Class: Hcr Fluids Swabs (HcrFluidsSwabsInterface)
hcr_fluids_swabs dh_interface
URI: nmdc_sub_schema:HcrFluidsSwabsInterface
classDiagram
class HcrFluidsSwabsInterface
DhMultiviewCommonColumnsMixin <|-- HcrFluidsSwabsInterface
DhInterface <|-- HcrFluidsSwabsInterface
HcrFluidsSwabsInterface : add_recov_method
HcrFluidsSwabsInterface : additional_info
HcrFluidsSwabsInterface : alkalinity
HcrFluidsSwabsInterface : alkalinity_method
HcrFluidsSwabsInterface : ammonium
HcrFluidsSwabsInterface : analysis_type
HcrFluidsSwabsInterface --|> AnalysisTypeEnum : analysis_type
HcrFluidsSwabsInterface : api
HcrFluidsSwabsInterface : aromatics_pc
HcrFluidsSwabsInterface : asphaltenes_pc
HcrFluidsSwabsInterface : basin
HcrFluidsSwabsInterface : benzene
HcrFluidsSwabsInterface : biocide
HcrFluidsSwabsInterface : biocide_admin_method
HcrFluidsSwabsInterface : calcium
HcrFluidsSwabsInterface : chem_administration
HcrFluidsSwabsInterface : chem_treat_method
HcrFluidsSwabsInterface : chem_treatment
HcrFluidsSwabsInterface : chloride
HcrFluidsSwabsInterface : collection_date
HcrFluidsSwabsInterface : density
HcrFluidsSwabsInterface : depos_env
HcrFluidsSwabsInterface --|> depos_env_enum : depos_env
HcrFluidsSwabsInterface : depth
HcrFluidsSwabsInterface : diss_carb_dioxide
HcrFluidsSwabsInterface : diss_inorg_carb
HcrFluidsSwabsInterface : diss_inorg_phosp
HcrFluidsSwabsInterface : diss_iron
HcrFluidsSwabsInterface : diss_org_carb
HcrFluidsSwabsInterface : diss_oxygen_fluid
HcrFluidsSwabsInterface : ecosystem
HcrFluidsSwabsInterface --|> EcosystemEnum : ecosystem
HcrFluidsSwabsInterface : ecosystem_category
HcrFluidsSwabsInterface --|> EcosystemCategoryEnum : ecosystem_category
HcrFluidsSwabsInterface : ecosystem_subtype
HcrFluidsSwabsInterface --|> EcosystemSubtypeEnum : ecosystem_subtype
HcrFluidsSwabsInterface : ecosystem_type
HcrFluidsSwabsInterface --|> EcosystemTypeEnum : ecosystem_type
HcrFluidsSwabsInterface : elev
HcrFluidsSwabsInterface : env_broad_scale
HcrFluidsSwabsInterface : env_local_scale
HcrFluidsSwabsInterface : env_medium
HcrFluidsSwabsInterface : ethylbenzene
HcrFluidsSwabsInterface : experimental_factor
HcrFluidsSwabsInterface : field
HcrFluidsSwabsInterface : geo_loc_name
HcrFluidsSwabsInterface : hc_produced
HcrFluidsSwabsInterface --|> hc_produced_enum : hc_produced
HcrFluidsSwabsInterface : hcr
HcrFluidsSwabsInterface --|> hcr_enum : hcr
HcrFluidsSwabsInterface : hcr_fw_salinity
HcrFluidsSwabsInterface : hcr_geol_age
HcrFluidsSwabsInterface --|> hcr_geol_age_enum : hcr_geol_age
HcrFluidsSwabsInterface : hcr_pressure
HcrFluidsSwabsInterface : hcr_temp
HcrFluidsSwabsInterface : iw_bt_date_well
HcrFluidsSwabsInterface : iwf
HcrFluidsSwabsInterface : lat_lon
HcrFluidsSwabsInterface : lithology
HcrFluidsSwabsInterface --|> lithology_enum : lithology
HcrFluidsSwabsInterface : magnesium
HcrFluidsSwabsInterface : misc_param
HcrFluidsSwabsInterface : nitrate
HcrFluidsSwabsInterface : nitrite
HcrFluidsSwabsInterface : org_count_qpcr_info
HcrFluidsSwabsInterface : organism_count
HcrFluidsSwabsInterface : oxy_stat_samp
HcrFluidsSwabsInterface --|> OxyStatSampEnum : oxy_stat_samp
HcrFluidsSwabsInterface : ph
HcrFluidsSwabsInterface : ph_meth
HcrFluidsSwabsInterface : potassium
HcrFluidsSwabsInterface : pour_point
HcrFluidsSwabsInterface : pressure
HcrFluidsSwabsInterface : prod_rate
HcrFluidsSwabsInterface : prod_start_date
HcrFluidsSwabsInterface : reservoir
HcrFluidsSwabsInterface : resins_pc
HcrFluidsSwabsInterface : salinity
HcrFluidsSwabsInterface : samp_collec_device
HcrFluidsSwabsInterface : samp_collec_method
HcrFluidsSwabsInterface : samp_collect_point
HcrFluidsSwabsInterface --|> samp_collect_point_enum : samp_collect_point
HcrFluidsSwabsInterface : samp_loc_corr_rate
HcrFluidsSwabsInterface : samp_mat_process
HcrFluidsSwabsInterface : samp_name
HcrFluidsSwabsInterface : samp_preserv
HcrFluidsSwabsInterface : samp_size
HcrFluidsSwabsInterface : samp_store_dur
HcrFluidsSwabsInterface : samp_store_loc
HcrFluidsSwabsInterface : samp_store_temp
HcrFluidsSwabsInterface : samp_subtype
HcrFluidsSwabsInterface --|> samp_subtype_enum : samp_subtype
HcrFluidsSwabsInterface : samp_transport_cond
HcrFluidsSwabsInterface : samp_type
HcrFluidsSwabsInterface : samp_well_name
HcrFluidsSwabsInterface : sample_link
HcrFluidsSwabsInterface : saturates_pc
HcrFluidsSwabsInterface : size_frac
HcrFluidsSwabsInterface : sodium
HcrFluidsSwabsInterface : source_mat_id
HcrFluidsSwabsInterface : specific_ecosystem
HcrFluidsSwabsInterface --|> SpecificEcosystemEnum : specific_ecosystem
HcrFluidsSwabsInterface : sulfate
HcrFluidsSwabsInterface : sulfate_fw
HcrFluidsSwabsInterface : sulfide
HcrFluidsSwabsInterface : suspend_solids
HcrFluidsSwabsInterface : tan
HcrFluidsSwabsInterface : temp
HcrFluidsSwabsInterface : toluene
HcrFluidsSwabsInterface : tot_iron
HcrFluidsSwabsInterface : tot_nitro
HcrFluidsSwabsInterface : tot_phosp
HcrFluidsSwabsInterface : tot_sulfur
HcrFluidsSwabsInterface : tvdss_of_hcr_press
HcrFluidsSwabsInterface : tvdss_of_hcr_temp
HcrFluidsSwabsInterface : vfa
HcrFluidsSwabsInterface : vfa_fw
HcrFluidsSwabsInterface : viscosity
HcrFluidsSwabsInterface : water_cut
HcrFluidsSwabsInterface : water_prod_rate
HcrFluidsSwabsInterface : win
HcrFluidsSwabsInterface : xylene
Inheritance
- DhInterface
- HcrFluidsSwabsInterface [ DhMultiviewCommonColumnsMixin]
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
add_recov_method | 0..1 String |
Additional (i | direct |
additional_info | 0..1 String |
Information that doesn't fit anywhere else | direct |
alkalinity | 0..1 String |
Alkalinity, the ability of a solution to neutralize acids to the equivalence ... | direct |
alkalinity_method | 0..1 String |
Method used for alkalinity measurement | direct |
ammonium | 0..1 String |
Concentration of ammonium in the sample | direct |
api | 0..1 String |
API gravity is a measure of how heavy or light a petroleum liquid is compared... | direct |
aromatics_pc | 0..1 String |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | direct |
asphaltenes_pc | 0..1 String |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | direct |
basin | 0..1 String |
Name of the basin (e | direct |
benzene | 0..1 String |
Concentration of benzene in the sample | direct |
biocide | 0..1 String |
List of biocides (commercial name of product and supplier) and date of admini... | direct |
biocide_admin_method | 0..1 String |
Method of biocide administration (dose, frequency, duration, time elapsed bet... | direct |
calcium | 0..1 String |
Concentration of calcium in the sample | direct |
chem_administration | 0..1 recommended String |
List of chemical compounds administered to the host or site where sampling oc... | direct |
chem_treat_method | 0..1 String |
Method of chemical administration(dose, frequency, duration, time elapsed bet... | direct |
chem_treatment | 0..1 String |
List of chemical compounds administered upstream the sampling location where ... | direct |
chloride | 0..1 String |
Concentration of chloride in the sample | direct |
collection_date | 1..1 String |
The date of sampling | direct |
density | 0..1 String |
Density of the sample, which is its mass per unit volume (aka volumetric mass... | direct |
depos_env | 0..1 DeposEnvEnum |
Main depositional environment (https://en | direct |
depth | 0..1 recommended String |
The vertical distance below local surface, e | direct |
diss_carb_dioxide | 0..1 String |
Concentration of dissolved carbon dioxide in the sample or liquid portion of ... | direct |
diss_inorg_carb | 0..1 String |
Dissolved inorganic carbon concentration in the sample, typically measured af... | direct |
diss_inorg_phosp | 0..1 String |
Concentration of dissolved inorganic phosphorus in the sample | direct |
diss_iron | 0..1 String |
Concentration of dissolved iron in the sample | direct |
diss_org_carb | 0..1 String |
Concentration of dissolved organic carbon in the sample, liquid portion of th... | direct |
diss_oxygen_fluid | 0..1 String |
Concentration of dissolved oxygen in the oil field produced fluids as it cont... | 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 |
ethylbenzene | 0..1 String |
Concentration of ethylbenzene in the sample | direct |
experimental_factor | 0..1 String |
Experimental factors are essentially the variable aspects of an experiment de... | direct |
field | 0..1 String |
Name of the hydrocarbon field (e | direct |
geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | direct |
hc_produced | 0..1 HcProducedEnum |
Main hydrocarbon type produced from resource (i | direct |
hcr | 0..1 HcrEnum |
Main Hydrocarbon Resource type | direct |
hcr_fw_salinity | 0..1 String |
Original formation water salinity (prior to secondary recovery e | direct |
hcr_geol_age | 0..1 HcrGeolAgeEnum |
Geological age of hydrocarbon resource (Additional info: https://en | direct |
hcr_pressure | 0..1 String |
Original pressure of the hydrocarbon resource | direct |
hcr_temp | 0..1 String |
Original temperature of the hydrocarbon resource | direct |
iw_bt_date_well | 0..1 String |
Injection water breakthrough date per well following a secondary and/or terti... | direct |
iwf | 0..1 String |
Proportion of the produced fluids derived from injected water at the time of ... | direct |
lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | direct |
lithology | 0..1 LithologyEnum |
Hydrocarbon resource main lithology (Additional information: http://petrowiki | direct |
magnesium | 0..1 String |
Concentration of magnesium in the sample | direct |
misc_param | 0..1 String |
Any other measurement performed or parameter collected, that is not listed he... | direct |
nitrate | 0..1 String |
Concentration of nitrate in the sample | direct |
nitrite | 0..1 String |
Concentration of nitrite in the sample | direct |
org_count_qpcr_info | 0..1 String |
If qpcr was used for the cell count, the target gene name, the primer sequenc... | 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 |
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 |
potassium | 0..1 String |
Concentration of potassium in the sample | direct |
pour_point | 0..1 String |
Temperature at which a liquid becomes semi solid and loses its flow character... | direct |
pressure | 0..1 String |
Pressure to which the sample is subject to, in atmospheres | direct |
prod_rate | 0..1 String |
Oil and/or gas production rates per well (e | direct |
prod_start_date | 0..1 String |
Date of field's first production | direct |
reservoir | 0..1 String |
Name of the reservoir (e | direct |
resins_pc | 0..1 String |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | 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_collect_point | 0..1 SampCollectPointEnum |
Sampling point on the asset were sample was collected (e | direct |
samp_loc_corr_rate | 0..1 String |
Metal corrosion rate is the speed of metal deterioration due to environmental... | direct |
samp_mat_process | 0..1 String |
A brief description of any processing applied to the sample during or after r... | direct |
samp_preserv | 0..1 String |
Preservative added to the sample (e | 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 |
samp_subtype | 0..1 SampSubtypeEnum |
Name of sample sub-type | direct |
samp_transport_cond | 0..1 String |
Sample transport duration (in days or hrs) and temperature the sample was exp... | direct |
samp_type | 0..1 String |
The type of material from which the sample was obtained | direct |
samp_well_name | 0..1 String |
Name of the well (e | direct |
sample_link | 0..1 recommended String |
A unique identifier to assign parent-child, subsample, or sibling samples | direct |
saturates_pc | 0..1 String |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | 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 |
sulfate_fw | 0..1 String |
Original sulfate concentration in the hydrocarbon resource | direct |
sulfide | 0..1 String |
Concentration of sulfide in the sample | direct |
suspend_solids | 0..1 String |
Concentration of substances including a wide variety of material, such as sil... | direct |
tan | 0..1 String |
Total Acid Number (TAN) is a measurement of acidity that is determined by th... | direct |
temp | 0..1 String |
Temperature of the sample at the time of sampling | direct |
toluene | 0..1 String |
Concentration of toluene in the sample | direct |
tot_iron | 0..1 String |
Concentration of total iron in the sample | direct |
tot_nitro | 0..1 String |
Total nitrogen concentration of water samples, calculated by: total nitrogen ... | direct |
tot_phosp | 0..1 String |
Total phosphorus concentration in the sample, calculated by: total phosphorus... | direct |
tot_sulfur | 0..1 String |
Concentration of total sulfur in the sample | direct |
tvdss_of_hcr_press | 0..1 String |
True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... | direct |
tvdss_of_hcr_temp | 0..1 String |
True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... | direct |
vfa | 0..1 String |
Concentration of Volatile Fatty Acids in the sample | direct |
vfa_fw | 0..1 String |
Original volatile fatty acid concentration in the hydrocarbon resource | direct |
viscosity | 0..1 String |
A measure of oil's resistance to gradual deformation by shear stress or t... | direct |
water_cut | 0..1 String |
Current amount of water (%) in a produced fluid stream; or the average of the... | direct |
water_prod_rate | 0..1 String |
Water production rates per well (e | direct |
win | 0..1 String |
A unique identifier of a well or wellbore | direct |
xylene | 0..1 String |
Concentration of xylene in the sample | direct |
analysis_type | 1..* AnalysisTypeEnum |
Select all the data types associated or available for this biosample | DhMultiviewCommonColumnsMixin |
samp_name | 1..1 String |
A local identifier or name that for the material sample collected | DhMultiviewCommonColumnsMixin |
source_mat_id | 0..1 String |
A globally unique identifier assigned to the biological sample | DhMultiviewCommonColumnsMixin |
Identifier and Mapping Information
Annotations
property | value |
---|---|
excel_worksheet_name | hcr fluids swab |
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:HcrFluidsSwabsInterface |
native | nmdc_sub_schema:HcrFluidsSwabsInterface |
LinkML Source
Direct
name: HcrFluidsSwabsInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: hcr fluids swab
description: hcr_fluids_swabs dh_interface
title: Hcr Fluids Swabs
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slots:
- add_recov_method
- additional_info
- alkalinity
- alkalinity_method
- ammonium
- api
- aromatics_pc
- asphaltenes_pc
- basin
- benzene
- biocide
- biocide_admin_method
- calcium
- chem_administration
- chem_treat_method
- chem_treatment
- chloride
- collection_date
- density
- depos_env
- depth
- diss_carb_dioxide
- diss_inorg_carb
- diss_inorg_phosp
- diss_iron
- diss_org_carb
- diss_oxygen_fluid
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- elev
- env_broad_scale
- env_local_scale
- env_medium
- ethylbenzene
- experimental_factor
- field
- geo_loc_name
- hc_produced
- hcr
- hcr_fw_salinity
- hcr_geol_age
- hcr_pressure
- hcr_temp
- iw_bt_date_well
- iwf
- lat_lon
- lithology
- magnesium
- misc_param
- nitrate
- nitrite
- org_count_qpcr_info
- organism_count
- oxy_stat_samp
- ph
- ph_meth
- potassium
- pour_point
- pressure
- prod_rate
- prod_start_date
- reservoir
- resins_pc
- salinity
- samp_collec_device
- samp_collec_method
- samp_collect_point
- samp_loc_corr_rate
- samp_mat_process
- samp_preserv
- samp_size
- samp_store_dur
- samp_store_loc
- samp_store_temp
- samp_subtype
- samp_transport_cond
- samp_type
- samp_well_name
- sample_link
- saturates_pc
- size_frac
- sodium
- specific_ecosystem
- sulfate
- sulfate_fw
- sulfide
- suspend_solids
- tan
- temp
- toluene
- tot_iron
- tot_nitro
- tot_phosp
- tot_sulfur
- tvdss_of_hcr_press
- tvdss_of_hcr_temp
- vfa
- vfa_fw
- viscosity
- water_cut
- water_prod_rate
- win
- xylene
slot_usage:
add_recov_method:
name: add_recov_method
annotations:
expected_value:
tag: expected_value
value: enumeration;timestamp
occurrence:
tag: occurrence
value: '1'
description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed
for increase of hydrocarbon recovery from resource and start date for each one
of them. If "other" is specified, please propose entry in "additional info"
field
title: secondary and tertiary recovery methods and start date
examples:
- value: Polymer Addition;2018-06-21T14:30Z
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- secondary and tertiary recovery methods and start date
rank: 289
is_a: core field
slot_uri: MIXS:0001009
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
additional_info:
name: additional_info
annotations:
expected_value:
tag: expected_value
value: text
occurrence:
tag: occurrence
value: '1'
description: Information that doesn't fit anywhere else. Can also be used to propose
new entries for fields with controlled vocabulary
title: additional info
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- additional info
rank: 290
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000300
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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.*$
alkalinity_method:
name: alkalinity_method
annotations:
expected_value:
tag: expected_value
value: description of method
occurrence:
tag: occurrence
value: '1'
description: Method used for alkalinity measurement
title: alkalinity method
examples:
- value: titration
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkalinity method
rank: 218
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000298
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
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.*$
api:
name: api
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degrees API
occurrence:
tag: occurrence
value: '1'
description: 'API gravity is a measure of how heavy or light a petroleum liquid
is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.
31.1° API)'
title: API gravity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- API gravity
rank: 291
is_a: core field
slot_uri: MIXS:0000157
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
aromatics_pc:
name: aromatics_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: aromatics wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aromatics wt%
rank: 292
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000133
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
asphaltenes_pc:
name: asphaltenes_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: asphaltenes wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- asphaltenes wt%
rank: 293
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000135
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
basin:
name: basin
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the basin (e.g. Campos)
title: basin name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- basin name
rank: 294
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000290
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
benzene:
name: benzene
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 benzene in the sample
title: benzene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- benzene
rank: 295
is_a: core field
slot_uri: MIXS:0000153
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
biocide:
name: biocide
annotations:
expected_value:
tag: expected_value
value: name;name;timestamp
occurrence:
tag: occurrence
value: '1'
description: List of biocides (commercial name of product and supplier) and date
of administration
title: biocide administration
examples:
- value: ALPHA 1427;Baker Hughes;2008-01-23
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biocide administration
rank: 297
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001011
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
biocide_admin_method:
name: biocide_admin_method
annotations:
expected_value:
tag: expected_value
value: measurement value;frequency;duration;duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Method of biocide administration (dose, frequency, duration, time
elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3
days)
title: biocide administration method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biocide administration method
rank: 298
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'
slot_uri: MIXS:0000456
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
calcium:
name: calcium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of calcium in the sample
title: calcium
examples:
- value: 0.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- calcium
rank: 9
is_a: core field
slot_uri: MIXS:0000432
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chem_administration:
name: chem_administration
annotations:
expected_value:
tag: expected_value
value: CHEBI;timestamp
occurrence:
tag: occurrence
value: m
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
- value: agar [CHEBI:2509];2018-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 17
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
chem_treat_method:
name: chem_treat_method
annotations:
expected_value:
tag: expected_value
value: measurement value;frequency;duration;duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Method of chemical administration(dose, frequency, duration, time
elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1
hr; 0 days)
title: chemical treatment method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical treatment method
rank: 302
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'
slot_uri: MIXS:0000457
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
chem_treatment:
name: chem_treatment
annotations:
expected_value:
tag: expected_value
value: name;name;timestamp
occurrence:
tag: occurrence
value: '1'
description: List of chemical compounds administered upstream the sampling location
where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,
demulsifiers, and other production chemicals etc.). The commercial name of the
product and name of the supplier should be provided. The date of administration
should also be included
title: chemical treatment
examples:
- value: ACCENT 1125;DOW;2010-11-17
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical treatment
rank: 303
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001012
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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.*$
collection_date:
name: collection_date
annotations:
expected_value:
tag: expected_value
value: date and time
description: The date of sampling
title: collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
- Use modified term (amended definition)
examples:
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- collection date
rank: 3
is_a: environment field
string_serialization: '{date, arbitrary precision}'
slot_uri: MIXS:0000011
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
density:
name: density
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter, gram per cubic centimeter
occurrence:
tag: occurrence
value: '1'
description: Density of the sample, which is its mass per unit volume (aka volumetric
mass density)
title: density
examples:
- value: 1000 kilogram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- density
rank: 12
is_a: core field
slot_uri: MIXS:0000435
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
depos_env:
name: depos_env
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).
If "other" is specified, please propose entry in "additional info" field
title: depositional environment
examples:
- value: Continental - Alluvial
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depositional environment
rank: 304
is_a: core field
slot_uri: MIXS:0000992
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: depos_env_enum
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]+)?)?$
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_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_inorg_phosp:
name: diss_inorg_phosp
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: Concentration of dissolved inorganic phosphorus in the sample
title: dissolved inorganic phosphorus
examples:
- value: 56.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic phosphorus
rank: 224
is_a: core field
slot_uri: MIXS:0000106
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_iron:
name: diss_iron
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved iron in the sample
title: dissolved iron
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved iron
rank: 305
is_a: core field
slot_uri: MIXS:0000139
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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_oxygen_fluid:
name: diss_oxygen_fluid
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 in the oil field produced fluids
as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
title: dissolved oxygen in fluids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen in fluids
rank: 306
is_a: core field
slot_uri: MIXS:0000438
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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+ \[[a-zA-Z]{2,}:\d+\]$
ethylbenzene:
name: ethylbenzene
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 ethylbenzene in the sample
title: ethylbenzene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ethylbenzene
rank: 309
is_a: core field
slot_uri: MIXS:0000155
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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
field:
name: field
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the hydrocarbon field (e.g. Albacora)
title: field name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- field name
rank: 310
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000291
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
hc_produced:
name: hc_produced
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,
etc). If "other" is specified, please propose entry in "additional info" field
title: hydrocarbon type produced
examples:
- value: Gas
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon type produced
rank: 313
is_a: core field
slot_uri: MIXS:0000989
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hc_produced_enum
hcr:
name: hcr
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR
defined as a natural environmental feature containing large amounts of hydrocarbons
at high concentrations potentially suitable for commercial exploitation. This
term should not be confused with the Hydrocarbon Occurrence term which also
includes hydrocarbon-rich environments with currently limited commercial interest
such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose
entry in "additional info" field
title: hydrocarbon resource type
examples:
- value: Oil Sand
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource type
rank: 314
is_a: core field
slot_uri: MIXS:0000988
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hcr_enum
hcr_fw_salinity:
name: hcr_fw_salinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original formation water salinity (prior to secondary recovery e.g.
Waterflooding) expressed as TDS
title: formation water salinity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- formation water salinity
rank: 315
is_a: core field
slot_uri: MIXS:0000406
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
hcr_geol_age:
name: hcr_geol_age
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).
If "other" is specified, please propose entry in "additional info" field'
title: hydrocarbon resource geological age
examples:
- value: Silurian
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource geological age
rank: 316
is_a: core field
slot_uri: MIXS:0000993
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hcr_geol_age_enum
hcr_pressure:
name: hcr_pressure
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: atmosphere, kilopascal
occurrence:
tag: occurrence
value: '1'
description: Original pressure of the hydrocarbon resource
title: hydrocarbon resource original pressure
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource original pressure
rank: 317
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000395
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
hcr_temp:
name: hcr_temp
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Original temperature of the hydrocarbon resource
title: hydrocarbon resource original temperature
examples:
- value: 150-295 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource original temperature
rank: 318
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000393
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
iw_bt_date_well:
name: iw_bt_date_well
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: Injection water breakthrough date per well following a secondary
and/or tertiary recovery
title: injection water breakthrough date of specific well
examples:
- value: '2018-05-11'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- injection water breakthrough date of specific well
rank: 334
is_a: core field
slot_uri: MIXS:0001010
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
iwf:
name: iwf
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: Proportion of the produced fluids derived from injected water at
the time of sampling. (e.g. 87%)
title: injection water fraction
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- injection water fraction
rank: 335
is_a: core field
slot_uri: MIXS:0000455
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
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+)?)$
lithology:
name: lithology
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).
If "other" is specified, please propose entry in "additional info" field'
title: lithology
examples:
- value: Volcanic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- lithology
rank: 336
is_a: core field
slot_uri: MIXS:0000990
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: lithology_enum
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.*$
misc_param:
name: misc_param
annotations:
expected_value:
tag: expected_value
value: parameter name;measurement value
occurrence:
tag: occurrence
value: m
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- miscellaneous parameter
rank: 23
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
nitrate:
name: nitrate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrate
rank: 26
is_a: core field
slot_uri: MIXS:0000425
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitrite:
name: nitrite
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrite in the sample
title: nitrite
examples:
- value: 0.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrite
rank: 27
is_a: core field
slot_uri: MIXS:0000426
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_count_qpcr_info:
name: org_count_qpcr_info
annotations:
expected_value:
tag: expected_value
value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial
denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes; total cycles
preferred_unit:
tag: preferred_unit
value: number of cells per gram (or ml or cm^2)
occurrence:
tag: occurrence
value: '1'
description: 'If qpcr was used for the cell count, the target gene name, the primer
sequence and the cycling conditions should also be provided. (Example: 16S rrna;
FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;
annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;
30 cycles)'
title: organism count qPCR information
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organism count qPCR information
rank: 337
is_a: core field
string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes; total cycles'
slot_uri: MIXS:0000099
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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
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
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.*$
pour_point:
name: pour_point
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 a liquid becomes semi solid and loses its flow
characteristics. In crude oil a high pour point is generally associated with
a high paraffin content, typically found in crude deriving from a larger proportion
of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'
title: pour point
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pour point
rank: 341
is_a: core field
slot_uri: MIXS:0000127
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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.*$
prod_rate:
name: prod_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Oil and/or gas production rates per well (e.g. 524 m3 / day)
title: production rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- production rate
rank: 344
is_a: core field
slot_uri: MIXS:0000452
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
prod_start_date:
name: prod_start_date
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: Date of field's first production
title: production start date
examples:
- value: '2018-05-11'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- production start date
rank: 345
is_a: core field
slot_uri: MIXS:0001008
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
reservoir:
name: reservoir
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the reservoir (e.g. Carapebus)
title: reservoir name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- reservoir name
rank: 347
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000303
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
resins_pc:
name: resins_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: resins wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- resins wt%
rank: 348
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000134
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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_collect_point:
name: samp_collect_point
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Sampling point on the asset were sample was collected (e.g. Wellhead,
storage tank, separator, etc). If "other" is specified, please propose entry
in "additional info" field
title: sample collection point
examples:
- value: well
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection point
rank: 349
is_a: core field
slot_uri: MIXS:0001015
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: samp_collect_point_enum
samp_loc_corr_rate:
name: samp_loc_corr_rate
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: millimeter per year
occurrence:
tag: occurrence
value: '1'
description: Metal corrosion rate is the speed of metal deterioration due to environmental
conditions. As environmental conditions change corrosion rates change accordingly.
Therefore, long term corrosion rates are generally more informative than short
term rates and for that reason they are preferred during reporting. In the case
of suspected MIC, corrosion rate measurements at the time of sampling might
provide insights into the involvement of certain microbial community members
in MIC as well as potential microbial interplays
title: corrosion rate at sample location
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- corrosion rate at sample location
rank: 350
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000136
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_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_preserv:
name: samp_preserv
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: milliliter
occurrence:
tag: occurrence
value: '1'
description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,
etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
title: preservative added to sample
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- preservative added to sample
rank: 352
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000463
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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.*$
samp_subtype:
name: samp_subtype
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Name of sample sub-type. For example if "sample type" is "Produced
Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified,
please propose entry in "additional info" field
title: sample subtype
examples:
- value: biofilm
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample subtype
rank: 354
is_a: core field
slot_uri: MIXS:0000999
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: samp_subtype_enum
samp_transport_cond:
name: samp_transport_cond
annotations:
expected_value:
tag: expected_value
value: measurement value;measurement value
preferred_unit:
tag: preferred_unit
value: days;degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Sample transport duration (in days or hrs) and temperature the sample
was exposed to (e.g. 5.5 days; 20 °C)
title: sample transport conditions
examples:
- value: 5 days;-20 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample transport conditions
rank: 355
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000410
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
samp_type:
name: samp_type
annotations:
expected_value:
tag: expected_value
value: GENEPIO:0001246
occurrence:
tag: occurrence
value: '1'
description: The type of material from which the sample was obtained. For the
Hydrocarbon package, samples include types like core, rock trimmings, drill
cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,
produced water, injected water, swabs, etc. For the Food Package, samples are
usually categorized as food, body products or tissues, or environmental material.
This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
title: sample type
examples:
- value: built environment sample [GENEPIO:0001248]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample type
rank: 357
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000998
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
samp_well_name:
name: samp_well_name
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the well (e.g. BXA1123) where sample was taken
title: sample well name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample well name
rank: 358
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000296
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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]+'
saturates_pc:
name: saturates_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: saturates wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- saturates wt%
rank: 359
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000131
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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.*$
sulfate_fw:
name: sulfate_fw
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original sulfate concentration in the hydrocarbon resource
title: sulfate in formation water
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfate in formation water
rank: 370
is_a: core field
slot_uri: MIXS:0000407
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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.*$
suspend_solids:
name: suspend_solids
annotations:
expected_value:
tag: expected_value
value: suspended solid name;measurement value
preferred_unit:
tag: preferred_unit
value: gram, microgram, milligram per liter, mole per liter, gram per liter,
part per million
occurrence:
tag: occurrence
value: m
description: Concentration of substances including a wide variety of material,
such as silt, decaying plant and animal matter; can include multiple substances
title: suspended solids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- suspended solids
rank: 372
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000150
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WastewaterSludgeInterface
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]+)$
tan:
name: tan
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total Acid Number (TAN) is a measurement of acidity that is determined
by the amount of potassium hydroxide in milligrams that is needed to neutralize
the acids in one gram of oil. It is an important quality measurement of crude
oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'
title: total acid number
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total acid number
rank: 373
is_a: core field
slot_uri: MIXS:0000120
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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.*$
toluene:
name: toluene
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 toluene in the sample
title: toluene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- toluene
rank: 375
is_a: core field
slot_uri: MIXS:0000154
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_iron:
name: tot_iron
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, milligram per kilogram
occurrence:
tag: occurrence
value: '1'
description: Concentration of total iron in the sample
title: total iron
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total iron
rank: 376
is_a: core field
slot_uri: MIXS:0000105
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_nitro:
name: tot_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total nitrogen concentration of water samples, calculated by: total
nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
without filtering, reported as nitrogen'
title: total nitrogen concentration
examples:
- value: 50 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total nitrogen concentration
rank: 377
is_a: core field
slot_uri: MIXS:0000102
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_phosp:
name: tot_phosp
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: 'Total phosphorus concentration in the sample, calculated by: total
phosphorus = total dissolved phosphorus + particulate phosphorus'
title: total phosphorus
examples:
- value: 0.03 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total phosphorus
rank: 52
is_a: core field
slot_uri: MIXS:0000117
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_sulfur:
name: tot_sulfur
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 total sulfur in the sample
title: total sulfur
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total sulfur
rank: 379
is_a: core field
slot_uri: MIXS:0000419
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tvdss_of_hcr_press:
name: tvdss_of_hcr_press
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
the original pressure was measured (e.g. 1578 m).
title: depth (TVDSS) of hydrocarbon resource pressure
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth (TVDSS) of hydrocarbon resource pressure
rank: 380
is_a: core field
slot_uri: MIXS:0000397
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tvdss_of_hcr_temp:
name: tvdss_of_hcr_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
the original temperature was measured (e.g. 1345 m).
title: depth (TVDSS) of hydrocarbon resource temperature
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth (TVDSS) of hydrocarbon resource temperature
rank: 381
is_a: core field
slot_uri: MIXS:0000394
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
vfa:
name: vfa
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 Volatile Fatty Acids in the sample
title: volatile fatty acids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- volatile fatty acids
rank: 382
is_a: core field
slot_uri: MIXS:0000152
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
vfa_fw:
name: vfa_fw
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original volatile fatty acid concentration in the hydrocarbon resource
title: vfa in formation water
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- vfa in formation water
rank: 383
is_a: core field
slot_uri: MIXS:0000408
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
viscosity:
name: viscosity
annotations:
expected_value:
tag: expected_value
value: measurement value;measurement value
preferred_unit:
tag: preferred_unit
value: cP at degree Celsius
occurrence:
tag: occurrence
value: '1'
description: A measure of oil's resistance to gradual deformation by shear stress or tensile
stress (e.g. 3.5 cp; 100 °C)
title: viscosity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- viscosity
rank: 384
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000126
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
water_cut:
name: water_cut
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: Current amount of water (%) in a produced fluid stream; or the average
of the combined streams
title: water cut
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water cut
rank: 386
is_a: core field
slot_uri: MIXS:0000454
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_prod_rate:
name: water_prod_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Water production rates per well (e.g. 987 m3 / day)
title: water production rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water production rate
rank: 387
is_a: core field
slot_uri: MIXS:0000453
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
win:
name: win
annotations:
expected_value:
tag: expected_value
value: text
occurrence:
tag: occurrence
value: '1'
description: 'A unique identifier of a well or wellbore. This is part of the Global
Framework for Well Identification initiative which is compiled by the Professional
Petroleum Data Management Association (PPDM) in an effort to improve well identification
systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'
title: well identification number
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- well identification number
rank: 388
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000297
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
xylene:
name: xylene
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 xylene in the sample
title: xylene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- xylene
rank: 389
is_a: core field
slot_uri: MIXS:0000156
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
horizon_meth:
name: horizon_meth
title: horizon method
Induced
name: HcrFluidsSwabsInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: hcr fluids swab
description: hcr_fluids_swabs dh_interface
title: Hcr Fluids Swabs
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slot_usage:
add_recov_method:
name: add_recov_method
annotations:
expected_value:
tag: expected_value
value: enumeration;timestamp
occurrence:
tag: occurrence
value: '1'
description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed
for increase of hydrocarbon recovery from resource and start date for each one
of them. If "other" is specified, please propose entry in "additional info"
field
title: secondary and tertiary recovery methods and start date
examples:
- value: Polymer Addition;2018-06-21T14:30Z
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- secondary and tertiary recovery methods and start date
rank: 289
is_a: core field
slot_uri: MIXS:0001009
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
additional_info:
name: additional_info
annotations:
expected_value:
tag: expected_value
value: text
occurrence:
tag: occurrence
value: '1'
description: Information that doesn't fit anywhere else. Can also be used to propose
new entries for fields with controlled vocabulary
title: additional info
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- additional info
rank: 290
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000300
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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.*$
alkalinity_method:
name: alkalinity_method
annotations:
expected_value:
tag: expected_value
value: description of method
occurrence:
tag: occurrence
value: '1'
description: Method used for alkalinity measurement
title: alkalinity method
examples:
- value: titration
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkalinity method
rank: 218
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000298
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
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.*$
api:
name: api
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degrees API
occurrence:
tag: occurrence
value: '1'
description: 'API gravity is a measure of how heavy or light a petroleum liquid
is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.
31.1° API)'
title: API gravity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- API gravity
rank: 291
is_a: core field
slot_uri: MIXS:0000157
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
aromatics_pc:
name: aromatics_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: aromatics wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aromatics wt%
rank: 292
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000133
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
asphaltenes_pc:
name: asphaltenes_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: asphaltenes wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- asphaltenes wt%
rank: 293
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000135
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
basin:
name: basin
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the basin (e.g. Campos)
title: basin name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- basin name
rank: 294
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000290
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
benzene:
name: benzene
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 benzene in the sample
title: benzene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- benzene
rank: 295
is_a: core field
slot_uri: MIXS:0000153
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
biocide:
name: biocide
annotations:
expected_value:
tag: expected_value
value: name;name;timestamp
occurrence:
tag: occurrence
value: '1'
description: List of biocides (commercial name of product and supplier) and date
of administration
title: biocide administration
examples:
- value: ALPHA 1427;Baker Hughes;2008-01-23
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biocide administration
rank: 297
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001011
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
biocide_admin_method:
name: biocide_admin_method
annotations:
expected_value:
tag: expected_value
value: measurement value;frequency;duration;duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Method of biocide administration (dose, frequency, duration, time
elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3
days)
title: biocide administration method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biocide administration method
rank: 298
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'
slot_uri: MIXS:0000456
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
calcium:
name: calcium
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of calcium in the sample
title: calcium
examples:
- value: 0.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- calcium
rank: 9
is_a: core field
slot_uri: MIXS:0000432
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chem_administration:
name: chem_administration
annotations:
expected_value:
tag: expected_value
value: CHEBI;timestamp
occurrence:
tag: occurrence
value: m
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
- value: agar [CHEBI:2509];2018-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 17
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
chem_treat_method:
name: chem_treat_method
annotations:
expected_value:
tag: expected_value
value: measurement value;frequency;duration;duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Method of chemical administration(dose, frequency, duration, time
elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1
hr; 0 days)
title: chemical treatment method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical treatment method
rank: 302
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'
slot_uri: MIXS:0000457
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
chem_treatment:
name: chem_treatment
annotations:
expected_value:
tag: expected_value
value: name;name;timestamp
occurrence:
tag: occurrence
value: '1'
description: List of chemical compounds administered upstream the sampling location
where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,
demulsifiers, and other production chemicals etc.). The commercial name of the
product and name of the supplier should be provided. The date of administration
should also be included
title: chemical treatment
examples:
- value: ACCENT 1125;DOW;2010-11-17
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical treatment
rank: 303
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001012
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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.*$
collection_date:
name: collection_date
annotations:
expected_value:
tag: expected_value
value: date and time
description: The date of sampling
title: collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only
- Use modified term (amended definition)
examples:
- value: '2021-04-15'
- value: 2021-04
- value: '2021'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- collection date
rank: 3
is_a: environment field
string_serialization: '{date, arbitrary precision}'
slot_uri: MIXS:0000011
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
density:
name: density
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter, gram per cubic centimeter
occurrence:
tag: occurrence
value: '1'
description: Density of the sample, which is its mass per unit volume (aka volumetric
mass density)
title: density
examples:
- value: 1000 kilogram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- density
rank: 12
is_a: core field
slot_uri: MIXS:0000435
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
depos_env:
name: depos_env
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).
If "other" is specified, please propose entry in "additional info" field
title: depositional environment
examples:
- value: Continental - Alluvial
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depositional environment
rank: 304
is_a: core field
slot_uri: MIXS:0000992
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: depos_env_enum
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]+)?)?$
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_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_inorg_phosp:
name: diss_inorg_phosp
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: Concentration of dissolved inorganic phosphorus in the sample
title: dissolved inorganic phosphorus
examples:
- value: 56.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic phosphorus
rank: 224
is_a: core field
slot_uri: MIXS:0000106
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_iron:
name: diss_iron
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved iron in the sample
title: dissolved iron
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved iron
rank: 305
is_a: core field
slot_uri: MIXS:0000139
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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_oxygen_fluid:
name: diss_oxygen_fluid
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 in the oil field produced fluids
as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
title: dissolved oxygen in fluids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen in fluids
rank: 306
is_a: core field
slot_uri: MIXS:0000438
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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+ \[[a-zA-Z]{2,}:\d+\]$
ethylbenzene:
name: ethylbenzene
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 ethylbenzene in the sample
title: ethylbenzene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ethylbenzene
rank: 309
is_a: core field
slot_uri: MIXS:0000155
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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
field:
name: field
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the hydrocarbon field (e.g. Albacora)
title: field name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- field name
rank: 310
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000291
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
hc_produced:
name: hc_produced
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,
etc). If "other" is specified, please propose entry in "additional info" field
title: hydrocarbon type produced
examples:
- value: Gas
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon type produced
rank: 313
is_a: core field
slot_uri: MIXS:0000989
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hc_produced_enum
hcr:
name: hcr
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR
defined as a natural environmental feature containing large amounts of hydrocarbons
at high concentrations potentially suitable for commercial exploitation. This
term should not be confused with the Hydrocarbon Occurrence term which also
includes hydrocarbon-rich environments with currently limited commercial interest
such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose
entry in "additional info" field
title: hydrocarbon resource type
examples:
- value: Oil Sand
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource type
rank: 314
is_a: core field
slot_uri: MIXS:0000988
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hcr_enum
hcr_fw_salinity:
name: hcr_fw_salinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original formation water salinity (prior to secondary recovery e.g.
Waterflooding) expressed as TDS
title: formation water salinity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- formation water salinity
rank: 315
is_a: core field
slot_uri: MIXS:0000406
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
hcr_geol_age:
name: hcr_geol_age
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).
If "other" is specified, please propose entry in "additional info" field'
title: hydrocarbon resource geological age
examples:
- value: Silurian
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource geological age
rank: 316
is_a: core field
slot_uri: MIXS:0000993
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hcr_geol_age_enum
hcr_pressure:
name: hcr_pressure
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: atmosphere, kilopascal
occurrence:
tag: occurrence
value: '1'
description: Original pressure of the hydrocarbon resource
title: hydrocarbon resource original pressure
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource original pressure
rank: 317
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000395
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
hcr_temp:
name: hcr_temp
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Original temperature of the hydrocarbon resource
title: hydrocarbon resource original temperature
examples:
- value: 150-295 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource original temperature
rank: 318
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000393
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
iw_bt_date_well:
name: iw_bt_date_well
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: Injection water breakthrough date per well following a secondary
and/or tertiary recovery
title: injection water breakthrough date of specific well
examples:
- value: '2018-05-11'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- injection water breakthrough date of specific well
rank: 334
is_a: core field
slot_uri: MIXS:0001010
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
iwf:
name: iwf
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: Proportion of the produced fluids derived from injected water at
the time of sampling. (e.g. 87%)
title: injection water fraction
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- injection water fraction
rank: 335
is_a: core field
slot_uri: MIXS:0000455
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
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+)?)$
lithology:
name: lithology
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).
If "other" is specified, please propose entry in "additional info" field'
title: lithology
examples:
- value: Volcanic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- lithology
rank: 336
is_a: core field
slot_uri: MIXS:0000990
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: lithology_enum
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.*$
misc_param:
name: misc_param
annotations:
expected_value:
tag: expected_value
value: parameter name;measurement value
occurrence:
tag: occurrence
value: m
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- miscellaneous parameter
rank: 23
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: false
owner: Biosample
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
nitrate:
name: nitrate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrate
rank: 26
is_a: core field
slot_uri: MIXS:0000425
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
nitrite:
name: nitrite
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrite in the sample
title: nitrite
examples:
- value: 0.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrite
rank: 27
is_a: core field
slot_uri: MIXS:0000426
multivalued: false
owner: Biosample
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_count_qpcr_info:
name: org_count_qpcr_info
annotations:
expected_value:
tag: expected_value
value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial
denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes; total cycles
preferred_unit:
tag: preferred_unit
value: number of cells per gram (or ml or cm^2)
occurrence:
tag: occurrence
value: '1'
description: 'If qpcr was used for the cell count, the target gene name, the primer
sequence and the cycling conditions should also be provided. (Example: 16S rrna;
FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;
annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;
30 cycles)'
title: organism count qPCR information
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organism count qPCR information
rank: 337
is_a: core field
string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes; total cycles'
slot_uri: MIXS:0000099
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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
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
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.*$
pour_point:
name: pour_point
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 a liquid becomes semi solid and loses its flow
characteristics. In crude oil a high pour point is generally associated with
a high paraffin content, typically found in crude deriving from a larger proportion
of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'
title: pour point
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pour point
rank: 341
is_a: core field
slot_uri: MIXS:0000127
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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.*$
prod_rate:
name: prod_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Oil and/or gas production rates per well (e.g. 524 m3 / day)
title: production rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- production rate
rank: 344
is_a: core field
slot_uri: MIXS:0000452
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
prod_start_date:
name: prod_start_date
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: Date of field's first production
title: production start date
examples:
- value: '2018-05-11'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- production start date
rank: 345
is_a: core field
slot_uri: MIXS:0001008
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
reservoir:
name: reservoir
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the reservoir (e.g. Carapebus)
title: reservoir name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- reservoir name
rank: 347
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000303
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
resins_pc:
name: resins_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: resins wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- resins wt%
rank: 348
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000134
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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_collect_point:
name: samp_collect_point
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Sampling point on the asset were sample was collected (e.g. Wellhead,
storage tank, separator, etc). If "other" is specified, please propose entry
in "additional info" field
title: sample collection point
examples:
- value: well
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection point
rank: 349
is_a: core field
slot_uri: MIXS:0001015
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: samp_collect_point_enum
samp_loc_corr_rate:
name: samp_loc_corr_rate
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: millimeter per year
occurrence:
tag: occurrence
value: '1'
description: Metal corrosion rate is the speed of metal deterioration due to environmental
conditions. As environmental conditions change corrosion rates change accordingly.
Therefore, long term corrosion rates are generally more informative than short
term rates and for that reason they are preferred during reporting. In the case
of suspected MIC, corrosion rate measurements at the time of sampling might
provide insights into the involvement of certain microbial community members
in MIC as well as potential microbial interplays
title: corrosion rate at sample location
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- corrosion rate at sample location
rank: 350
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000136
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_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_preserv:
name: samp_preserv
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: milliliter
occurrence:
tag: occurrence
value: '1'
description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,
etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
title: preservative added to sample
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- preservative added to sample
rank: 352
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000463
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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.*$
samp_subtype:
name: samp_subtype
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Name of sample sub-type. For example if "sample type" is "Produced
Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified,
please propose entry in "additional info" field
title: sample subtype
examples:
- value: biofilm
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample subtype
rank: 354
is_a: core field
slot_uri: MIXS:0000999
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: samp_subtype_enum
samp_transport_cond:
name: samp_transport_cond
annotations:
expected_value:
tag: expected_value
value: measurement value;measurement value
preferred_unit:
tag: preferred_unit
value: days;degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Sample transport duration (in days or hrs) and temperature the sample
was exposed to (e.g. 5.5 days; 20 °C)
title: sample transport conditions
examples:
- value: 5 days;-20 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample transport conditions
rank: 355
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000410
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
samp_type:
name: samp_type
annotations:
expected_value:
tag: expected_value
value: GENEPIO:0001246
occurrence:
tag: occurrence
value: '1'
description: The type of material from which the sample was obtained. For the
Hydrocarbon package, samples include types like core, rock trimmings, drill
cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,
produced water, injected water, swabs, etc. For the Food Package, samples are
usually categorized as food, body products or tissues, or environmental material.
This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
title: sample type
examples:
- value: built environment sample [GENEPIO:0001248]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample type
rank: 357
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000998
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
samp_well_name:
name: samp_well_name
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the well (e.g. BXA1123) where sample was taken
title: sample well name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample well name
rank: 358
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000296
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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]+'
saturates_pc:
name: saturates_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: saturates wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- saturates wt%
rank: 359
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000131
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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.*$
sulfate_fw:
name: sulfate_fw
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original sulfate concentration in the hydrocarbon resource
title: sulfate in formation water
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfate in formation water
rank: 370
is_a: core field
slot_uri: MIXS:0000407
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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.*$
suspend_solids:
name: suspend_solids
annotations:
expected_value:
tag: expected_value
value: suspended solid name;measurement value
preferred_unit:
tag: preferred_unit
value: gram, microgram, milligram per liter, mole per liter, gram per liter,
part per million
occurrence:
tag: occurrence
value: m
description: Concentration of substances including a wide variety of material,
such as silt, decaying plant and animal matter; can include multiple substances
title: suspended solids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- suspended solids
rank: 372
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000150
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WastewaterSludgeInterface
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]+)$
tan:
name: tan
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total Acid Number (TAN) is a measurement of acidity that is determined
by the amount of potassium hydroxide in milligrams that is needed to neutralize
the acids in one gram of oil. It is an important quality measurement of crude
oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'
title: total acid number
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total acid number
rank: 373
is_a: core field
slot_uri: MIXS:0000120
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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.*$
toluene:
name: toluene
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 toluene in the sample
title: toluene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- toluene
rank: 375
is_a: core field
slot_uri: MIXS:0000154
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_iron:
name: tot_iron
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, milligram per kilogram
occurrence:
tag: occurrence
value: '1'
description: Concentration of total iron in the sample
title: total iron
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total iron
rank: 376
is_a: core field
slot_uri: MIXS:0000105
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_nitro:
name: tot_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total nitrogen concentration of water samples, calculated by: total
nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
without filtering, reported as nitrogen'
title: total nitrogen concentration
examples:
- value: 50 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total nitrogen concentration
rank: 377
is_a: core field
slot_uri: MIXS:0000102
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_phosp:
name: tot_phosp
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: 'Total phosphorus concentration in the sample, calculated by: total
phosphorus = total dissolved phosphorus + particulate phosphorus'
title: total phosphorus
examples:
- value: 0.03 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total phosphorus
rank: 52
is_a: core field
slot_uri: MIXS:0000117
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_sulfur:
name: tot_sulfur
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 total sulfur in the sample
title: total sulfur
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total sulfur
rank: 379
is_a: core field
slot_uri: MIXS:0000419
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tvdss_of_hcr_press:
name: tvdss_of_hcr_press
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
the original pressure was measured (e.g. 1578 m).
title: depth (TVDSS) of hydrocarbon resource pressure
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth (TVDSS) of hydrocarbon resource pressure
rank: 380
is_a: core field
slot_uri: MIXS:0000397
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tvdss_of_hcr_temp:
name: tvdss_of_hcr_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
the original temperature was measured (e.g. 1345 m).
title: depth (TVDSS) of hydrocarbon resource temperature
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth (TVDSS) of hydrocarbon resource temperature
rank: 381
is_a: core field
slot_uri: MIXS:0000394
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
vfa:
name: vfa
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 Volatile Fatty Acids in the sample
title: volatile fatty acids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- volatile fatty acids
rank: 382
is_a: core field
slot_uri: MIXS:0000152
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
vfa_fw:
name: vfa_fw
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original volatile fatty acid concentration in the hydrocarbon resource
title: vfa in formation water
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- vfa in formation water
rank: 383
is_a: core field
slot_uri: MIXS:0000408
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
viscosity:
name: viscosity
annotations:
expected_value:
tag: expected_value
value: measurement value;measurement value
preferred_unit:
tag: preferred_unit
value: cP at degree Celsius
occurrence:
tag: occurrence
value: '1'
description: A measure of oil's resistance to gradual deformation by shear stress or tensile
stress (e.g. 3.5 cp; 100 °C)
title: viscosity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- viscosity
rank: 384
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000126
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
water_cut:
name: water_cut
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: Current amount of water (%) in a produced fluid stream; or the average
of the combined streams
title: water cut
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water cut
rank: 386
is_a: core field
slot_uri: MIXS:0000454
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_prod_rate:
name: water_prod_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Water production rates per well (e.g. 987 m3 / day)
title: water production rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water production rate
rank: 387
is_a: core field
slot_uri: MIXS:0000453
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
win:
name: win
annotations:
expected_value:
tag: expected_value
value: text
occurrence:
tag: occurrence
value: '1'
description: 'A unique identifier of a well or wellbore. This is part of the Global
Framework for Well Identification initiative which is compiled by the Professional
Petroleum Data Management Association (PPDM) in an effort to improve well identification
systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'
title: well identification number
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- well identification number
rank: 388
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000297
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
xylene:
name: xylene
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 xylene in the sample
title: xylene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- xylene
rank: 389
is_a: core field
slot_uri: MIXS:0000156
multivalued: false
owner: Biosample
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
horizon_meth:
name: horizon_meth
title: horizon method
attributes:
add_recov_method:
name: add_recov_method
annotations:
expected_value:
tag: expected_value
value: enumeration;timestamp
occurrence:
tag: occurrence
value: '1'
description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed
for increase of hydrocarbon recovery from resource and start date for each one
of them. If "other" is specified, please propose entry in "additional info"
field
title: secondary and tertiary recovery methods and start date
examples:
- value: Polymer Addition;2018-06-21T14:30Z
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- secondary and tertiary recovery methods and start date
rank: 289
is_a: core field
slot_uri: MIXS:0001009
multivalued: false
alias: add_recov_method
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
additional_info:
name: additional_info
annotations:
expected_value:
tag: expected_value
value: text
occurrence:
tag: occurrence
value: '1'
description: Information that doesn't fit anywhere else. Can also be used to propose
new entries for fields with controlled vocabulary
title: additional info
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- additional info
rank: 290
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000300
multivalued: false
alias: additional_info
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
alkalinity_method:
name: alkalinity_method
annotations:
expected_value:
tag: expected_value
value: description of method
occurrence:
tag: occurrence
value: '1'
description: Method used for alkalinity measurement
title: alkalinity method
examples:
- value: titration
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkalinity method
rank: 218
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000298
multivalued: false
alias: alkalinity_method
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
api:
name: api
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degrees API
occurrence:
tag: occurrence
value: '1'
description: 'API gravity is a measure of how heavy or light a petroleum liquid
is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.
31.1° API)'
title: API gravity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- API gravity
rank: 291
is_a: core field
slot_uri: MIXS:0000157
multivalued: false
alias: api
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
aromatics_pc:
name: aromatics_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: aromatics wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aromatics wt%
rank: 292
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000133
multivalued: false
alias: aromatics_pc
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
asphaltenes_pc:
name: asphaltenes_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: asphaltenes wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- asphaltenes wt%
rank: 293
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000135
multivalued: false
alias: asphaltenes_pc
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
basin:
name: basin
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the basin (e.g. Campos)
title: basin name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- basin name
rank: 294
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000290
multivalued: false
alias: basin
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
benzene:
name: benzene
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 benzene in the sample
title: benzene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- benzene
rank: 295
is_a: core field
slot_uri: MIXS:0000153
multivalued: false
alias: benzene
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
biocide:
name: biocide
annotations:
expected_value:
tag: expected_value
value: name;name;timestamp
occurrence:
tag: occurrence
value: '1'
description: List of biocides (commercial name of product and supplier) and date
of administration
title: biocide administration
examples:
- value: ALPHA 1427;Baker Hughes;2008-01-23
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biocide administration
rank: 297
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001011
multivalued: false
alias: biocide
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
biocide_admin_method:
name: biocide_admin_method
annotations:
expected_value:
tag: expected_value
value: measurement value;frequency;duration;duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Method of biocide administration (dose, frequency, duration, time
elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3
days)
title: biocide administration method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biocide administration method
rank: 298
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'
slot_uri: MIXS:0000456
multivalued: false
alias: biocide_admin_method
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
chem_administration:
name: chem_administration
annotations:
expected_value:
tag: expected_value
value: CHEBI;timestamp
occurrence:
tag: occurrence
value: m
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
examples:
- value: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22
- value: agar [CHEBI:2509];2018-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 17
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: false
alias: chem_administration
owner: HcrFluidsSwabsInterface
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)?)?)?)?$
chem_treat_method:
name: chem_treat_method
annotations:
expected_value:
tag: expected_value
value: measurement value;frequency;duration;duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Method of chemical administration(dose, frequency, duration, time
elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1
hr; 0 days)
title: chemical treatment method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical treatment method
rank: 302
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'
slot_uri: MIXS:0000457
multivalued: false
alias: chem_treat_method
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
chem_treatment:
name: chem_treatment
annotations:
expected_value:
tag: expected_value
value: name;name;timestamp
occurrence:
tag: occurrence
value: '1'
description: List of chemical compounds administered upstream the sampling location
where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,
demulsifiers, and other production chemicals etc.). The commercial name of the
product and name of the supplier should be provided. The date of administration
should also be included
title: chemical treatment
examples:
- value: ACCENT 1125;DOW;2010-11-17
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical treatment
rank: 303
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001012
multivalued: false
alias: chem_treatment
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- 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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
required: true
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
density:
name: density
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter, gram per cubic centimeter
occurrence:
tag: occurrence
value: '1'
description: Density of the sample, which is its mass per unit volume (aka volumetric
mass density)
title: density
examples:
- value: 1000 kilogram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- density
rank: 12
is_a: core field
slot_uri: MIXS:0000435
multivalued: false
alias: density
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
depos_env:
name: depos_env
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).
If "other" is specified, please propose entry in "additional info" field
title: depositional environment
examples:
- value: Continental - Alluvial
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depositional environment
rank: 304
is_a: core field
slot_uri: MIXS:0000992
multivalued: false
alias: depos_env
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: depos_env_enum
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: HcrFluidsSwabsInterface
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]+)?)?$
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- 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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_inorg_phosp:
name: diss_inorg_phosp
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: Concentration of dissolved inorganic phosphorus in the sample
title: dissolved inorganic phosphorus
examples:
- value: 56.5 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic phosphorus
rank: 224
is_a: core field
slot_uri: MIXS:0000106
multivalued: false
alias: diss_inorg_phosp
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_iron:
name: diss_iron
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved iron in the sample
title: dissolved iron
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved iron
rank: 305
is_a: core field
slot_uri: MIXS:0000139
multivalued: false
alias: diss_iron
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
diss_oxygen_fluid:
name: diss_oxygen_fluid
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 in the oil field produced fluids
as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
title: dissolved oxygen in fluids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen in fluids
rank: 306
is_a: core field
slot_uri: MIXS:0000438
multivalued: false
alias: diss_oxygen_fluid
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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+ \[[a-zA-Z]{2,}:\d+\]$
ethylbenzene:
name: ethylbenzene
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 ethylbenzene in the sample
title: ethylbenzene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ethylbenzene
rank: 309
is_a: core field
slot_uri: MIXS:0000155
multivalued: false
alias: ethylbenzene
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
field:
name: field
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the hydrocarbon field (e.g. Albacora)
title: field name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- field name
rank: 310
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000291
multivalued: false
alias: field
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_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: HcrFluidsSwabsInterface
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: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$'
hc_produced:
name: hc_produced
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,
etc). If "other" is specified, please propose entry in "additional info" field
title: hydrocarbon type produced
examples:
- value: Gas
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon type produced
rank: 313
is_a: core field
slot_uri: MIXS:0000989
multivalued: false
alias: hc_produced
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hc_produced_enum
hcr:
name: hcr
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR
defined as a natural environmental feature containing large amounts of hydrocarbons
at high concentrations potentially suitable for commercial exploitation. This
term should not be confused with the Hydrocarbon Occurrence term which also
includes hydrocarbon-rich environments with currently limited commercial interest
such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose
entry in "additional info" field
title: hydrocarbon resource type
examples:
- value: Oil Sand
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource type
rank: 314
is_a: core field
slot_uri: MIXS:0000988
multivalued: false
alias: hcr
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hcr_enum
hcr_fw_salinity:
name: hcr_fw_salinity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original formation water salinity (prior to secondary recovery e.g.
Waterflooding) expressed as TDS
title: formation water salinity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- formation water salinity
rank: 315
is_a: core field
slot_uri: MIXS:0000406
multivalued: false
alias: hcr_fw_salinity
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
hcr_geol_age:
name: hcr_geol_age
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).
If "other" is specified, please propose entry in "additional info" field'
title: hydrocarbon resource geological age
examples:
- value: Silurian
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource geological age
rank: 316
is_a: core field
slot_uri: MIXS:0000993
multivalued: false
alias: hcr_geol_age
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: hcr_geol_age_enum
hcr_pressure:
name: hcr_pressure
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: atmosphere, kilopascal
occurrence:
tag: occurrence
value: '1'
description: Original pressure of the hydrocarbon resource
title: hydrocarbon resource original pressure
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource original pressure
rank: 317
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000395
multivalued: false
alias: hcr_pressure
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
hcr_temp:
name: hcr_temp
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Original temperature of the hydrocarbon resource
title: hydrocarbon resource original temperature
examples:
- value: 150-295 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hydrocarbon resource original temperature
rank: 318
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000393
multivalued: false
alias: hcr_temp
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
iw_bt_date_well:
name: iw_bt_date_well
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: Injection water breakthrough date per well following a secondary
and/or tertiary recovery
title: injection water breakthrough date of specific well
examples:
- value: '2018-05-11'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- injection water breakthrough date of specific well
rank: 334
is_a: core field
slot_uri: MIXS:0001010
multivalued: false
alias: iw_bt_date_well
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
iwf:
name: iwf
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: Proportion of the produced fluids derived from injected water at
the time of sampling. (e.g. 87%)
title: injection water fraction
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- injection water fraction
rank: 335
is_a: core field
slot_uri: MIXS:0000455
multivalued: false
alias: iwf
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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+)?)$
lithology:
name: lithology
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).
If "other" is specified, please propose entry in "additional info" field'
title: lithology
examples:
- value: Volcanic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- lithology
rank: 336
is_a: core field
slot_uri: MIXS:0000990
multivalued: false
alias: lithology
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: lithology_enum
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SedimentInterface
- WaterInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
[^;\t\r\x0A]+)$
nitrate:
name: nitrate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, milligram per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrate
rank: 26
is_a: core field
slot_uri: MIXS:0000425
multivalued: false
alias: nitrate
owner: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
org_count_qpcr_info:
name: org_count_qpcr_info
annotations:
expected_value:
tag: expected_value
value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial
denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes; total cycles
preferred_unit:
tag: preferred_unit
value: number of cells per gram (or ml or cm^2)
occurrence:
tag: occurrence
value: '1'
description: 'If qpcr was used for the cell count, the target gene name, the primer
sequence and the cycling conditions should also be provided. (Example: 16S rrna;
FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;
annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;
30 cycles)'
title: organism count qPCR information
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organism count qPCR information
rank: 337
is_a: core field
string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes; total cycles'
slot_uri: MIXS:0000099
multivalued: false
alias: org_count_qpcr_info
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: OxyStatSampEnum
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_section
range: string
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
pour_point:
name: pour_point
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 a liquid becomes semi solid and loses its flow
characteristics. In crude oil a high pour point is generally associated with
a high paraffin content, typically found in crude deriving from a larger proportion
of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'
title: pour point
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pour point
rank: 341
is_a: core field
slot_uri: MIXS:0000127
multivalued: false
alias: pour_point
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
prod_rate:
name: prod_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Oil and/or gas production rates per well (e.g. 524 m3 / day)
title: production rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- production rate
rank: 344
is_a: core field
slot_uri: MIXS:0000452
multivalued: false
alias: prod_rate
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
prod_start_date:
name: prod_start_date
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: Date of field's first production
title: production start date
examples:
- value: '2018-05-11'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- production start date
rank: 345
is_a: core field
slot_uri: MIXS:0001008
multivalued: false
alias: prod_start_date
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
reservoir:
name: reservoir
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the reservoir (e.g. Carapebus)
title: reservoir name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- reservoir name
rank: 347
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000303
multivalued: false
alias: reservoir
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
resins_pc:
name: resins_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: resins wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- resins wt%
rank: 348
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000134
multivalued: false
alias: resins_pc
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_collect_point:
name: samp_collect_point
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Sampling point on the asset were sample was collected (e.g. Wellhead,
storage tank, separator, etc). If "other" is specified, please propose entry
in "additional info" field
title: sample collection point
examples:
- value: well
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection point
rank: 349
is_a: core field
slot_uri: MIXS:0001015
multivalued: false
alias: samp_collect_point
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: samp_collect_point_enum
samp_loc_corr_rate:
name: samp_loc_corr_rate
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: millimeter per year
occurrence:
tag: occurrence
value: '1'
description: Metal corrosion rate is the speed of metal deterioration due to environmental
conditions. As environmental conditions change corrosion rates change accordingly.
Therefore, long term corrosion rates are generally more informative than short
term rates and for that reason they are preferred during reporting. In the case
of suspected MIC, corrosion rate measurements at the time of sampling might
provide insights into the involvement of certain microbial community members
in MIC as well as potential microbial interplays
title: corrosion rate at sample location
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- corrosion rate at sample location
rank: 350
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000136
multivalued: false
alias: samp_loc_corr_rate
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
samp_preserv:
name: samp_preserv
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: milliliter
occurrence:
tag: occurrence
value: '1'
description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,
etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
title: preservative added to sample
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- preservative added to sample
rank: 352
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000463
multivalued: false
alias: samp_preserv
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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.*$
samp_subtype:
name: samp_subtype
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Name of sample sub-type. For example if "sample type" is "Produced
Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified,
please propose entry in "additional info" field
title: sample subtype
examples:
- value: biofilm
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample subtype
rank: 354
is_a: core field
slot_uri: MIXS:0000999
multivalued: false
alias: samp_subtype
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: samp_subtype_enum
samp_transport_cond:
name: samp_transport_cond
annotations:
expected_value:
tag: expected_value
value: measurement value;measurement value
preferred_unit:
tag: preferred_unit
value: days;degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Sample transport duration (in days or hrs) and temperature the sample
was exposed to (e.g. 5.5 days; 20 °C)
title: sample transport conditions
examples:
- value: 5 days;-20 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample transport conditions
rank: 355
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000410
multivalued: false
alias: samp_transport_cond
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
samp_type:
name: samp_type
annotations:
expected_value:
tag: expected_value
value: GENEPIO:0001246
occurrence:
tag: occurrence
value: '1'
description: The type of material from which the sample was obtained. For the
Hydrocarbon package, samples include types like core, rock trimmings, drill
cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,
produced water, injected water, swabs, etc. For the Food Package, samples are
usually categorized as food, body products or tissues, or environmental material.
This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
title: sample type
examples:
- value: built environment sample [GENEPIO:0001248]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample type
rank: 357
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000998
multivalued: false
alias: samp_type
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
samp_well_name:
name: samp_well_name
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Name of the well (e.g. BXA1123) where sample was taken
title: sample well name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample well name
rank: 358
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000296
multivalued: false
alias: samp_well_name
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
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: HcrFluidsSwabsInterface
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]+'
saturates_pc:
name: saturates_pc
annotations:
expected_value:
tag: expected_value
value: name;measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: 'Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis
method that divides crude oil components according to their polarizability
and polarity. There are three main methods to obtain SARA results. The most
popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:
https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'
title: saturates wt%
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- saturates wt%
rank: 359
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000131
multivalued: false
alias: saturates_pc
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
sulfate_fw:
name: sulfate_fw
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original sulfate concentration in the hydrocarbon resource
title: sulfate in formation water
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sulfate in formation water
rank: 370
is_a: core field
slot_uri: MIXS:0000407
multivalued: false
alias: sulfate_fw
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- MiscEnvsInterface
- SedimentInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
suspend_solids:
name: suspend_solids
annotations:
expected_value:
tag: expected_value
value: suspended solid name;measurement value
preferred_unit:
tag: preferred_unit
value: gram, microgram, milligram per liter, mole per liter, gram per liter,
part per million
occurrence:
tag: occurrence
value: m
description: Concentration of substances including a wide variety of material,
such as silt, decaying plant and animal matter; can include multiple substances
title: suspended solids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- suspended solids
rank: 372
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000150
multivalued: false
alias: suspend_solids
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WastewaterSludgeInterface
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]+)$
tan:
name: tan
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total Acid Number (TAN) is a measurement of acidity that is determined
by the amount of potassium hydroxide in milligrams that is needed to neutralize
the acids in one gram of oil. It is an important quality measurement of crude
oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'
title: total acid number
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total acid number
rank: 373
is_a: core field
slot_uri: MIXS:0000120
multivalued: false
alias: tan
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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.*$
toluene:
name: toluene
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 toluene in the sample
title: toluene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- toluene
rank: 375
is_a: core field
slot_uri: MIXS:0000154
multivalued: false
alias: toluene
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_iron:
name: tot_iron
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter, milligram per kilogram
occurrence:
tag: occurrence
value: '1'
description: Concentration of total iron in the sample
title: total iron
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total iron
rank: 376
is_a: core field
slot_uri: MIXS:0000105
multivalued: false
alias: tot_iron
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_nitro:
name: tot_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total nitrogen concentration of water samples, calculated by: total
nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
without filtering, reported as nitrogen'
title: total nitrogen concentration
examples:
- value: 50 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total nitrogen concentration
rank: 377
is_a: core field
slot_uri: MIXS:0000102
multivalued: false
alias: tot_nitro
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_phosp:
name: tot_phosp
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: 'Total phosphorus concentration in the sample, calculated by: total
phosphorus = total dissolved phosphorus + particulate phosphorus'
title: total phosphorus
examples:
- value: 0.03 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total phosphorus
rank: 52
is_a: core field
slot_uri: MIXS:0000117
multivalued: false
alias: tot_phosp
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
- SoilInterface
- WaterInterface
slot_group: mixs_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tot_sulfur:
name: tot_sulfur
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 total sulfur in the sample
title: total sulfur
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total sulfur
rank: 379
is_a: core field
slot_uri: MIXS:0000419
multivalued: false
alias: tot_sulfur
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tvdss_of_hcr_press:
name: tvdss_of_hcr_press
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
the original pressure was measured (e.g. 1578 m).
title: depth (TVDSS) of hydrocarbon resource pressure
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth (TVDSS) of hydrocarbon resource pressure
rank: 380
is_a: core field
slot_uri: MIXS:0000397
multivalued: false
alias: tvdss_of_hcr_press
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
tvdss_of_hcr_temp:
name: tvdss_of_hcr_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where
the original temperature was measured (e.g. 1345 m).
title: depth (TVDSS) of hydrocarbon resource temperature
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth (TVDSS) of hydrocarbon resource temperature
rank: 381
is_a: core field
slot_uri: MIXS:0000394
multivalued: false
alias: tvdss_of_hcr_temp
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
vfa:
name: vfa
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 Volatile Fatty Acids in the sample
title: volatile fatty acids
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- volatile fatty acids
rank: 382
is_a: core field
slot_uri: MIXS:0000152
multivalued: false
alias: vfa
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
vfa_fw:
name: vfa_fw
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Original volatile fatty acid concentration in the hydrocarbon resource
title: vfa in formation water
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- vfa in formation water
rank: 383
is_a: core field
slot_uri: MIXS:0000408
multivalued: false
alias: vfa_fw
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
viscosity:
name: viscosity
annotations:
expected_value:
tag: expected_value
value: measurement value;measurement value
preferred_unit:
tag: preferred_unit
value: cP at degree Celsius
occurrence:
tag: occurrence
value: '1'
description: A measure of oil's resistance to gradual deformation by shear stress or tensile
stress (e.g. 3.5 cp; 100 °C)
title: viscosity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- viscosity
rank: 384
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000126
multivalued: false
alias: viscosity
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
water_cut:
name: water_cut
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percent
occurrence:
tag: occurrence
value: '1'
description: Current amount of water (%) in a produced fluid stream; or the average
of the combined streams
title: water cut
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water cut
rank: 386
is_a: core field
slot_uri: MIXS:0000454
multivalued: false
alias: water_cut
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
water_prod_rate:
name: water_prod_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Water production rates per well (e.g. 987 m3 / day)
title: water production rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water production rate
rank: 387
is_a: core field
slot_uri: MIXS:0000453
multivalued: false
alias: water_prod_rate
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
win:
name: win
annotations:
expected_value:
tag: expected_value
value: text
occurrence:
tag: occurrence
value: '1'
description: 'A unique identifier of a well or wellbore. This is part of the Global
Framework for Well Identification initiative which is compiled by the Professional
Petroleum Data Management Association (PPDM) in an effort to improve well identification
systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'
title: well identification number
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- well identification number
rank: 388
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000297
multivalued: false
alias: win
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
xylene:
name: xylene
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 xylene in the sample
title: xylene
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- xylene
rank: 389
is_a: core field
slot_uri: MIXS:0000156
multivalued: false
alias: xylene
owner: HcrFluidsSwabsInterface
domain_of:
- Biosample
- HcrCoresInterface
- HcrFluidsSwabsInterface
slot_group: mixs_core_section
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$
analysis_type:
name: analysis_type
description: Select all the data types associated or available for this biosample
title: analysis/data type
examples:
- value: metagenomics; metabolomics; proteomics
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIxS:investigation_type
rank: 3
multivalued: true
alias: analysis_type
owner: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
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: HcrFluidsSwabsInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
pattern: '[^\:\n\r]+\:[^\:\n\r]+'