic nitrogen
title: organic nitrogen method
comments:
- required if "org_nitro" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(85)90144-0
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000338
- MIXS:0000205
rank: 14
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
other_treatment:
name: other_treatment
description: Other treatments applied to your samples that are not applicable
to the provided fields
title: other treatments
notes:
- Values entered here will be used to determine potential new slots.
comments:
- This is an open text field to provide any treatments that cannot be captured
in the provided slots.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000300
rank: 15
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
start_date_inc:
name: start_date_inc
description: Date the incubation was started. Only relevant for incubation samples.
title: incubation start date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 4
string_serialization: '{date, arbitrary precision}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
start_time_inc:
name: start_time_inc
description: Time the incubation was started. Only relevant for incubation samples.
title: incubation start time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 5
string_serialization: '{time, seconds optional}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
Induced
name: SoilMixsInspiredMixin
description: Mixin with SoilMixsInspired Terms
title: Soil MIxS Inspired Mixin
from_schema: https://example.com/nmdc_submission_schema
mixin: true
slot_usage:
collection_date_inc:
name: collection_date_inc
description: Date the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 2
string_serialization: '{date, arbitrary precision}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
collection_time:
name: collection_time
description: The time of sampling, either as an instance (single point) or interval.
title: collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 1
string_serialization: '{time, seconds optional}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
collection_time_inc:
name: collection_time_inc
description: Time the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 3
string_serialization: '{time, seconds optional}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
experimental_factor_other:
name: experimental_factor_other
description: Other details about your sample that you feel can't be accurately
represented in the available columns.
title: experimental factor- other
comments:
- This slot accepts open-ended text about your sample.
- We recommend using key:value pairs.
- Provided pairs will be considered for inclusion as future slots/terms in this
data collection template.
examples:
- value: 'experimental treatment: value'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000008
- MIXS:0000300
rank: 7
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
filter_method:
name: filter_method
description: Type of filter used or how the sample was filtered
title: filter method
comments:
- describe the filter or provide a catalog number and manufacturer
examples:
- value: C18
- value: Basix PES, 13-100-106 FisherSci
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000765
rank: 6
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
isotope_exposure:
name: isotope_exposure
description: List isotope exposure or addition applied to your sample.
title: isotope exposure/addition
todos:
- Can we make the H218O correctly super and subscripted?
comments:
- This is required when your experimental design includes the use of isotopically
labeled compounds
examples:
- value: 13C glucose
- value: H218O
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000751
rank: 16
string_serialization: '{termLabel} {[termID]}; {timestamp}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
micro_biomass_c_meth:
name: micro_biomass_c_meth
description: Reference or method used in determining microbial biomass carbon
title: microbial biomass carbon method
todos:
- How should we separate values? | or ;? lets be consistent
comments:
- required if "microbial_biomass_c" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 1004
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
micro_biomass_n_meth:
name: micro_biomass_n_meth
description: Reference or method used in determining microbial biomass nitrogen
title: microbial biomass nitrogen method
comments:
- required if "microbial_biomass_n" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 1004
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
microbial_biomass_c:
name: microbial_biomass_c
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass carbon
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug C/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 1004
string_serialization: '{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
microbial_biomass_n:
name: microbial_biomass_n
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass nitrogen
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug N/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 1004
string_serialization: '{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
non_microb_biomass:
name: non_microb_biomass
description: Amount of biomass; should include the name for the part of biomass
measured, e.g.insect, plant, total. Can include multiple measurements separated
by ;
title: non-microbial biomass
examples:
- value: insect 0.23 ug; plant 1g
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000174
- MIXS:0000650
rank: 8
string_serialization: '{text};{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
non_microb_biomass_method:
name: non_microb_biomass_method
description: Reference or method used in determining biomass
title: non-microbial biomass method
comments:
- required if "non-microbial biomass" is provided
examples:
- value: https://doi.org/10.1038/s41467-021-26181-3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 9
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
org_nitro_method:
name: org_nitro_method
description: Method used for obtaining organic nitrogen
title: organic nitrogen method
comments:
- required if "org_nitro" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(85)90144-0
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000338
- MIXS:0000205
rank: 14
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
other_treatment:
name: other_treatment
description: Other treatments applied to your samples that are not applicable
to the provided fields
title: other treatments
notes:
- Values entered here will be used to determine potential new slots.
comments:
- This is an open text field to provide any treatments that cannot be captured
in the provided slots.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000300
rank: 15
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
start_date_inc:
name: start_date_inc
description: Date the incubation was started. Only relevant for incubation samples.
title: incubation start date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 4
string_serialization: '{date, arbitrary precision}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
start_time_inc:
name: start_time_inc
description: Time the incubation was started. Only relevant for incubation samples.
title: incubation start time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 5
string_serialization: '{time, seconds optional}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
attributes:
collection_date_inc:
name: collection_date_inc
description: Date the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 2
string_serialization: '{date, arbitrary precision}'
multivalued: false
alias: collection_date_inc
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
collection_time:
name: collection_time
description: The time of sampling, either as an instance (single point) or interval.
title: collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 1
string_serialization: '{time, seconds optional}'
multivalued: false
alias: collection_time
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
collection_time_inc:
name: collection_time_inc
description: Time the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 3
string_serialization: '{time, seconds optional}'
multivalued: false
alias: collection_time_inc
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$
experimental_factor_other:
name: experimental_factor_other
description: Other details about your sample that you feel can't be accurately
represented in the available columns.
title: experimental factor- other
comments:
- This slot accepts open-ended text about your sample.
- We recommend using key:value pairs.
- Provided pairs will be considered for inclusion as future slots/terms in this
data collection template.
examples:
- value: 'experimental treatment: value'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000008
- MIXS:0000300
rank: 7
string_serialization: '{text}'
multivalued: false
alias: experimental_factor_other
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
filter_method:
name: filter_method
description: Type of filter used or how the sample was filtered
title: filter method
comments:
- describe the filter or provide a catalog number and manufacturer
examples:
- value: C18
- value: Basix PES, 13-100-106 FisherSci
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000765
rank: 6
string_serialization: '{text}'
multivalued: false
alias: filter_method
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
isotope_exposure:
name: isotope_exposure
description: List isotope exposure or addition applied to your sample.
title: isotope exposure/addition
todos:
- Can we make the H218O correctly super and subscripted?
comments:
- This is required when your experimental design includes the use of isotopically
labeled compounds
examples:
- value: 13C glucose
- value: H218O
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000751
rank: 16
string_serialization: '{termLabel} {[termID]}; {timestamp}'
multivalued: false
alias: isotope_exposure
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
micro_biomass_c_meth:
name: micro_biomass_c_meth
description: Reference or method used in determining microbial biomass carbon
title: microbial biomass carbon method
todos:
- How should we separate values? | or ;? lets be consistent
comments:
- required if "microbial_biomass_c" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 1004
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
alias: micro_biomass_c_meth
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
micro_biomass_n_meth:
name: micro_biomass_n_meth
description: Reference or method used in determining microbial biomass nitrogen
title: microbial biomass nitrogen method
comments:
- required if "microbial_biomass_n" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 1004
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
alias: micro_biomass_n_meth
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
microbial_biomass_c:
name: microbial_biomass_c
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass carbon
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug C/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 1004
string_serialization: '{float} {unit}'
multivalued: false
alias: microbial_biomass_c
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
microbial_biomass_n:
name: microbial_biomass_n
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass nitrogen
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug N/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 1004
string_serialization: '{float} {unit}'
multivalued: false
alias: microbial_biomass_n
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
non_microb_biomass:
name: non_microb_biomass
description: Amount of biomass; should include the name for the part of biomass
measured, e.g.insect, plant, total. Can include multiple measurements separated
by ;
title: non-microbial biomass
examples:
- value: insect 0.23 ug; plant 1g
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000174
- MIXS:0000650
rank: 8
string_serialization: '{text};{float} {unit}'
multivalued: false
alias: non_microb_biomass
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
non_microb_biomass_method:
name: non_microb_biomass_method
description: Reference or method used in determining biomass
title: non-microbial biomass method
comments:
- required if "non-microbial biomass" is provided
examples:
- value: https://doi.org/10.1038/s41467-021-26181-3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 9
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
alias: non_microb_biomass_method
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
org_nitro_method:
name: org_nitro_method
description: Method used for obtaining organic nitrogen
title: organic nitrogen method
comments:
- required if "org_nitro" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(85)90144-0
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000338
- MIXS:0000205
rank: 14
string_serialization: '{PMID}|{DOI}|{URL}'
multivalued: false
alias: org_nitro_method
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SedimentInterface
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
other_treatment:
name: other_treatment
description: Other treatments applied to your samples that are not applicable
to the provided fields
title: other treatments
notes:
- Values entered here will be used to determine potential new slots.
comments:
- This is an open text field to provide any treatments that cannot be captured
in the provided slots.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000300
rank: 15
string_serialization: '{text}'
multivalued: false
alias: other_treatment
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
start_date_inc:
name: start_date_inc
description: Date the incubation was started. Only relevant for incubation samples.
title: incubation start date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 4
string_serialization: '{date, arbitrary precision}'
multivalued: false
alias: start_date_inc
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WaterInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
start_time_inc:
name: start_time_inc
description: Time the incubation was started. Only relevant for incubation samples.
title: incubation start time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 5
string_serialization: '{time, seconds optional}'
multivalued: false
alias: start_time_inc
owner: SoilMixsInspiredMixin
domain_of:
- Biosample
- SoilInterface
- SoilMixsInspiredMixin
slot_group: mixs_inspired_section
range: string
recommended: true
pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$