Class: Biofilm (BiofilmInterface)
biofilm dh_interface
URI: nmdc_sub_schema:BiofilmInterface
classDiagram
class BiofilmInterface
DhMultiviewCommonColumnsMixin <|-- BiofilmInterface
SampIdNewTermsMixin <|-- BiofilmInterface
DhInterface <|-- BiofilmInterface
BiofilmInterface : alkalinity
BiofilmInterface : alkyl_diethers
BiofilmInterface : alt
BiofilmInterface : aminopept_act
BiofilmInterface : ammonium
BiofilmInterface : analysis_type
BiofilmInterface --|> AnalysisTypeEnum : analysis_type
BiofilmInterface : bacteria_carb_prod
BiofilmInterface : biomass
BiofilmInterface : bishomohopanol
BiofilmInterface : bromide
BiofilmInterface : calcium
BiofilmInterface : carb_nitro_ratio
BiofilmInterface : chem_administration
BiofilmInterface : chloride
BiofilmInterface : chlorophyll
BiofilmInterface : collection_date
BiofilmInterface : depth
BiofilmInterface : diether_lipids
BiofilmInterface : diss_carb_dioxide
BiofilmInterface : diss_hydrogen
BiofilmInterface : diss_inorg_carb
BiofilmInterface : diss_org_carb
BiofilmInterface : diss_org_nitro
BiofilmInterface : diss_oxygen
BiofilmInterface : ecosystem
BiofilmInterface --|> EcosystemEnum : ecosystem
BiofilmInterface : ecosystem_category
BiofilmInterface --|> EcosystemCategoryEnum : ecosystem_category
BiofilmInterface : ecosystem_subtype
BiofilmInterface --|> EcosystemSubtypeEnum : ecosystem_subtype
BiofilmInterface : ecosystem_type
BiofilmInterface --|> EcosystemTypeEnum : ecosystem_type
BiofilmInterface : elev
BiofilmInterface : env_broad_scale
BiofilmInterface : env_local_scale
BiofilmInterface : env_medium
BiofilmInterface : experimental_factor
BiofilmInterface : geo_loc_name
BiofilmInterface : glucosidase_act
BiofilmInterface : lat_lon
BiofilmInterface : magnesium
BiofilmInterface : mean_frict_vel
BiofilmInterface : mean_peak_frict_vel
BiofilmInterface : methane
BiofilmInterface : misc_param
BiofilmInterface : n_alkanes
BiofilmInterface : nitrate
BiofilmInterface : nitrite
BiofilmInterface : nitro
BiofilmInterface : org_carb
BiofilmInterface : org_matter
BiofilmInterface : org_nitro
BiofilmInterface : organism_count
BiofilmInterface : oxy_stat_samp
BiofilmInterface --|> OxyStatSampEnum : oxy_stat_samp
BiofilmInterface : part_org_carb
BiofilmInterface : perturbation
BiofilmInterface : petroleum_hydrocarb
BiofilmInterface : ph
BiofilmInterface : ph_meth
BiofilmInterface : phaeopigments
BiofilmInterface : phosphate
BiofilmInterface : phosplipid_fatt_acid
BiofilmInterface : potassium
BiofilmInterface : pressure
BiofilmInterface : redox_potential
BiofilmInterface : salinity
BiofilmInterface : samp_collec_device
BiofilmInterface : samp_collec_method
BiofilmInterface : samp_mat_process
BiofilmInterface : samp_name
BiofilmInterface : samp_size
BiofilmInterface : samp_store_dur
BiofilmInterface : samp_store_loc
BiofilmInterface : samp_store_temp
BiofilmInterface : sample_link
BiofilmInterface : silicate
BiofilmInterface : size_frac
BiofilmInterface : sodium
BiofilmInterface : source_mat_id
BiofilmInterface : specific_ecosystem
BiofilmInterface --|> SpecificEcosystemEnum : specific_ecosystem
BiofilmInterface : sulfate
BiofilmInterface : sulfide
BiofilmInterface : temp
BiofilmInterface : tot_carb
BiofilmInterface : tot_nitro_content
BiofilmInterface : tot_org_carb
BiofilmInterface : turbidity
BiofilmInterface : water_content
Inheritance
- DhInterface
- BiofilmInterface [ DhMultiviewCommonColumnsMixin SampIdNewTermsMixin]
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
alkalinity | 0..1 String |
Alkalinity, the ability of a solution to neutralize acids to the equivalence ... | direct |
alkyl_diethers | 0..1 String |
Concentration of alkyl diethers | direct |
alt | 0..1 recommended String |
Altitude is a term used to identify heights of objects such as airplanes, spa... | direct |
aminopept_act | 0..1 String |
Measurement of aminopeptidase activity | direct |
ammonium | 0..1 String |
Concentration of ammonium in the sample | direct |
bacteria_carb_prod | 0..1 String |
Measurement of bacterial carbon production | direct |
biomass | 0..1 String |
Amount of biomass; should include the name for the part of biomass measured, ... | direct |
bishomohopanol | 0..1 String |
Concentration of bishomohopanol | direct |
bromide | 0..1 String |
Concentration of bromide | direct |
calcium | 0..1 String |
Concentration of calcium in the sample | direct |
carb_nitro_ratio | 0..1 Float |
Ratio of amount or concentrations of carbon to nitrogen | 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 |
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_carb | 0..1 String |
Concentration of dissolved organic carbon in the sample, liquid portion of th... | 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 |
glucosidase_act | 0..1 String |
Measurement of glucosidase activity | direct |
lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | direct |
magnesium | 0..1 String |
Concentration of magnesium in the sample | direct |
mean_frict_vel | 0..1 String |
Measurement of mean friction velocity | direct |
mean_peak_frict_vel | 0..1 String |
Measurement of mean peak friction velocity | direct |
methane | 0..1 String |
Methane (gas) amount or concentration at the time of sampling | direct |
misc_param | 0..1 String |
Any other measurement performed or parameter collected, that is not listed he... | direct |
n_alkanes | 0..1 String |
Concentration of n-alkanes; can include multiple n-alkanes | 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 |
part_org_carb | 0..1 String |
Concentration of particulate organic carbon | direct |
perturbation | 0..1 String |
Type of perturbation, e | direct |
petroleum_hydrocarb | 0..1 String |
Concentration of petroleum hydrocarbon | 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 |
phaeopigments | 0..1 String |
Concentration of phaeopigments; can include multiple phaeopigments | 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 |
redox_potential | 0..1 String |
Redox potential, measured relative to a hydrogen cell, indicating oxidation o... | 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 |
tot_carb | 0..1 String |
Total carbon content | direct |
tot_nitro_content | 0..1 String |
Total nitrogen content of the sample | direct |
tot_org_carb | 0..1 String |
Definition for soil: total organic carbon content of the soil, definition oth... | direct |
turbidity | 0..1 String |
Measure of the amount of cloudiness or haziness in water caused by individual... | direct |
water_content | 0..1 String |
Water content measurement | 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 |
Usages
used by | used in | type | used |
---|---|---|---|
SampleData | biofilm_data | range | BiofilmInterface |
Identifier and Mapping Information
Annotations
property | value |
---|---|
excel_worksheet_name | microbial mat_biofilm |
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:BiofilmInterface |
native | nmdc_sub_schema:BiofilmInterface |
LinkML Source
Direct
name: BiofilmInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: microbial mat_biofilm
description: biofilm dh_interface
title: Biofilm
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
slots:
- alkalinity
- alkyl_diethers
- alt
- aminopept_act
- ammonium
- bacteria_carb_prod
- biomass
- bishomohopanol
- bromide
- calcium
- carb_nitro_ratio
- chem_administration
- chloride
- chlorophyll
- collection_date
- depth
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_org_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
- glucosidase_act
- lat_lon
- magnesium
- mean_frict_vel
- mean_peak_frict_vel
- methane
- misc_param
- n_alkanes
- nitrate
- nitrite
- nitro
- org_carb
- org_matter
- org_nitro
- organism_count
- oxy_stat_samp
- part_org_carb
- perturbation
- petroleum_hydrocarb
- ph
- ph_meth
- phaeopigments
- phosphate
- phosplipid_fatt_acid
- potassium
- pressure
- redox_potential
- 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
- tot_carb
- tot_nitro_content
- tot_org_carb
- turbidity
- water_content
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.*$
alkyl_diethers:
name: alkyl_diethers
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of alkyl diethers
title: alkyl diethers
examples:
- value: 0.005 mole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkyl diethers
rank: 2
is_a: core field
slot_uri: MIXS:0000490
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- 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.*$
aminopept_act:
name: aminopept_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of aminopeptidase activity
title: aminopeptidase activity
examples:
- value: 0.269 mole per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aminopeptidase activity
rank: 3
is_a: core field
slot_uri: MIXS:0000172
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
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.*$
bacteria_carb_prod:
name: bacteria_carb_prod
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of bacterial carbon production
title: bacterial carbon production
examples:
- value: 2.53 microgram per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bacterial carbon production
rank: 5
is_a: core field
slot_uri: MIXS:0000173
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
bishomohopanol:
name: bishomohopanol
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, microgram per gram
occurrence:
tag: occurrence
value: '1'
description: Concentration of bishomohopanol
title: bishomohopanol
examples:
- value: 14 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bishomohopanol
rank: 7
is_a: core field
slot_uri: MIXS:0000175
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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.*$
carb_nitro_ratio:
name: carb_nitro_ratio
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Ratio of amount or concentrations of carbon to nitrogen
title: carbon/nitrogen ratio
examples:
- value: '0.417361111'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- carbon/nitrogen ratio
rank: 44
is_a: core field
slot_uri: MIXS:0000310
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: float
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]))?)?$
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_carb:
name: diss_org_carb
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 organic carbon in the sample, liquid portion
of the sample, or aqueous phase of the fluid
title: dissolved organic carbon
examples:
- value: 197 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic carbon
rank: 17
is_a: core field
slot_uri: MIXS:0000433
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- 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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
glucosidase_act:
name: glucosidase_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mol per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of glucosidase activity
title: glucosidase activity
examples:
- value: 5 mol per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- glucosidase activity
rank: 20
is_a: core field
slot_uri: MIXS:0000137
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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+)?)$
magnesium:
name: magnesium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter, milligram per liter, parts per million, micromole per
kilogram
occurrence:
tag: occurrence
value: '1'
description: Concentration of magnesium in the sample
title: magnesium
examples:
- value: 52.8 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- magnesium
rank: 21
is_a: core field
slot_uri: MIXS:0000431
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
mean_frict_vel:
name: mean_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean friction velocity
title: mean friction velocity
examples:
- value: 0.5 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean friction velocity
rank: 22
is_a: core field
slot_uri: MIXS:0000498
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
mean_peak_frict_vel:
name: mean_peak_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean peak friction velocity
title: mean peak friction velocity
examples:
- value: 1 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean peak friction velocity
rank: 23
is_a: core field
slot_uri: MIXS:0000502
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
methane:
name: methane
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, parts per billion, parts per million
occurrence:
tag: occurrence
value: '1'
description: Methane (gas) amount or concentration at the time of sampling
title: methane
examples:
- value: 1800 parts per billion
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- methane
rank: 24
is_a: core field
slot_uri: MIXS:0000101
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- SedimentInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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]+)$
n_alkanes:
name: n_alkanes
annotations:
expected_value:
tag: expected_value
value: n-alkane name;measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of n-alkanes; can include multiple n-alkanes
title: n-alkanes
examples:
- value: n-hexadecane;100 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- n-alkanes
rank: 25
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000503
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
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
part_org_carb:
name: part_org_carb
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 particulate organic carbon
title: particulate organic carbon
examples:
- value: 1.92 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- particulate organic carbon
rank: 31
is_a: core field
slot_uri: MIXS:0000515
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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
petroleum_hydrocarb:
name: petroleum_hydrocarb
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 petroleum hydrocarbon
title: petroleum hydrocarbon
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- petroleum hydrocarbon
rank: 34
is_a: core field
slot_uri: MIXS:0000516
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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
phaeopigments:
name: phaeopigments
annotations:
expected_value:
tag: expected_value
value: phaeopigment name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter
occurrence:
tag: occurrence
value: m
description: Concentration of phaeopigments; can include multiple phaeopigments
title: phaeopigments
examples:
- value: 2.5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phaeopigments
rank: 35
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000180
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
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.*$
redox_potential:
name: redox_potential
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millivolt
occurrence:
tag: occurrence
value: '1'
description: Redox potential, measured relative to a hydrogen cell, indicating
oxidation or reduction potential
title: redox potential
examples:
- value: 300 millivolt
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- redox potential
rank: 40
is_a: core field
slot_uri: MIXS:0000182
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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.*$
tot_carb:
name: tot_carb
description: Total carbon content
title: total carbon
todos:
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
examples:
- value: 1 ug/L
from_schema: https://w3id.org/nmdc/nmdc
rank: 47
is_a: core field
slot_uri: MIXS:0000525
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_nitro_content:
name: tot_nitro_content
description: Total nitrogen content of the sample
title: total nitrogen content
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
rank: 48
is_a: core field
slot_uri: MIXS:0000530
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_org_carb:
name: tot_org_carb
description: 'Definition for soil: total organic carbon content of the soil, definition
otherwise: total organic carbon content'
title: total organic carbon
todos:
- check description. How are they different?
- check description. How are they different?
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
rank: 50
is_a: core field
slot_uri: MIXS:0000533
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
turbidity:
name: turbidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: formazin turbidity unit, formazin nephelometric units
occurrence:
tag: occurrence
value: '1'
description: Measure of the amount of cloudiness or haziness in water caused by
individual particles
title: turbidity
examples:
- value: 0.3 nephelometric turbidity units
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- turbidity
rank: 47
is_a: core field
slot_uri: MIXS:0000191
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_content:
name: water_content
annotations:
expected_value:
tag: expected_value
value: string
preferred_unit:
tag: preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
description: Water content measurement
title: water content
todos:
- value in preferred unit is too limiting. need to change this
- check and correct validation so examples are accepted
- how to manage multiple water content methods?
examples:
- value: 0.75 g water/g dry soil
- value: 75% water holding capacity
- value: 1.1 g fresh weight/ dry weight
- value: 10% water filled pore space
from_schema: https://w3id.org/nmdc/nmdc
rank: 39
is_a: core field
string_serialization: '{float or pct} {unit}'
slot_uri: MIXS:0000185
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$
horizon_meth:
name: horizon_meth
title: horizon method
Induced
name: BiofilmInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: microbial mat_biofilm
description: biofilm dh_interface
title: Biofilm
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
- SampIdNewTermsMixin
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.*$
alkyl_diethers:
name: alkyl_diethers
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of alkyl diethers
title: alkyl diethers
examples:
- value: 0.005 mole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkyl diethers
rank: 2
is_a: core field
slot_uri: MIXS:0000490
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- 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.*$
aminopept_act:
name: aminopept_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of aminopeptidase activity
title: aminopeptidase activity
examples:
- value: 0.269 mole per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aminopeptidase activity
rank: 3
is_a: core field
slot_uri: MIXS:0000172
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
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.*$
bacteria_carb_prod:
name: bacteria_carb_prod
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of bacterial carbon production
title: bacterial carbon production
examples:
- value: 2.53 microgram per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bacterial carbon production
rank: 5
is_a: core field
slot_uri: MIXS:0000173
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
bishomohopanol:
name: bishomohopanol
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, microgram per gram
occurrence:
tag: occurrence
value: '1'
description: Concentration of bishomohopanol
title: bishomohopanol
examples:
- value: 14 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bishomohopanol
rank: 7
is_a: core field
slot_uri: MIXS:0000175
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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.*$
carb_nitro_ratio:
name: carb_nitro_ratio
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Ratio of amount or concentrations of carbon to nitrogen
title: carbon/nitrogen ratio
examples:
- value: '0.417361111'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- carbon/nitrogen ratio
rank: 44
is_a: core field
slot_uri: MIXS:0000310
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: float
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]))?)?$
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_carb:
name: diss_org_carb
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 organic carbon in the sample, liquid portion
of the sample, or aqueous phase of the fluid
title: dissolved organic carbon
examples:
- value: 197 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic carbon
rank: 17
is_a: core field
slot_uri: MIXS:0000433
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- 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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
glucosidase_act:
name: glucosidase_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mol per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of glucosidase activity
title: glucosidase activity
examples:
- value: 5 mol per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- glucosidase activity
rank: 20
is_a: core field
slot_uri: MIXS:0000137
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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+)?)$
magnesium:
name: magnesium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter, milligram per liter, parts per million, micromole per
kilogram
occurrence:
tag: occurrence
value: '1'
description: Concentration of magnesium in the sample
title: magnesium
examples:
- value: 52.8 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- magnesium
rank: 21
is_a: core field
slot_uri: MIXS:0000431
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
mean_frict_vel:
name: mean_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean friction velocity
title: mean friction velocity
examples:
- value: 0.5 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean friction velocity
rank: 22
is_a: core field
slot_uri: MIXS:0000498
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
mean_peak_frict_vel:
name: mean_peak_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean peak friction velocity
title: mean peak friction velocity
examples:
- value: 1 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean peak friction velocity
rank: 23
is_a: core field
slot_uri: MIXS:0000502
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
methane:
name: methane
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, parts per billion, parts per million
occurrence:
tag: occurrence
value: '1'
description: Methane (gas) amount or concentration at the time of sampling
title: methane
examples:
- value: 1800 parts per billion
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- methane
rank: 24
is_a: core field
slot_uri: MIXS:0000101
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- SedimentInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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]+)$
n_alkanes:
name: n_alkanes
annotations:
expected_value:
tag: expected_value
value: n-alkane name;measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of n-alkanes; can include multiple n-alkanes
title: n-alkanes
examples:
- value: n-hexadecane;100 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- n-alkanes
rank: 25
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000503
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
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
part_org_carb:
name: part_org_carb
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 particulate organic carbon
title: particulate organic carbon
examples:
- value: 1.92 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- particulate organic carbon
rank: 31
is_a: core field
slot_uri: MIXS:0000515
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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
petroleum_hydrocarb:
name: petroleum_hydrocarb
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 petroleum hydrocarbon
title: petroleum hydrocarbon
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- petroleum hydrocarbon
rank: 34
is_a: core field
slot_uri: MIXS:0000516
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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
phaeopigments:
name: phaeopigments
annotations:
expected_value:
tag: expected_value
value: phaeopigment name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter
occurrence:
tag: occurrence
value: m
description: Concentration of phaeopigments; can include multiple phaeopigments
title: phaeopigments
examples:
- value: 2.5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phaeopigments
rank: 35
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000180
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
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.*$
redox_potential:
name: redox_potential
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millivolt
occurrence:
tag: occurrence
value: '1'
description: Redox potential, measured relative to a hydrogen cell, indicating
oxidation or reduction potential
title: redox potential
examples:
- value: 300 millivolt
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- redox potential
rank: 40
is_a: core field
slot_uri: MIXS:0000182
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- 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.*$
tot_carb:
name: tot_carb
description: Total carbon content
title: total carbon
todos:
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
examples:
- value: 1 ug/L
from_schema: https://w3id.org/nmdc/nmdc
rank: 47
is_a: core field
slot_uri: MIXS:0000525
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_nitro_content:
name: tot_nitro_content
description: Total nitrogen content of the sample
title: total nitrogen content
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
rank: 48
is_a: core field
slot_uri: MIXS:0000530
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_org_carb:
name: tot_org_carb
description: 'Definition for soil: total organic carbon content of the soil, definition
otherwise: total organic carbon content'
title: total organic carbon
todos:
- check description. How are they different?
- check description. How are they different?
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
rank: 50
is_a: core field
slot_uri: MIXS:0000533
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
turbidity:
name: turbidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: formazin turbidity unit, formazin nephelometric units
occurrence:
tag: occurrence
value: '1'
description: Measure of the amount of cloudiness or haziness in water caused by
individual particles
title: turbidity
examples:
- value: 0.3 nephelometric turbidity units
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- turbidity
rank: 47
is_a: core field
slot_uri: MIXS:0000191
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_content:
name: water_content
annotations:
expected_value:
tag: expected_value
value: string
preferred_unit:
tag: preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
description: Water content measurement
title: water content
todos:
- value in preferred unit is too limiting. need to change this
- check and correct validation so examples are accepted
- how to manage multiple water content methods?
examples:
- value: 0.75 g water/g dry soil
- value: 75% water holding capacity
- value: 1.1 g fresh weight/ dry weight
- value: 10% water filled pore space
from_schema: https://w3id.org/nmdc/nmdc
rank: 39
is_a: core field
string_serialization: '{float or pct} {unit}'
slot_uri: MIXS:0000185
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[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: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
alkyl_diethers:
name: alkyl_diethers
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of alkyl diethers
title: alkyl diethers
examples:
- value: 0.005 mole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkyl diethers
rank: 2
is_a: core field
slot_uri: MIXS:0000490
multivalued: false
alias: alkyl_diethers
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- 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: BiofilmInterface
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.*$
aminopept_act:
name: aminopept_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of aminopeptidase activity
title: aminopeptidase activity
examples:
- value: 0.269 mole per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aminopeptidase activity
rank: 3
is_a: core field
slot_uri: MIXS:0000172
multivalued: false
alias: aminopept_act
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
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: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
bacteria_carb_prod:
name: bacteria_carb_prod
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of bacterial carbon production
title: bacterial carbon production
examples:
- value: 2.53 microgram per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bacterial carbon production
rank: 5
is_a: core field
slot_uri: MIXS:0000173
multivalued: false
alias: bacteria_carb_prod
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- 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: BiofilmInterface
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]+)$
bishomohopanol:
name: bishomohopanol
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, microgram per gram
occurrence:
tag: occurrence
value: '1'
description: Concentration of bishomohopanol
title: bishomohopanol
examples:
- value: 14 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bishomohopanol
rank: 7
is_a: core field
slot_uri: MIXS:0000175
multivalued: false
alias: bishomohopanol
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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: BiofilmInterface
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: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
carb_nitro_ratio:
name: carb_nitro_ratio
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Ratio of amount or concentrations of carbon to nitrogen
title: carbon/nitrogen ratio
examples:
- value: '0.417361111'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- carbon/nitrogen ratio
rank: 44
is_a: core field
slot_uri: MIXS:0000310
multivalued: false
alias: carb_nitro_ratio
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: float
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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]))?)?$
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_org_carb:
name: diss_org_carb
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 organic carbon in the sample, liquid portion
of the sample, or aqueous phase of the fluid
title: dissolved organic carbon
examples:
- value: 197 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic carbon
rank: 17
is_a: core field
slot_uri: MIXS:0000433
multivalued: false
alias: diss_org_carb
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- 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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
glucosidase_act:
name: glucosidase_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mol per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of glucosidase activity
title: glucosidase activity
examples:
- value: 5 mol per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- glucosidase activity
rank: 20
is_a: core field
slot_uri: MIXS:0000137
multivalued: false
alias: glucosidase_act
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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: BiofilmInterface
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+)?)$
magnesium:
name: magnesium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter, milligram per liter, parts per million, micromole per
kilogram
occurrence:
tag: occurrence
value: '1'
description: Concentration of magnesium in the sample
title: magnesium
examples:
- value: 52.8 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- magnesium
rank: 21
is_a: core field
slot_uri: MIXS:0000431
multivalued: false
alias: magnesium
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
mean_frict_vel:
name: mean_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean friction velocity
title: mean friction velocity
examples:
- value: 0.5 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean friction velocity
rank: 22
is_a: core field
slot_uri: MIXS:0000498
multivalued: false
alias: mean_frict_vel
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
mean_peak_frict_vel:
name: mean_peak_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean peak friction velocity
title: mean peak friction velocity
examples:
- value: 1 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean peak friction velocity
rank: 23
is_a: core field
slot_uri: MIXS:0000502
multivalued: false
alias: mean_peak_frict_vel
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
methane:
name: methane
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, parts per billion, parts per million
occurrence:
tag: occurrence
value: '1'
description: Methane (gas) amount or concentration at the time of sampling
title: methane
examples:
- value: 1800 parts per billion
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- methane
rank: 24
is_a: core field
slot_uri: MIXS:0000101
multivalued: false
alias: methane
owner: BiofilmInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- SedimentInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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: BiofilmInterface
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]+)$
n_alkanes:
name: n_alkanes
annotations:
expected_value:
tag: expected_value
value: n-alkane name;measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of n-alkanes; can include multiple n-alkanes
title: n-alkanes
examples:
- value: n-hexadecane;100 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- n-alkanes
rank: 25
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000503
multivalued: false
alias: n_alkanes
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: OxyStatSampEnum
part_org_carb:
name: part_org_carb
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 particulate organic carbon
title: particulate organic carbon
examples:
- value: 1.92 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- particulate organic carbon
rank: 31
is_a: core field
slot_uri: MIXS:0000515
multivalued: false
alias: part_org_carb
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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: BiofilmInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
petroleum_hydrocarb:
name: petroleum_hydrocarb
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 petroleum hydrocarbon
title: petroleum hydrocarbon
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- petroleum hydrocarbon
rank: 34
is_a: core field
slot_uri: MIXS:0000516
multivalued: false
alias: petroleum_hydrocarb
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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: BiofilmInterface
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: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
phaeopigments:
name: phaeopigments
annotations:
expected_value:
tag: expected_value
value: phaeopigment name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter
occurrence:
tag: occurrence
value: m
description: Concentration of phaeopigments; can include multiple phaeopigments
title: phaeopigments
examples:
- value: 2.5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phaeopigments
rank: 35
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000180
multivalued: false
alias: phaeopigments
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- 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]+)$
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
redox_potential:
name: redox_potential
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millivolt
occurrence:
tag: occurrence
value: '1'
description: Redox potential, measured relative to a hydrogen cell, indicating
oxidation or reduction potential
title: redox potential
examples:
- value: 300 millivolt
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- redox potential
rank: 40
is_a: core field
slot_uri: MIXS:0000182
multivalued: false
alias: redox_potential
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- 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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
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.*$
tot_carb:
name: tot_carb
description: Total carbon content
title: total carbon
todos:
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
examples:
- value: 1 ug/L
from_schema: https://w3id.org/nmdc/nmdc
rank: 47
is_a: core field
slot_uri: MIXS:0000525
multivalued: false
alias: tot_carb
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_nitro_content:
name: tot_nitro_content
description: Total nitrogen content of the sample
title: total nitrogen content
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
rank: 48
is_a: core field
slot_uri: MIXS:0000530
multivalued: false
alias: tot_nitro_content
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_org_carb:
name: tot_org_carb
description: 'Definition for soil: total organic carbon content of the soil, definition
otherwise: total organic carbon content'
title: total organic carbon
todos:
- check description. How are they different?
- check description. How are they different?
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
rank: 50
is_a: core field
slot_uri: MIXS:0000533
multivalued: false
alias: tot_org_carb
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
turbidity:
name: turbidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: formazin turbidity unit, formazin nephelometric units
occurrence:
tag: occurrence
value: '1'
description: Measure of the amount of cloudiness or haziness in water caused by
individual particles
title: turbidity
examples:
- value: 0.3 nephelometric turbidity units
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- turbidity
rank: 47
is_a: core field
slot_uri: MIXS:0000191
multivalued: false
alias: turbidity
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_content:
name: water_content
annotations:
expected_value:
tag: expected_value
value: string
preferred_unit:
tag: preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
description: Water content measurement
title: water content
todos:
- value in preferred unit is too limiting. need to change this
- check and correct validation so examples are accepted
- how to manage multiple water content methods?
examples:
- value: 0.75 g water/g dry soil
- value: 75% water holding capacity
- value: 1.1 g fresh weight/ dry weight
- value: 10% water filled pore space
from_schema: https://w3id.org/nmdc/nmdc
rank: 39
is_a: core field
string_serialization: '{float or pct} {unit}'
slot_uri: MIXS:0000185
multivalued: false
alias: water_content
owner: BiofilmInterface
domain_of:
- Biosample
- BiofilmInterface
- SedimentInterface
- SoilInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[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: BiofilmInterface
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: BiofilmInterface
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: BiofilmInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
pattern: '[^\:\n\r]+\:[^\:\n\r]+'