Class: Misc Envs (MiscEnvsInterface)
misc_envs dh_interface
URI: nmdc_sub_schema:MiscEnvsInterface
classDiagram
class MiscEnvsInterface
DhMultiviewCommonColumnsMixin <|-- MiscEnvsInterface
DhInterface <|-- MiscEnvsInterface
MiscEnvsInterface : alkalinity
MiscEnvsInterface : alt
MiscEnvsInterface : ammonium
MiscEnvsInterface : analysis_type
MiscEnvsInterface --|> AnalysisTypeEnum : analysis_type
MiscEnvsInterface : biomass
MiscEnvsInterface : bromide
MiscEnvsInterface : calcium
MiscEnvsInterface : chem_administration
MiscEnvsInterface : chloride
MiscEnvsInterface : chlorophyll
MiscEnvsInterface : collection_date
MiscEnvsInterface : density
MiscEnvsInterface : depth
MiscEnvsInterface : diether_lipids
MiscEnvsInterface : diss_carb_dioxide
MiscEnvsInterface : diss_hydrogen
MiscEnvsInterface : diss_inorg_carb
MiscEnvsInterface : diss_org_nitro
MiscEnvsInterface : diss_oxygen
MiscEnvsInterface : ecosystem
MiscEnvsInterface --|> EcosystemEnum : ecosystem
MiscEnvsInterface : ecosystem_category
MiscEnvsInterface --|> EcosystemCategoryEnum : ecosystem_category
MiscEnvsInterface : ecosystem_subtype
MiscEnvsInterface --|> EcosystemSubtypeEnum : ecosystem_subtype
MiscEnvsInterface : ecosystem_type
MiscEnvsInterface --|> EcosystemTypeEnum : ecosystem_type
MiscEnvsInterface : elev
MiscEnvsInterface : env_broad_scale
MiscEnvsInterface : env_local_scale
MiscEnvsInterface : env_medium
MiscEnvsInterface : experimental_factor
MiscEnvsInterface : geo_loc_name
MiscEnvsInterface : lat_lon
MiscEnvsInterface : misc_param
MiscEnvsInterface : nitrate
MiscEnvsInterface : nitrite
MiscEnvsInterface : nitro
MiscEnvsInterface : org_carb
MiscEnvsInterface : org_matter
MiscEnvsInterface : org_nitro
MiscEnvsInterface : organism_count
MiscEnvsInterface : oxy_stat_samp
MiscEnvsInterface --|> OxyStatSampEnum : oxy_stat_samp
MiscEnvsInterface : perturbation
MiscEnvsInterface : ph
MiscEnvsInterface : ph_meth
MiscEnvsInterface : phosphate
MiscEnvsInterface : phosplipid_fatt_acid
MiscEnvsInterface : potassium
MiscEnvsInterface : pressure
MiscEnvsInterface : salinity
MiscEnvsInterface : samp_collec_device
MiscEnvsInterface : samp_collec_method
MiscEnvsInterface : samp_mat_process
MiscEnvsInterface : samp_name
MiscEnvsInterface : samp_size
MiscEnvsInterface : samp_store_dur
MiscEnvsInterface : samp_store_loc
MiscEnvsInterface : samp_store_temp
MiscEnvsInterface : sample_link
MiscEnvsInterface : silicate
MiscEnvsInterface : size_frac
MiscEnvsInterface : sodium
MiscEnvsInterface : source_mat_id
MiscEnvsInterface : specific_ecosystem
MiscEnvsInterface --|> SpecificEcosystemEnum : specific_ecosystem
MiscEnvsInterface : sulfate
MiscEnvsInterface : sulfide
MiscEnvsInterface : temp
MiscEnvsInterface : water_current
Inheritance
- DhInterface
- MiscEnvsInterface [ DhMultiviewCommonColumnsMixin]
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
alkalinity | 0..1 String |
Alkalinity, the ability of a solution to neutralize acids to the equivalence ... | direct |
alt | 0..1 recommended String |
Altitude is a term used to identify heights of objects such as airplanes, spa... | direct |
ammonium | 0..1 String |
Concentration of ammonium in the sample | direct |
biomass | 0..1 String |
Amount of biomass; should include the name for the part of biomass measured, ... | direct |
bromide | 0..1 String |
Concentration of bromide | direct |
calcium | 0..1 String |
Concentration of calcium in the sample | direct |
chem_administration | 0..1 recommended String |
List of chemical compounds administered to the host or site where sampling oc... | direct |
chloride | 0..1 String |
Concentration of chloride in the sample | direct |
chlorophyll | 0..1 String |
Concentration of chlorophyll | direct |
collection_date | 1..1 String |
The date of sampling | direct |
density | 0..1 String |
Density of the sample, which is its mass per unit volume (aka volumetric mass... | direct |
depth | 0..1 recommended String |
The vertical distance below local surface, e | direct |
diether_lipids | 0..1 String |
Concentration of diether lipids; can include multiple types of diether lipids | direct |
diss_carb_dioxide | 0..1 String |
Concentration of dissolved carbon dioxide in the sample or liquid portion of ... | direct |
diss_hydrogen | 0..1 String |
Concentration of dissolved hydrogen | direct |
diss_inorg_carb | 0..1 String |
Dissolved inorganic carbon concentration in the sample, typically measured af... | direct |
diss_org_nitro | 0..1 String |
Dissolved organic nitrogen concentration measured as; total dissolved nitroge... | direct |
diss_oxygen | 0..1 String |
Concentration of dissolved oxygen | direct |
ecosystem | 0..1 recommended EcosystemEnum |
An ecosystem is a combination of a physical environment (abiotic factors) and... | direct |
ecosystem_category | 0..1 recommended EcosystemCategoryEnum |
Ecosystem categories represent divisions within the ecosystem based on specif... | direct |
ecosystem_subtype | 0..1 recommended EcosystemSubtypeEnum |
Ecosystem subtypes represent further subdivision of Ecosystem types into more... | direct |
ecosystem_type | 0..1 recommended EcosystemTypeEnum |
Ecosystem types represent things having common characteristics within the Eco... | direct |
elev | 1..1 Float |
Elevation of the sampling site is its height above a fixed reference point, m... | direct |
env_broad_scale | 1..1 String |
In this field, report which major environmental system your sample or specime... | direct |
env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen’s local vic... | direct |
env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | direct |
experimental_factor | 0..1 String |
Experimental factors are essentially the variable aspects of an experiment de... | direct |
geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | direct |
lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | direct |
misc_param | 0..1 String |
Any other measurement performed or parameter collected, that is not listed he... | direct |
nitrate | 0..1 String |
Concentration of nitrate in the sample | direct |
nitrite | 0..1 String |
Concentration of nitrite in the sample | direct |
nitro | 0..1 String |
Concentration of nitrogen (total) | direct |
org_carb | 0..1 String |
Concentration of organic carbon | direct |
org_matter | 0..1 String |
Concentration of organic matter | direct |
org_nitro | 0..1 String |
Concentration of organic nitrogen | direct |
organism_count | 0..1 String |
Total cell count of any organism (or group of organisms) per gram, volume or ... | direct |
oxy_stat_samp | 0..1 OxyStatSampEnum |
Oxygenation status of sample | direct |
perturbation | 0..1 String |
Type of perturbation, e | direct |
ph | 0..1 recommended Float |
pH measurement of the sample, or liquid portion of sample, or aqueous phase o... | direct |
ph_meth | 0..1 String |
Reference or method used in determining ph | direct |
phosphate | 0..1 String |
Concentration of phosphate | direct |
phosplipid_fatt_acid | 0..1 String |
Concentration of phospholipid fatty acids; can include multiple values | direct |
potassium | 0..1 String |
Concentration of potassium in the sample | direct |
pressure | 0..1 String |
Pressure to which the sample is subject to, in atmospheres | direct |
salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample | direct |
samp_collec_device | 0..1 recommended String |
The device used to collect an environmental sample | direct |
samp_collec_method | 0..1 String |
The method employed for collecting the sample | direct |
samp_mat_process | 0..1 String |
A brief description of any processing applied to the sample during or after r... | direct |
samp_size | 0..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | direct |
samp_store_dur | 0..1 String |
Duration for which the sample was stored | direct |
samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room | direct |
samp_store_temp | 1..1 String |
Temperature at which the sample was stored (degrees are assumed) | direct |
sample_link | 0..1 recommended String |
A unique identifier to assign parent-child, subsample, or sibling samples | direct |
silicate | 0..1 String |
Concentration of silicate | direct |
size_frac | 0..1 String |
Filtering pore size used in sample preparation | direct |
sodium | 0..1 String |
Sodium concentration in the sample | direct |
specific_ecosystem | 0..1 recommended SpecificEcosystemEnum |
Specific ecosystems represent specific features of the environment like aphot... | direct |
sulfate | 0..1 String |
Concentration of sulfate in the sample | direct |
sulfide | 0..1 String |
Concentration of sulfide in the sample | direct |
temp | 0..1 String |
Temperature of the sample at the time of sampling | direct |
water_current | 0..1 String |
Measurement of magnitude and direction of flow within a fluid | direct |
analysis_type | 1..* AnalysisTypeEnum |
Select all the data types associated or available for this biosample | DhMultiviewCommonColumnsMixin |
samp_name | 1..1 String |
A local identifier or name that for the material sample collected | DhMultiviewCommonColumnsMixin |
source_mat_id | 0..1 String |
A globally unique identifier assigned to the biological sample | DhMultiviewCommonColumnsMixin |
Identifier and Mapping Information
Annotations
property | value |
---|---|
excel_worksheet_name | misc natural or artificial |
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:MiscEnvsInterface |
native | nmdc_sub_schema:MiscEnvsInterface |
LinkML Source
Direct
name: MiscEnvsInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: misc natural or artificial
description: misc_envs dh_interface
title: Misc Envs
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slots:
- alkalinity
- alt
- ammonium
- biomass
- bromide
- calcium
- chem_administration
- chloride
- chlorophyll
- collection_date
- density
- depth
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_org_nitro
- diss_oxygen
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- elev
- env_broad_scale
- env_local_scale
- env_medium
- experimental_factor
- geo_loc_name
- lat_lon
- misc_param
- nitrate
- nitrite
- nitro
- org_carb
- org_matter
- org_nitro
- organism_count
- oxy_stat_samp
- perturbation
- ph
- ph_meth
- phosphate
- phosplipid_fatt_acid
- potassium
- pressure
- salinity
- samp_collec_device
- samp_collec_method
- samp_mat_process
- samp_size
- samp_store_dur
- samp_store_loc
- samp_store_temp
- sample_link
- silicate
- size_frac
- sodium
- specific_ecosystem
- sulfate
- sulfide
- temp
- water_current
slot_usage:
alkalinity:
name: alkalinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milliequivalent per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Alkalinity, the ability of a solution to neutralize acids to the
equivalence point of carbonate or bicarbonate
title: alkalinity
examples:
- value: 50 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkalinity
rank: 1
is_a: core field
slot_uri: MIXS:0000421
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
alt:
name: alt
annotations:
expected_value:
tag: expected_value
value: measurement value
description: Altitude is a term used to identify heights of objects such as airplanes,
space shuttles, rockets, atmospheric balloons and heights of places such as
atmospheric layers and clouds. It is used to measure the height of an object
which is above the earth's surface. In this context, the altitude measurement
is the vertical distance between the earth's surface above sea level and the
sampled position in the air
title: altitude
examples:
- value: 100 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- altitude
rank: 26
is_a: environment field
slot_uri: MIXS:0000094
multivalued: false
owner: Biosample
domain_of:
- agriculture
- air
- built environment
- core
- food-animal and animal feed
- food-farm environment
- food-food production facility
- food-human foods
- host-associated
- human-associated
- human-gut
- human-oral
- human-skin
- human-vaginal
- hydrocarbon resources-cores
- hydrocarbon resources-fluids_swabs
- microbial mat_biofilm
- miscellaneous natural or artificial environment
- plant-associated
- sediment
- soil
- symbiont-associated
- wastewater_sludge
- water
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HostAssociatedInterface
- MiscEnvsInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
ammonium:
name: ammonium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of ammonium in the sample
title: ammonium
examples:
- value: 1.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ammonium
rank: 4
is_a: core field
slot_uri: MIXS:0000427
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
biomass:
name: biomass
annotations:
expected_value:
tag: expected_value
value: biomass type;measurement value
preferred_unit:
tag: preferred_unit
value: ton, kilogram, gram
occurrence:
tag: occurrence
value: m
description: Amount of biomass; should include the name for the part of biomass
measured, e.g. Microbial, total. Can include multiple measurements
title: biomass
examples:
- value: total;20 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biomass
rank: 6
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000174
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
bromide:
name: bromide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of bromide
title: bromide
examples:
- value: 0.05 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bromide
rank: 8
is_a: core field
slot_uri: MIXS:0000176
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
calcium:
name: calcium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of calcium in the sample
title: calcium
examples:
- value: 0.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- calcium
rank: 9
is_a: core field
slot_uri: MIXS:0000432
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chem_administration:
name: chem_administration
annotations:
expected_value:
tag: expected_value
value: CHEBI;timestamp
occurrence:
tag: occurrence
value: m
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
- value: agar [CHEBI:2509];2018-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 17
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_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)?)?)?)?$
chloride:
name: chloride
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of chloride in the sample
title: chloride
examples:
- value: 5000 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chloride
rank: 10
is_a: core field
slot_uri: MIXS:0000429
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chlorophyll:
name: chlorophyll
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter, microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of chlorophyll
title: chlorophyll
examples:
- value: 5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chlorophyll
rank: 11
is_a: core field
slot_uri: MIXS:0000177
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
collection_date:
name: collection_date
annotations:
expected_value:
tag: expected_value
value: date and time
description: The date of sampling
title: collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
- Use modified term (amended definition)
examples:
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- collection date
rank: 3
is_a: environment field
string_serialization: '{date, arbitrary precision}'
slot_uri: MIXS:0000011
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
density:
name: density
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter, gram per cubic centimeter
occurrence:
tag: occurrence
value: '1'
description: Density of the sample, which is its mass per unit volume (aka volumetric
mass density)
title: density
examples:
- value: 1000 kilogram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- density
rank: 12
is_a: core field
slot_uri: MIXS:0000435
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
depth:
name: depth
annotations:
expected_value:
tag: expected_value
value: measurement value
description: The vertical distance below local surface, e.g. for sediment or soil
samples depth is measured from sediment or soil surface, respectively. Depth
can be reported as an interval for subsurface samples.
title: depth, meters
notes:
- Use modified term
comments:
- All depths must be reported in meters. Provide the numerical portion only.
examples:
- value: 0 - 0.1
- value: '1'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth
rank: 9
is_a: environment field
string_serialization: '{float}|{float}-{float}'
slot_uri: MIXS:0000018
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?(\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)?$
diether_lipids:
name: diether_lipids
annotations:
expected_value:
tag: expected_value
value: diether lipid name;measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of diether lipids; can include multiple types of diether
lipids
title: diether lipids
examples:
- value: 0.2 nanogram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- diether lipids
rank: 13
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000178
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
diss_carb_dioxide:
name: diss_carb_dioxide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved carbon dioxide in the sample or liquid
portion of the sample
title: dissolved carbon dioxide
examples:
- value: 5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved carbon dioxide
rank: 14
is_a: core field
slot_uri: MIXS:0000436
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_hydrogen:
name: diss_hydrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved hydrogen
title: dissolved hydrogen
examples:
- value: 0.3 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved hydrogen
rank: 15
is_a: core field
slot_uri: MIXS:0000179
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_inorg_carb:
name: diss_inorg_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Dissolved inorganic carbon concentration in the sample, typically
measured after filtering the sample using a 0.45 micrometer filter
title: dissolved inorganic carbon
examples:
- value: 2059 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic carbon
rank: 16
is_a: core field
slot_uri: MIXS:0000434
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_org_nitro:
name: diss_org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Dissolved organic nitrogen concentration measured as; total dissolved
nitrogen - NH4 - NO3 - NO2
title: dissolved organic nitrogen
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic nitrogen
rank: 18
is_a: core field
slot_uri: MIXS:0000162
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_oxygen:
name: diss_oxygen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per kilogram, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved oxygen
title: dissolved oxygen
examples:
- value: 175 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen
rank: 19
is_a: core field
slot_uri: MIXS:0000119
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
ecosystem:
name: ecosystem
description: An ecosystem is a combination of a physical environment (abiotic
factors) and all the organisms (biotic factors) that interact with this environment.
Ecosystem is in position 1/5 in a GOLD path.
comments:
- The abiotic factors play a profound role on the type and composition of organisms
in a given environment. The GOLD Ecosystem at the top of the five-level classification
system is aimed at capturing the broader environment from which an organism
or environmental sample is collected. The three broad groups under Ecosystem
are Environmental, Host-associated, and Engineered. They represent samples collected
from a natural environment or from another organism or from engineered environments
like bioreactors respectively.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 9
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemEnum
recommended: true
ecosystem_category:
name: ecosystem_category
description: Ecosystem categories represent divisions within the ecosystem based
on specific characteristics of the environment from where an organism or sample
is isolated. Ecosystem category is in position 2/5 in a GOLD path.
comments:
- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.
Ecosystem categories for Host-associated samples can be individual hosts or
phyla and for engineered samples it may be manipulated environments like bioreactors,
solid waste etc.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 10
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemCategoryEnum
recommended: true
ecosystem_subtype:
name: ecosystem_subtype
description: Ecosystem subtypes represent further subdivision of Ecosystem types
into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
path.
comments:
- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided
(for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in
the Ecosystem subtype category.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 12
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemSubtypeEnum
recommended: true
ecosystem_type:
name: ecosystem_type
description: Ecosystem types represent things having common characteristics within
the Ecosystem Category. These common characteristics based grouping is still
broad but specific to the characteristics of a given environment. Ecosystem
type is in position 3/5 in a GOLD path.
comments:
- The Aquatic ecosystem category (for example) may have ecosystem types like Marine
or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor
air as different Ecosystem Types. In the case of Host-associated samples, ecosystem
type can represent Respiratory system, Digestive system, Roots etc.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 11
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemTypeEnum
recommended: true
elev:
name: elev
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit.
title: elevation, meters
comments:
- All elevations must be reported in meters. Provide the numerical portion only.
- Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
if needed, to help estimate the elevation based on latitude and longitude coordinates.
examples:
- value: '225'
- value: '0'
- value: '1250'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
is_a: environment field
slot_uri: MIXS:0000093
multivalued: false
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: float
required: true
env_broad_scale:
name: env_broad_scale
description: 'In this field, report which major environmental system your sample
or specimen came from. The systems identified should have a coarse spatial grain,
to provide the general environmental context of where the sampling was done
(e.g. were you in the desert or a rainforest?). We recommend using subclasses
of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
(one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
[termID]|termLabel [termID]. Example: Annotating a water sample from the photic
zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
[ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
title: broad-scale environmental context
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
env_local_scale:
name: env_local_scale
description: 'Report the entity or entities which are in the sample or specimen’s
local vicinity and which you believe have significant causal influences on your
sample or specimen. We recommend using EnvO terms which are of smaller spatial
grain than your entry for env_broad_scale. Terms, such as anatomical sites,
from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
title: local environmental context
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
examples:
- value: canopy [ENVO:00000047]
- value: herb and fern layer [ENVO:01000337]
- value: litter layer [ENVO:01000338]
- value: understory [01000335]
- value: shrub layer [ENVO:01000336]
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top).'
title: environmental medium
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
examples:
- value: soil [ENVO:00001998]
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000014
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
experimental_factor:
name: experimental_factor
annotations:
expected_value:
tag: expected_value
value: text or EFO and/or OBI
description: Experimental factors are essentially the variable aspects of an experiment
design which can be used to describe an experiment, or set of experiments, in
an increasingly detailed manner. This field accepts ontology terms from Experimental
Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
title: experimental factor
examples:
- value: time series design [EFO:EFO_0001779]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- experimental factor
rank: 12
is_a: investigation field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000008
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
geo_loc_name:
name: geo_loc_name
annotations:
expected_value:
tag: expected_value
value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
name'
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name.
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- geographic location (country and/or sea,region)
rank: 4
is_a: environment field
string_serialization: '{text}: {text}, {text}'
slot_uri: MIXS:0000010
multivalued: false
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
notes:
- This is currently a required field but it's not clear if this should be required
for human hosts
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
is_a: environment field
string_serialization: '{lat lon}'
slot_uri: MIXS:0000009
multivalued: false
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$
misc_param:
name: misc_param
annotations:
expected_value:
tag: expected_value
value: parameter name;measurement value
occurrence:
tag: occurrence
value: m
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- miscellaneous parameter
rank: 23
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
nitrate:
name: nitrate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrate
rank: 26
is_a: core field
slot_uri: MIXS:0000425
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitrite:
name: nitrite
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrite in the sample
title: nitrite
examples:
- value: 0.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrite
rank: 27
is_a: core field
slot_uri: MIXS:0000426
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitro:
name: nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrogen (total)
title: nitrogen
examples:
- value: 4.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrogen
rank: 28
is_a: core field
slot_uri: MIXS:0000504
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_carb:
name: org_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic carbon
title: organic carbon
examples:
- value: 1.5 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic carbon
rank: 29
is_a: core field
slot_uri: MIXS:0000508
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_matter:
name: org_matter
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic matter
title: organic matter
examples:
- value: 1.75 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic matter
rank: 45
is_a: core field
slot_uri: MIXS:0000204
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_nitro:
name: org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic nitrogen
title: organic nitrogen
examples:
- value: 4 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic nitrogen
rank: 46
is_a: core field
slot_uri: MIXS:0000205
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
organism_count:
name: organism_count
annotations:
expected_value:
tag: expected_value
value: organism name;measurement value;enumeration
preferred_unit:
tag: preferred_unit
value: number of cells per cubic meter, number of cells per milliliter, number
of cells per cubic centimeter
occurrence:
tag: occurrence
value: m
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organism count
rank: 30
is_a: core field
slot_uri: MIXS:0000103
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
oxy_stat_samp:
name: oxy_stat_samp
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- oxygenation status of sample
rank: 25
is_a: core field
slot_uri: MIXS:0000753
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: OxyStatSampEnum
perturbation:
name: perturbation
annotations:
expected_value:
tag: expected_value
value: perturbation type name;perturbation interval and duration
occurrence:
tag: occurrence
value: m
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- perturbation
rank: 33
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
ph:
name: ph
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: pH measurement of the sample, or liquid portion of sample, or aqueous
phase of the fluid
title: pH
notes:
- Use modified term
examples:
- value: '7.2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pH
rank: 27
is_a: core field
string_serialization: '{float}'
slot_uri: MIXS:0001001
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: float
recommended: true
minimum_value: 0
maximum_value: 14
ph_meth:
name: ph_meth
description: Reference or method used in determining ph
title: pH method
comments:
- This can include a link to the instrument used or a citation for the method.
examples:
- value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
- value: https://doi.org/10.2136/sssabookser5.3.c16
from_schema: https://w3id.org/nmdc/nmdc
rank: 41
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0001106
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
phosphate:
name: phosphate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of phosphate
title: phosphate
examples:
- value: 0.7 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phosphate
rank: 53
is_a: core field
slot_uri: MIXS:0000505
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
phosplipid_fatt_acid:
name: phosplipid_fatt_acid
annotations:
expected_value:
tag: expected_value
value: phospholipid fatty acid name;measurement value
preferred_unit:
tag: preferred_unit
value: mole per gram, mole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of phospholipid fatty acids; can include multiple values
title: phospholipid fatty acid
examples:
- value: 2.98 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phospholipid fatty acid
rank: 36
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000181
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
potassium:
name: potassium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of potassium in the sample
title: potassium
examples:
- value: 463 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- potassium
rank: 38
is_a: core field
slot_uri: MIXS:0000430
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
pressure:
name: pressure
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: atmosphere
occurrence:
tag: occurrence
value: '1'
description: Pressure to which the sample is subject to, in atmospheres
title: pressure
examples:
- value: 50 atmosphere
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pressure
rank: 39
is_a: core field
slot_uri: MIXS:0000412
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
salinity:
name: salinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: practical salinity unit, percentage
occurrence:
tag: occurrence
value: '1'
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater.
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- salinity
rank: 54
is_a: core field
slot_uri: MIXS:0000183
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
samp_collec_device:
name: samp_collec_device
annotations:
expected_value:
tag: expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
title: sample collection device
comments:
- Report dimensions and details when applicable
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection device
rank: 14
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000002
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
samp_collec_method:
name: samp_collec_method
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url , or text
description: The method employed for collecting the sample.
title: sample collection method
comments:
- This can be a citation or description
examples:
- value: swabbing
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection method
rank: 15
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001225
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_mat_process:
name: samp_mat_process
annotations:
expected_value:
tag: expected_value
value: text
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed.
title: sample material processing
examples:
- value: filtering of seawater
- value: storing samples in ethanol
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample material processing
rank: 12
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000016
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_size:
name: samp_size
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millliter, gram, milligram, liter
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected.
title: amount or size of sample collected
comments:
- This refers to the TOTAL amount of sample collected from the experiment. NOT
the amount sent to each institution or collected for a specific analysis.
examples:
- value: 5 grams
- value: 10 mL
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- amount or size of sample collected
rank: 18
is_a: nucleic acid sequence source field
string_serialization: '{float} {unit}'
slot_uri: MIXS:0000001
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
samp_store_dur:
name: samp_store_dur
annotations:
expected_value:
tag: expected_value
value: duration
occurrence:
tag: occurrence
value: '1'
description: Duration for which the sample was stored
title: sample storage duration
examples:
- value: P1Y6M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage duration
rank: 353
is_a: core field
string_serialization: '{duration}'
slot_uri: MIXS:0000116
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
samp_store_loc:
name: samp_store_loc
annotations:
expected_value:
tag: expected_value
value: location name
occurrence:
tag: occurrence
value: '1'
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage location
rank: 41
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
samp_store_temp:
name: samp_store_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Temperature at which the sample was stored (degrees are assumed)
title: sample storage temperature
examples:
- value: -80 Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage temperature
rank: 7
is_a: core field
slot_uri: MIXS:0000110
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sample_link:
name: sample_link
description: A unique identifier to assign parent-child, subsample, or sibling
samples. This is relevant when a sample or other material was used to generate
the new sample.
title: sample linkage
notes:
- 'also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) >
1 and "placeholder" in slot_usage.keys():AttributeError: ''list'' object has
no attribute ''keys'''
comments:
- 'This field allows multiple entries separated by ; (Examples: Soil collected
from the field will link with the soil used in an incubation. The soil a plant
was grown in links to the plant sample. An original culture sample was transferred
to a new vial and generated a new sample)'
examples:
- value: IGSN:DSJ0284
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{text}:{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
- SampIdNewTermsMixin
slot_group: sample_id_section
range: string
recommended: true
pattern: '[^\:\n\r]+\:[^\:\n\r]+'
silicate:
name: silicate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of silicate
title: silicate
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- silicate
rank: 43
is_a: core field
slot_uri: MIXS:0000184
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
size_frac:
name: size_frac
annotations:
expected_value:
tag: expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- size fraction selected
rank: 285
is_a: nucleic acid sequence source field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
sodium:
name: sodium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Sodium concentration in the sample
title: sodium
examples:
- value: 10.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sodium
rank: 363
is_a: core field
slot_uri: MIXS:0000428
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
specific_ecosystem:
name: specific_ecosystem
description: Specific ecosystems represent specific features of the environment
like aphotic zone in an ocean or gastric mucosa within a host digestive system.
Specific ecosystem is in position 5/5 in a GOLD path.
comments:
- Specific ecosystems help to define samples based on very specific characteristics
of an environment under the five-level classification system.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 13
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: SpecificEcosystemEnum
recommended: true
sulfate:
name: sulfate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of sulfate in the sample
title: sulfate
examples:
- value: 5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfate
rank: 44
is_a: core field
slot_uri: MIXS:0000423
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sulfide:
name: sulfide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of sulfide in the sample
title: sulfide
examples:
- value: 2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfide
rank: 371
is_a: core field
slot_uri: MIXS:0000424
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
temp:
name: temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling.
title: temperature
examples:
- value: 25 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- temperature
rank: 37
is_a: environment field
slot_uri: MIXS:0000113
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_current:
name: water_current
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per second, knots
occurrence:
tag: occurrence
value: '1'
description: Measurement of magnitude and direction of flow within a fluid
title: water current
examples:
- value: 10 cubic meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water current
rank: 236
is_a: core field
slot_uri: MIXS:0000203
multivalued: false
owner: Biosample
domain_of:
- Biosample
- MiscEnvsInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
horizon_meth:
name: horizon_meth
title: horizon method
Induced
name: MiscEnvsInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: misc natural or artificial
description: misc_envs dh_interface
title: Misc Envs
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slot_usage:
alkalinity:
name: alkalinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milliequivalent per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Alkalinity, the ability of a solution to neutralize acids to the
equivalence point of carbonate or bicarbonate
title: alkalinity
examples:
- value: 50 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkalinity
rank: 1
is_a: core field
slot_uri: MIXS:0000421
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
alt:
name: alt
annotations:
expected_value:
tag: expected_value
value: measurement value
description: Altitude is a term used to identify heights of objects such as airplanes,
space shuttles, rockets, atmospheric balloons and heights of places such as
atmospheric layers and clouds. It is used to measure the height of an object
which is above the earth's surface. In this context, the altitude measurement
is the vertical distance between the earth's surface above sea level and the
sampled position in the air
title: altitude
examples:
- value: 100 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- altitude
rank: 26
is_a: environment field
slot_uri: MIXS:0000094
multivalued: false
owner: Biosample
domain_of:
- agriculture
- air
- built environment
- core
- food-animal and animal feed
- food-farm environment
- food-food production facility
- food-human foods
- host-associated
- human-associated
- human-gut
- human-oral
- human-skin
- human-vaginal
- hydrocarbon resources-cores
- hydrocarbon resources-fluids_swabs
- microbial mat_biofilm
- miscellaneous natural or artificial environment
- plant-associated
- sediment
- soil
- symbiont-associated
- wastewater_sludge
- water
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HostAssociatedInterface
- MiscEnvsInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
ammonium:
name: ammonium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of ammonium in the sample
title: ammonium
examples:
- value: 1.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ammonium
rank: 4
is_a: core field
slot_uri: MIXS:0000427
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
biomass:
name: biomass
annotations:
expected_value:
tag: expected_value
value: biomass type;measurement value
preferred_unit:
tag: preferred_unit
value: ton, kilogram, gram
occurrence:
tag: occurrence
value: m
description: Amount of biomass; should include the name for the part of biomass
measured, e.g. Microbial, total. Can include multiple measurements
title: biomass
examples:
- value: total;20 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biomass
rank: 6
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000174
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
bromide:
name: bromide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of bromide
title: bromide
examples:
- value: 0.05 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bromide
rank: 8
is_a: core field
slot_uri: MIXS:0000176
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
calcium:
name: calcium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of calcium in the sample
title: calcium
examples:
- value: 0.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- calcium
rank: 9
is_a: core field
slot_uri: MIXS:0000432
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chem_administration:
name: chem_administration
annotations:
expected_value:
tag: expected_value
value: CHEBI;timestamp
occurrence:
tag: occurrence
value: m
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
- value: agar [CHEBI:2509];2018-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 17
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_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)?)?)?)?$
chloride:
name: chloride
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of chloride in the sample
title: chloride
examples:
- value: 5000 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chloride
rank: 10
is_a: core field
slot_uri: MIXS:0000429
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chlorophyll:
name: chlorophyll
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter, microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of chlorophyll
title: chlorophyll
examples:
- value: 5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chlorophyll
rank: 11
is_a: core field
slot_uri: MIXS:0000177
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
collection_date:
name: collection_date
annotations:
expected_value:
tag: expected_value
value: date and time
description: The date of sampling
title: collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
- Use modified term (amended definition)
examples:
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- collection date
rank: 3
is_a: environment field
string_serialization: '{date, arbitrary precision}'
slot_uri: MIXS:0000011
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
density:
name: density
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter, gram per cubic centimeter
occurrence:
tag: occurrence
value: '1'
description: Density of the sample, which is its mass per unit volume (aka volumetric
mass density)
title: density
examples:
- value: 1000 kilogram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- density
rank: 12
is_a: core field
slot_uri: MIXS:0000435
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
depth:
name: depth
annotations:
expected_value:
tag: expected_value
value: measurement value
description: The vertical distance below local surface, e.g. for sediment or soil
samples depth is measured from sediment or soil surface, respectively. Depth
can be reported as an interval for subsurface samples.
title: depth, meters
notes:
- Use modified term
comments:
- All depths must be reported in meters. Provide the numerical portion only.
examples:
- value: 0 - 0.1
- value: '1'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth
rank: 9
is_a: environment field
string_serialization: '{float}|{float}-{float}'
slot_uri: MIXS:0000018
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?(\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)?$
diether_lipids:
name: diether_lipids
annotations:
expected_value:
tag: expected_value
value: diether lipid name;measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of diether lipids; can include multiple types of diether
lipids
title: diether lipids
examples:
- value: 0.2 nanogram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- diether lipids
rank: 13
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000178
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
diss_carb_dioxide:
name: diss_carb_dioxide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved carbon dioxide in the sample or liquid
portion of the sample
title: dissolved carbon dioxide
examples:
- value: 5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved carbon dioxide
rank: 14
is_a: core field
slot_uri: MIXS:0000436
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_hydrogen:
name: diss_hydrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved hydrogen
title: dissolved hydrogen
examples:
- value: 0.3 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved hydrogen
rank: 15
is_a: core field
slot_uri: MIXS:0000179
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_inorg_carb:
name: diss_inorg_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Dissolved inorganic carbon concentration in the sample, typically
measured after filtering the sample using a 0.45 micrometer filter
title: dissolved inorganic carbon
examples:
- value: 2059 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic carbon
rank: 16
is_a: core field
slot_uri: MIXS:0000434
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_org_nitro:
name: diss_org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Dissolved organic nitrogen concentration measured as; total dissolved
nitrogen - NH4 - NO3 - NO2
title: dissolved organic nitrogen
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic nitrogen
rank: 18
is_a: core field
slot_uri: MIXS:0000162
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_oxygen:
name: diss_oxygen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per kilogram, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved oxygen
title: dissolved oxygen
examples:
- value: 175 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen
rank: 19
is_a: core field
slot_uri: MIXS:0000119
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
ecosystem:
name: ecosystem
description: An ecosystem is a combination of a physical environment (abiotic
factors) and all the organisms (biotic factors) that interact with this environment.
Ecosystem is in position 1/5 in a GOLD path.
comments:
- The abiotic factors play a profound role on the type and composition of organisms
in a given environment. The GOLD Ecosystem at the top of the five-level classification
system is aimed at capturing the broader environment from which an organism
or environmental sample is collected. The three broad groups under Ecosystem
are Environmental, Host-associated, and Engineered. They represent samples collected
from a natural environment or from another organism or from engineered environments
like bioreactors respectively.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 9
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemEnum
recommended: true
ecosystem_category:
name: ecosystem_category
description: Ecosystem categories represent divisions within the ecosystem based
on specific characteristics of the environment from where an organism or sample
is isolated. Ecosystem category is in position 2/5 in a GOLD path.
comments:
- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.
Ecosystem categories for Host-associated samples can be individual hosts or
phyla and for engineered samples it may be manipulated environments like bioreactors,
solid waste etc.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 10
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemCategoryEnum
recommended: true
ecosystem_subtype:
name: ecosystem_subtype
description: Ecosystem subtypes represent further subdivision of Ecosystem types
into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
path.
comments:
- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided
(for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in
the Ecosystem subtype category.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 12
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemSubtypeEnum
recommended: true
ecosystem_type:
name: ecosystem_type
description: Ecosystem types represent things having common characteristics within
the Ecosystem Category. These common characteristics based grouping is still
broad but specific to the characteristics of a given environment. Ecosystem
type is in position 3/5 in a GOLD path.
comments:
- The Aquatic ecosystem category (for example) may have ecosystem types like Marine
or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor
air as different Ecosystem Types. In the case of Host-associated samples, ecosystem
type can represent Respiratory system, Digestive system, Roots etc.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 11
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemTypeEnum
recommended: true
elev:
name: elev
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit.
title: elevation, meters
comments:
- All elevations must be reported in meters. Provide the numerical portion only.
- Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
if needed, to help estimate the elevation based on latitude and longitude coordinates.
examples:
- value: '225'
- value: '0'
- value: '1250'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
is_a: environment field
slot_uri: MIXS:0000093
multivalued: false
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: float
required: true
env_broad_scale:
name: env_broad_scale
description: 'In this field, report which major environmental system your sample
or specimen came from. The systems identified should have a coarse spatial grain,
to provide the general environmental context of where the sampling was done
(e.g. were you in the desert or a rainforest?). We recommend using subclasses
of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
(one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
[termID]|termLabel [termID]. Example: Annotating a water sample from the photic
zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
[ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
title: broad-scale environmental context
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
env_local_scale:
name: env_local_scale
description: 'Report the entity or entities which are in the sample or specimen’s
local vicinity and which you believe have significant causal influences on your
sample or specimen. We recommend using EnvO terms which are of smaller spatial
grain than your entry for env_broad_scale. Terms, such as anatomical sites,
from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
title: local environmental context
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
examples:
- value: canopy [ENVO:00000047]
- value: herb and fern layer [ENVO:01000337]
- value: litter layer [ENVO:01000338]
- value: understory [01000335]
- value: shrub layer [ENVO:01000336]
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top).'
title: environmental medium
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
examples:
- value: soil [ENVO:00001998]
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000014
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
experimental_factor:
name: experimental_factor
annotations:
expected_value:
tag: expected_value
value: text or EFO and/or OBI
description: Experimental factors are essentially the variable aspects of an experiment
design which can be used to describe an experiment, or set of experiments, in
an increasingly detailed manner. This field accepts ontology terms from Experimental
Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
title: experimental factor
examples:
- value: time series design [EFO:EFO_0001779]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- experimental factor
rank: 12
is_a: investigation field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000008
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
geo_loc_name:
name: geo_loc_name
annotations:
expected_value:
tag: expected_value
value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
name'
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name.
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- geographic location (country and/or sea,region)
rank: 4
is_a: environment field
string_serialization: '{text}: {text}, {text}'
slot_uri: MIXS:0000010
multivalued: false
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
notes:
- This is currently a required field but it's not clear if this should be required
for human hosts
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
is_a: environment field
string_serialization: '{lat lon}'
slot_uri: MIXS:0000009
multivalued: false
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$
misc_param:
name: misc_param
annotations:
expected_value:
tag: expected_value
value: parameter name;measurement value
occurrence:
tag: occurrence
value: m
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- miscellaneous parameter
rank: 23
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
nitrate:
name: nitrate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrate
rank: 26
is_a: core field
slot_uri: MIXS:0000425
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitrite:
name: nitrite
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrite in the sample
title: nitrite
examples:
- value: 0.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrite
rank: 27
is_a: core field
slot_uri: MIXS:0000426
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitro:
name: nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrogen (total)
title: nitrogen
examples:
- value: 4.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrogen
rank: 28
is_a: core field
slot_uri: MIXS:0000504
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_carb:
name: org_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic carbon
title: organic carbon
examples:
- value: 1.5 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic carbon
rank: 29
is_a: core field
slot_uri: MIXS:0000508
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_matter:
name: org_matter
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic matter
title: organic matter
examples:
- value: 1.75 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic matter
rank: 45
is_a: core field
slot_uri: MIXS:0000204
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_nitro:
name: org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic nitrogen
title: organic nitrogen
examples:
- value: 4 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic nitrogen
rank: 46
is_a: core field
slot_uri: MIXS:0000205
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
organism_count:
name: organism_count
annotations:
expected_value:
tag: expected_value
value: organism name;measurement value;enumeration
preferred_unit:
tag: preferred_unit
value: number of cells per cubic meter, number of cells per milliliter, number
of cells per cubic centimeter
occurrence:
tag: occurrence
value: m
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organism count
rank: 30
is_a: core field
slot_uri: MIXS:0000103
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
oxy_stat_samp:
name: oxy_stat_samp
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- oxygenation status of sample
rank: 25
is_a: core field
slot_uri: MIXS:0000753
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: OxyStatSampEnum
perturbation:
name: perturbation
annotations:
expected_value:
tag: expected_value
value: perturbation type name;perturbation interval and duration
occurrence:
tag: occurrence
value: m
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- perturbation
rank: 33
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
ph:
name: ph
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: pH measurement of the sample, or liquid portion of sample, or aqueous
phase of the fluid
title: pH
notes:
- Use modified term
examples:
- value: '7.2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pH
rank: 27
is_a: core field
string_serialization: '{float}'
slot_uri: MIXS:0001001
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: float
recommended: true
minimum_value: 0
maximum_value: 14
ph_meth:
name: ph_meth
description: Reference or method used in determining ph
title: pH method
comments:
- This can include a link to the instrument used or a citation for the method.
examples:
- value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
- value: https://doi.org/10.2136/sssabookser5.3.c16
from_schema: https://w3id.org/nmdc/nmdc
rank: 41
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0001106
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
phosphate:
name: phosphate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of phosphate
title: phosphate
examples:
- value: 0.7 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phosphate
rank: 53
is_a: core field
slot_uri: MIXS:0000505
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
phosplipid_fatt_acid:
name: phosplipid_fatt_acid
annotations:
expected_value:
tag: expected_value
value: phospholipid fatty acid name;measurement value
preferred_unit:
tag: preferred_unit
value: mole per gram, mole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of phospholipid fatty acids; can include multiple values
title: phospholipid fatty acid
examples:
- value: 2.98 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phospholipid fatty acid
rank: 36
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000181
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
potassium:
name: potassium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of potassium in the sample
title: potassium
examples:
- value: 463 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- potassium
rank: 38
is_a: core field
slot_uri: MIXS:0000430
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
pressure:
name: pressure
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: atmosphere
occurrence:
tag: occurrence
value: '1'
description: Pressure to which the sample is subject to, in atmospheres
title: pressure
examples:
- value: 50 atmosphere
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pressure
rank: 39
is_a: core field
slot_uri: MIXS:0000412
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
salinity:
name: salinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: practical salinity unit, percentage
occurrence:
tag: occurrence
value: '1'
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater.
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- salinity
rank: 54
is_a: core field
slot_uri: MIXS:0000183
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
samp_collec_device:
name: samp_collec_device
annotations:
expected_value:
tag: expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
title: sample collection device
comments:
- Report dimensions and details when applicable
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection device
rank: 14
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000002
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
samp_collec_method:
name: samp_collec_method
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url , or text
description: The method employed for collecting the sample.
title: sample collection method
comments:
- This can be a citation or description
examples:
- value: swabbing
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection method
rank: 15
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001225
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_mat_process:
name: samp_mat_process
annotations:
expected_value:
tag: expected_value
value: text
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed.
title: sample material processing
examples:
- value: filtering of seawater
- value: storing samples in ethanol
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample material processing
rank: 12
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000016
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_size:
name: samp_size
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millliter, gram, milligram, liter
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected.
title: amount or size of sample collected
comments:
- This refers to the TOTAL amount of sample collected from the experiment. NOT
the amount sent to each institution or collected for a specific analysis.
examples:
- value: 5 grams
- value: 10 mL
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- amount or size of sample collected
rank: 18
is_a: nucleic acid sequence source field
string_serialization: '{float} {unit}'
slot_uri: MIXS:0000001
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
samp_store_dur:
name: samp_store_dur
annotations:
expected_value:
tag: expected_value
value: duration
occurrence:
tag: occurrence
value: '1'
description: Duration for which the sample was stored
title: sample storage duration
examples:
- value: P1Y6M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage duration
rank: 353
is_a: core field
string_serialization: '{duration}'
slot_uri: MIXS:0000116
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
samp_store_loc:
name: samp_store_loc
annotations:
expected_value:
tag: expected_value
value: location name
occurrence:
tag: occurrence
value: '1'
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage location
rank: 41
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
samp_store_temp:
name: samp_store_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Temperature at which the sample was stored (degrees are assumed)
title: sample storage temperature
examples:
- value: -80 Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage temperature
rank: 7
is_a: core field
slot_uri: MIXS:0000110
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sample_link:
name: sample_link
description: A unique identifier to assign parent-child, subsample, or sibling
samples. This is relevant when a sample or other material was used to generate
the new sample.
title: sample linkage
notes:
- 'also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) >
1 and "placeholder" in slot_usage.keys():AttributeError: ''list'' object has
no attribute ''keys'''
comments:
- 'This field allows multiple entries separated by ; (Examples: Soil collected
from the field will link with the soil used in an incubation. The soil a plant
was grown in links to the plant sample. An original culture sample was transferred
to a new vial and generated a new sample)'
examples:
- value: IGSN:DSJ0284
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{text}:{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
- SampIdNewTermsMixin
slot_group: sample_id_section
range: string
recommended: true
pattern: '[^\:\n\r]+\:[^\:\n\r]+'
silicate:
name: silicate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of silicate
title: silicate
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- silicate
rank: 43
is_a: core field
slot_uri: MIXS:0000184
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
size_frac:
name: size_frac
annotations:
expected_value:
tag: expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- size fraction selected
rank: 285
is_a: nucleic acid sequence source field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
sodium:
name: sodium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Sodium concentration in the sample
title: sodium
examples:
- value: 10.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sodium
rank: 363
is_a: core field
slot_uri: MIXS:0000428
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
specific_ecosystem:
name: specific_ecosystem
description: Specific ecosystems represent specific features of the environment
like aphotic zone in an ocean or gastric mucosa within a host digestive system.
Specific ecosystem is in position 5/5 in a GOLD path.
comments:
- Specific ecosystems help to define samples based on very specific characteristics
of an environment under the five-level classification system.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 13
is_a: gold_path_field
owner: Biosample
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: SpecificEcosystemEnum
recommended: true
sulfate:
name: sulfate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of sulfate in the sample
title: sulfate
examples:
- value: 5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfate
rank: 44
is_a: core field
slot_uri: MIXS:0000423
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sulfide:
name: sulfide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of sulfide in the sample
title: sulfide
examples:
- value: 2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfide
rank: 371
is_a: core field
slot_uri: MIXS:0000424
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
temp:
name: temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling.
title: temperature
examples:
- value: 25 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- temperature
rank: 37
is_a: environment field
slot_uri: MIXS:0000113
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_current:
name: water_current
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per second, knots
occurrence:
tag: occurrence
value: '1'
description: Measurement of magnitude and direction of flow within a fluid
title: water current
examples:
- value: 10 cubic meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water current
rank: 236
is_a: core field
slot_uri: MIXS:0000203
multivalued: false
owner: Biosample
domain_of:
- Biosample
- MiscEnvsInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
horizon_meth:
name: horizon_meth
title: horizon method
attributes:
alkalinity:
name: alkalinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milliequivalent per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Alkalinity, the ability of a solution to neutralize acids to the
equivalence point of carbonate or bicarbonate
title: alkalinity
examples:
- value: 50 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkalinity
rank: 1
is_a: core field
slot_uri: MIXS:0000421
multivalued: false
alias: alkalinity
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
alt:
name: alt
annotations:
expected_value:
tag: expected_value
value: measurement value
description: Altitude is a term used to identify heights of objects such as airplanes,
space shuttles, rockets, atmospheric balloons and heights of places such as
atmospheric layers and clouds. It is used to measure the height of an object
which is above the earth's surface. In this context, the altitude measurement
is the vertical distance between the earth's surface above sea level and the
sampled position in the air
title: altitude
examples:
- value: 100 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- altitude
rank: 26
is_a: environment field
slot_uri: MIXS:0000094
multivalued: false
alias: alt
owner: MiscEnvsInterface
domain_of:
- agriculture
- air
- built environment
- core
- food-animal and animal feed
- food-farm environment
- food-food production facility
- food-human foods
- host-associated
- human-associated
- human-gut
- human-oral
- human-skin
- human-vaginal
- hydrocarbon resources-cores
- hydrocarbon resources-fluids_swabs
- microbial mat_biofilm
- miscellaneous natural or artificial environment
- plant-associated
- sediment
- soil
- symbiont-associated
- wastewater_sludge
- water
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HostAssociatedInterface
- MiscEnvsInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
ammonium:
name: ammonium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of ammonium in the sample
title: ammonium
examples:
- value: 1.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ammonium
rank: 4
is_a: core field
slot_uri: MIXS:0000427
multivalued: false
alias: ammonium
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
biomass:
name: biomass
annotations:
expected_value:
tag: expected_value
value: biomass type;measurement value
preferred_unit:
tag: preferred_unit
value: ton, kilogram, gram
occurrence:
tag: occurrence
value: m
description: Amount of biomass; should include the name for the part of biomass
measured, e.g. Microbial, total. Can include multiple measurements
title: biomass
examples:
- value: total;20 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biomass
rank: 6
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000174
multivalued: false
alias: biomass
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
bromide:
name: bromide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of bromide
title: bromide
examples:
- value: 0.05 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bromide
rank: 8
is_a: core field
slot_uri: MIXS:0000176
multivalued: false
alias: bromide
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
calcium:
name: calcium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of calcium in the sample
title: calcium
examples:
- value: 0.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- calcium
rank: 9
is_a: core field
slot_uri: MIXS:0000432
multivalued: false
alias: calcium
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chem_administration:
name: chem_administration
annotations:
expected_value:
tag: expected_value
value: CHEBI;timestamp
occurrence:
tag: occurrence
value: m
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
- value: agar [CHEBI:2509];2018-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 17
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: false
alias: chem_administration
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_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)?)?)?)?$
chloride:
name: chloride
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of chloride in the sample
title: chloride
examples:
- value: 5000 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chloride
rank: 10
is_a: core field
slot_uri: MIXS:0000429
multivalued: false
alias: chloride
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chlorophyll:
name: chlorophyll
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter, microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of chlorophyll
title: chlorophyll
examples:
- value: 5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chlorophyll
rank: 11
is_a: core field
slot_uri: MIXS:0000177
multivalued: false
alias: chlorophyll
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
collection_date:
name: collection_date
annotations:
expected_value:
tag: expected_value
value: date and time
description: The date of sampling
title: collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
- Use modified term (amended definition)
examples:
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- collection date
rank: 3
is_a: environment field
string_serialization: '{date, arbitrary precision}'
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
density:
name: density
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter, gram per cubic centimeter
occurrence:
tag: occurrence
value: '1'
description: Density of the sample, which is its mass per unit volume (aka volumetric
mass density)
title: density
examples:
- value: 1000 kilogram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- density
rank: 12
is_a: core field
slot_uri: MIXS:0000435
multivalued: false
alias: density
owner: MiscEnvsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
depth:
name: depth
annotations:
expected_value:
tag: expected_value
value: measurement value
description: The vertical distance below local surface, e.g. for sediment or soil
samples depth is measured from sediment or soil surface, respectively. Depth
can be reported as an interval for subsurface samples.
title: depth, meters
notes:
- Use modified term
comments:
- All depths must be reported in meters. Provide the numerical portion only.
examples:
- value: 0 - 0.1
- value: '1'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth
rank: 9
is_a: environment field
string_serialization: '{float}|{float}-{float}'
slot_uri: MIXS:0000018
multivalued: false
alias: depth
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?(\s*-\s*[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)?$
diether_lipids:
name: diether_lipids
annotations:
expected_value:
tag: expected_value
value: diether lipid name;measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of diether lipids; can include multiple types of diether
lipids
title: diether lipids
examples:
- value: 0.2 nanogram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- diether lipids
rank: 13
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000178
multivalued: false
alias: diether_lipids
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
diss_carb_dioxide:
name: diss_carb_dioxide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved carbon dioxide in the sample or liquid
portion of the sample
title: dissolved carbon dioxide
examples:
- value: 5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved carbon dioxide
rank: 14
is_a: core field
slot_uri: MIXS:0000436
multivalued: false
alias: diss_carb_dioxide
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_hydrogen:
name: diss_hydrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved hydrogen
title: dissolved hydrogen
examples:
- value: 0.3 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved hydrogen
rank: 15
is_a: core field
slot_uri: MIXS:0000179
multivalued: false
alias: diss_hydrogen
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_inorg_carb:
name: diss_inorg_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Dissolved inorganic carbon concentration in the sample, typically
measured after filtering the sample using a 0.45 micrometer filter
title: dissolved inorganic carbon
examples:
- value: 2059 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic carbon
rank: 16
is_a: core field
slot_uri: MIXS:0000434
multivalued: false
alias: diss_inorg_carb
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_org_nitro:
name: diss_org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Dissolved organic nitrogen concentration measured as; total dissolved
nitrogen - NH4 - NO3 - NO2
title: dissolved organic nitrogen
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic nitrogen
rank: 18
is_a: core field
slot_uri: MIXS:0000162
multivalued: false
alias: diss_org_nitro
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_oxygen:
name: diss_oxygen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per kilogram, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved oxygen
title: dissolved oxygen
examples:
- value: 175 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen
rank: 19
is_a: core field
slot_uri: MIXS:0000119
multivalued: false
alias: diss_oxygen
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
ecosystem:
name: ecosystem
description: An ecosystem is a combination of a physical environment (abiotic
factors) and all the organisms (biotic factors) that interact with this environment.
Ecosystem is in position 1/5 in a GOLD path.
comments:
- The abiotic factors play a profound role on the type and composition of organisms
in a given environment. The GOLD Ecosystem at the top of the five-level classification
system is aimed at capturing the broader environment from which an organism
or environmental sample is collected. The three broad groups under Ecosystem
are Environmental, Host-associated, and Engineered. They represent samples collected
from a natural environment or from another organism or from engineered environments
like bioreactors respectively.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 9
is_a: gold_path_field
alias: ecosystem
owner: MiscEnvsInterface
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemEnum
recommended: true
ecosystem_category:
name: ecosystem_category
description: Ecosystem categories represent divisions within the ecosystem based
on specific characteristics of the environment from where an organism or sample
is isolated. Ecosystem category is in position 2/5 in a GOLD path.
comments:
- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.
Ecosystem categories for Host-associated samples can be individual hosts or
phyla and for engineered samples it may be manipulated environments like bioreactors,
solid waste etc.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 10
is_a: gold_path_field
alias: ecosystem_category
owner: MiscEnvsInterface
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemCategoryEnum
recommended: true
ecosystem_subtype:
name: ecosystem_subtype
description: Ecosystem subtypes represent further subdivision of Ecosystem types
into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD
path.
comments:
- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided
(for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in
the Ecosystem subtype category.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 12
is_a: gold_path_field
alias: ecosystem_subtype
owner: MiscEnvsInterface
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemSubtypeEnum
recommended: true
ecosystem_type:
name: ecosystem_type
description: Ecosystem types represent things having common characteristics within
the Ecosystem Category. These common characteristics based grouping is still
broad but specific to the characteristics of a given environment. Ecosystem
type is in position 3/5 in a GOLD path.
comments:
- The Aquatic ecosystem category (for example) may have ecosystem types like Marine
or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor
air as different Ecosystem Types. In the case of Host-associated samples, ecosystem
type can represent Respiratory system, Digestive system, Roots etc.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 11
is_a: gold_path_field
alias: ecosystem_type
owner: MiscEnvsInterface
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: EcosystemTypeEnum
recommended: true
elev:
name: elev
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit.
title: elevation, meters
comments:
- All elevations must be reported in meters. Provide the numerical portion only.
- Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
if needed, to help estimate the elevation based on latitude and longitude coordinates.
examples:
- value: '225'
- value: '0'
- value: '1250'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
is_a: environment field
slot_uri: MIXS:0000093
multivalued: false
alias: elev
owner: MiscEnvsInterface
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: float
required: true
env_broad_scale:
name: env_broad_scale
description: 'In this field, report which major environmental system your sample
or specimen came from. The systems identified should have a coarse spatial grain,
to provide the general environmental context of where the sampling was done
(e.g. were you in the desert or a rainforest?). We recommend using subclasses
of ENVO''s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format
(one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel
[termID]|termLabel [termID]. Example: Annotating a water sample from the photic
zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome
[ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider:
tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new
terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
title: broad-scale environmental context
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
env_local_scale:
name: env_local_scale
description: 'Report the entity or entities which are in the sample or specimen’s
local vicinity and which you believe have significant causal influences on your
sample or specimen. We recommend using EnvO terms which are of smaller spatial
grain than your entry for env_broad_scale. Terms, such as anatomical sites,
from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
title: local environmental context
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
examples:
- value: canopy [ENVO:00000047]
- value: herb and fern layer [ENVO:01000337]
- value: litter layer [ENVO:01000338]
- value: understory [01000335]
- value: shrub layer [ENVO:01000336]
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top).'
title: environmental medium
notes:
- range changed to enumeration late in makefile, so this is modified (but "sample
ID" anyway)
examples:
- value: soil [ENVO:00001998]
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
experimental_factor:
name: experimental_factor
annotations:
expected_value:
tag: expected_value
value: text or EFO and/or OBI
description: Experimental factors are essentially the variable aspects of an experiment
design which can be used to describe an experiment, or set of experiments, in
an increasingly detailed manner. This field accepts ontology terms from Experimental
Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
title: experimental factor
examples:
- value: time series design [EFO:EFO_0001779]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- experimental factor
rank: 12
is_a: investigation field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000008
multivalued: false
alias: experimental_factor
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
geo_loc_name:
name: geo_loc_name
annotations:
expected_value:
tag: expected_value
value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
name'
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name.
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- geographic location (country and/or sea,region)
rank: 4
is_a: environment field
string_serialization: '{text}: {text}, {text}'
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: MiscEnvsInterface
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
notes:
- This is currently a required field but it's not clear if this should be required
for human hosts
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
is_a: environment field
string_serialization: '{lat lon}'
slot_uri: MIXS:0000009
multivalued: false
alias: lat_lon
owner: MiscEnvsInterface
domain_of:
- FieldResearchSite
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$
misc_param:
name: misc_param
annotations:
expected_value:
tag: expected_value
value: parameter name;measurement value
occurrence:
tag: occurrence
value: m
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- miscellaneous parameter
rank: 23
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: false
alias: misc_param
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
nitrate:
name: nitrate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrate
rank: 26
is_a: core field
slot_uri: MIXS:0000425
multivalued: false
alias: nitrate
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitrite:
name: nitrite
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrite in the sample
title: nitrite
examples:
- value: 0.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrite
rank: 27
is_a: core field
slot_uri: MIXS:0000426
multivalued: false
alias: nitrite
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitro:
name: nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrogen (total)
title: nitrogen
examples:
- value: 4.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrogen
rank: 28
is_a: core field
slot_uri: MIXS:0000504
multivalued: false
alias: nitro
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_carb:
name: org_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic carbon
title: organic carbon
examples:
- value: 1.5 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic carbon
rank: 29
is_a: core field
slot_uri: MIXS:0000508
multivalued: false
alias: org_carb
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_matter:
name: org_matter
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic matter
title: organic matter
examples:
- value: 1.75 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic matter
rank: 45
is_a: core field
slot_uri: MIXS:0000204
multivalued: false
alias: org_matter
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_nitro:
name: org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic nitrogen
title: organic nitrogen
examples:
- value: 4 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic nitrogen
rank: 46
is_a: core field
slot_uri: MIXS:0000205
multivalued: false
alias: org_nitro
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
organism_count:
name: organism_count
annotations:
expected_value:
tag: expected_value
value: organism name;measurement value;enumeration
preferred_unit:
tag: preferred_unit
value: number of cells per cubic meter, number of cells per milliliter, number
of cells per cubic centimeter
occurrence:
tag: occurrence
value: m
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organism count
rank: 30
is_a: core field
slot_uri: MIXS:0000103
multivalued: false
alias: organism_count
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$
oxy_stat_samp:
name: oxy_stat_samp
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- oxygenation status of sample
rank: 25
is_a: core field
slot_uri: MIXS:0000753
multivalued: false
alias: oxy_stat_samp
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: OxyStatSampEnum
perturbation:
name: perturbation
annotations:
expected_value:
tag: expected_value
value: perturbation type name;perturbation interval and duration
occurrence:
tag: occurrence
value: m
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- perturbation
rank: 33
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: false
alias: perturbation
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
ph:
name: ph
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: pH measurement of the sample, or liquid portion of sample, or aqueous
phase of the fluid
title: pH
notes:
- Use modified term
examples:
- value: '7.2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pH
rank: 27
is_a: core field
string_serialization: '{float}'
slot_uri: MIXS:0001001
multivalued: false
alias: ph
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: float
recommended: true
minimum_value: 0
maximum_value: 14
ph_meth:
name: ph_meth
description: Reference or method used in determining ph
title: pH method
comments:
- This can include a link to the instrument used or a citation for the method.
examples:
- value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB
- value: https://doi.org/10.2136/sssabookser5.3.c16
from_schema: https://w3id.org/nmdc/nmdc
rank: 41
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0001106
multivalued: false
alias: ph_meth
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
phosphate:
name: phosphate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of phosphate
title: phosphate
examples:
- value: 0.7 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phosphate
rank: 53
is_a: core field
slot_uri: MIXS:0000505
multivalued: false
alias: phosphate
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
phosplipid_fatt_acid:
name: phosplipid_fatt_acid
annotations:
expected_value:
tag: expected_value
value: phospholipid fatty acid name;measurement value
preferred_unit:
tag: preferred_unit
value: mole per gram, mole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of phospholipid fatty acids; can include multiple values
title: phospholipid fatty acid
examples:
- value: 2.98 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phospholipid fatty acid
rank: 36
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000181
multivalued: false
alias: phosplipid_fatt_acid
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
potassium:
name: potassium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of potassium in the sample
title: potassium
examples:
- value: 463 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- potassium
rank: 38
is_a: core field
slot_uri: MIXS:0000430
multivalued: false
alias: potassium
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
pressure:
name: pressure
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: atmosphere
occurrence:
tag: occurrence
value: '1'
description: Pressure to which the sample is subject to, in atmospheres
title: pressure
examples:
- value: 50 atmosphere
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pressure
rank: 39
is_a: core field
slot_uri: MIXS:0000412
multivalued: false
alias: pressure
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
salinity:
name: salinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: practical salinity unit, percentage
occurrence:
tag: occurrence
value: '1'
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater.
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- salinity
rank: 54
is_a: core field
slot_uri: MIXS:0000183
multivalued: false
alias: salinity
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
samp_collec_device:
name: samp_collec_device
annotations:
expected_value:
tag: expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
title: sample collection device
comments:
- Report dimensions and details when applicable
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection device
rank: 14
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collec_device
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
samp_collec_method:
name: samp_collec_method
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url , or text
description: The method employed for collecting the sample.
title: sample collection method
comments:
- This can be a citation or description
examples:
- value: swabbing
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection method
rank: 15
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collec_method
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_mat_process:
name: samp_mat_process
annotations:
expected_value:
tag: expected_value
value: text
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed.
title: sample material processing
examples:
- value: filtering of seawater
- value: storing samples in ethanol
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample material processing
rank: 12
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_size:
name: samp_size
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millliter, gram, milligram, liter
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected.
title: amount or size of sample collected
comments:
- This refers to the TOTAL amount of sample collected from the experiment. NOT
the amount sent to each institution or collected for a specific analysis.
examples:
- value: 5 grams
- value: 10 mL
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- amount or size of sample collected
rank: 18
is_a: nucleic acid sequence source field
string_serialization: '{float} {unit}'
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
samp_store_dur:
name: samp_store_dur
annotations:
expected_value:
tag: expected_value
value: duration
occurrence:
tag: occurrence
value: '1'
description: Duration for which the sample was stored
title: sample storage duration
examples:
- value: P1Y6M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage duration
rank: 353
is_a: core field
string_serialization: '{duration}'
slot_uri: MIXS:0000116
multivalued: false
alias: samp_store_dur
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
samp_store_loc:
name: samp_store_loc
annotations:
expected_value:
tag: expected_value
value: location name
occurrence:
tag: occurrence
value: '1'
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage location
rank: 41
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
alias: samp_store_loc
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
samp_store_temp:
name: samp_store_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Temperature at which the sample was stored (degrees are assumed)
title: sample storage temperature
examples:
- value: -80 Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage temperature
rank: 7
is_a: core field
slot_uri: MIXS:0000110
multivalued: false
alias: samp_store_temp
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sample_link:
name: sample_link
description: A unique identifier to assign parent-child, subsample, or sibling
samples. This is relevant when a sample or other material was used to generate
the new sample.
title: sample linkage
notes:
- 'also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) >
1 and "placeholder" in slot_usage.keys():AttributeError: ''list'' object has
no attribute ''keys'''
comments:
- 'This field allows multiple entries separated by ; (Examples: Soil collected
from the field will link with the soil used in an incubation. The soil a plant
was grown in links to the plant sample. An original culture sample was transferred
to a new vial and generated a new sample)'
examples:
- value: IGSN:DSJ0284
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{text}:{text}'
multivalued: false
alias: sample_link
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
- SampIdNewTermsMixin
slot_group: sample_id_section
range: string
recommended: true
pattern: '[^\:\n\r]+\:[^\:\n\r]+'
silicate:
name: silicate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of silicate
title: silicate
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- silicate
rank: 43
is_a: core field
slot_uri: MIXS:0000184
multivalued: false
alias: silicate
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
size_frac:
name: size_frac
annotations:
expected_value:
tag: expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- size fraction selected
rank: 285
is_a: nucleic acid sequence source field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
alias: size_frac
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
sodium:
name: sodium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Sodium concentration in the sample
title: sodium
examples:
- value: 10.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sodium
rank: 363
is_a: core field
slot_uri: MIXS:0000428
multivalued: false
alias: sodium
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
specific_ecosystem:
name: specific_ecosystem
description: Specific ecosystems represent specific features of the environment
like aphotic zone in an ocean or gastric mucosa within a host digestive system.
Specific ecosystem is in position 5/5 in a GOLD path.
comments:
- Specific ecosystems help to define samples based on very specific characteristics
of an environment under the five-level classification system.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://gold.jgi.doe.gov/help
rank: 13
is_a: gold_path_field
alias: specific_ecosystem
owner: MiscEnvsInterface
domain_of:
- Biosample
- Study
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: SpecificEcosystemEnum
recommended: true
sulfate:
name: sulfate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of sulfate in the sample
title: sulfate
examples:
- value: 5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfate
rank: 44
is_a: core field
slot_uri: MIXS:0000423
multivalued: false
alias: sulfate
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sulfide:
name: sulfide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of sulfide in the sample
title: sulfide
examples:
- value: 2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfide
rank: 371
is_a: core field
slot_uri: MIXS:0000424
multivalued: false
alias: sulfide
owner: MiscEnvsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
temp:
name: temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling.
title: temperature
examples:
- value: 25 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- temperature
rank: 37
is_a: environment field
slot_uri: MIXS:0000113
multivalued: false
alias: temp
owner: MiscEnvsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_current:
name: water_current
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per second, knots
occurrence:
tag: occurrence
value: '1'
description: Measurement of magnitude and direction of flow within a fluid
title: water current
examples:
- value: 10 cubic meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water current
rank: 236
is_a: core field
slot_uri: MIXS:0000203
multivalued: false
alias: water_current
owner: MiscEnvsInterface
domain_of:
- Biosample
- MiscEnvsInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
analysis_type:
name: analysis_type
description: Select all the data types associated or available for this biosample
title: analysis/data type
examples:
- value: metagenomics; metabolomics; proteomics
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIxS:investigation_type
rank: 3
multivalued: true
alias: analysis_type
owner: MiscEnvsInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: AnalysisTypeEnum
required: true
recommended: false
samp_name:
name: samp_name
annotations:
expected_value:
tag: expected_value
value: text
description: A local identifier or name that for the material sample collected.
Refers to the original material collected or to any derived sub-samples.
title: sample name
comments:
- It can have any format, but we suggest that you make it concise, unique and
consistent within your lab, and as informative as possible.
examples:
- value: Rock core CB1178(5-6) from NSW
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample name
rank: 1
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0001107
multivalued: false
identifier: true
alias: samp_name
owner: MiscEnvsInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
required: true
source_mat_id:
name: source_mat_id
description: A globally unique identifier assigned to the biological sample.
title: source material identifier
todos:
- Currently, the comments say to use UUIDs. However, if we implement assigning
NMDC identifiers with the minter we dont need to require a GUID. It can be an
optional field to fill out only if they already have a resolvable ID.
- Currently, the comments say to use UUIDs. However, if we implement assigning
NMDC identifiers with the minter we dont need to require a GUID. It can be an
optional field to fill out only if they already have a resolvable ID.
notes:
- The source material IS the Globally Unique ID
comments:
- Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),
NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These
IDs enable linking to derived analytes and subsamples. If you have not assigned
FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).
- Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),
NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These
IDs enable linking to derived analytes and subsamples. If you have not assigned
FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).
examples:
- value: IGSN:AU1243
- value: UUID:24f1467a-40f4-11ed-b878-0242ac120002
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
is_a: nucleic acid sequence source field
string_serialization: '{text}:{text}'
slot_uri: MIXS:0000026
multivalued: false
alias: source_mat_id
owner: MiscEnvsInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
pattern: '[^\:\n\r]+\:[^\:\n\r]+'