Class: Biosample
Biological source material which can be characterized by an experiment.
URI: nmdc:Biosample
Note
Mermaid class diagram too large to render.
Inheritance
- NamedThing
- MaterialEntity
- Biosample
- MaterialEntity
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| associated_studies | 1..* Study |
The study associated with a resource | direct |
| biosample_categories | * BiosampleCategoryEnum |
direct | |
| collected_from | 0..1 FieldResearchSite |
The Site from which a Biosample was collected | direct |
| embargoed | 0..1 recommended Boolean |
If true, the data are embargoed and not available for public access | direct |
| host_disease_stat | 0..1 TextValue |
List of diseases with which the host has been diagnosed; can include multiple... | direct |
| host_taxid | 0..1 ControlledIdentifiedTermValue |
NCBI taxon id of the host, e | direct |
| img_identifiers | * ExternalIdentifier |
A list of identifiers that relate the biosample to records in the IMG databas... | direct |
| neon_biosample_identifiers | * ExternalIdentifier |
direct | |
| samp_name | 0..1 String |
A local identifier or name that for the material sample used for extracting n... | direct |
| gold_biosample_identifiers | * Uriorcurie |
Unique identifier for a biosample submitted to GOLD that matches the NMDC sub... | direct |
| insdc_biosample_identifiers | * ExternalIdentifier |
identifiers for corresponding sample in INSDC | direct |
| emsl_biosample_identifiers | * ExternalIdentifier |
A list of identifiers for the biosample from the EMSL database | direct |
| igsn_biosample_identifiers | * ExternalIdentifier |
A list of identifiers for the biosample from the IGSN database | direct |
| abs_air_humidity | 0..1 QuantityValue |
Actual mass of water vapor - mh20 - present in the air water vapor mixture | direct |
| add_recov_method | 0..1 TextValue |
Additional (i | direct |
| additional_info | 0..1 TextValue |
Information that doesn't fit anywhere else | direct |
| address | 0..1 TextValue |
The street name and building number where the sampling occurred | direct |
| adj_room | 0..1 TextValue |
List of rooms (room number, room name) immediately adjacent to the sampling r... | direct |
| aero_struc | 0..1 TextValue |
Aerospace structures typically consist of thin plates with stiffeners for the... | direct |
| agrochem_addition | * TextValue |
Addition of fertilizers, pesticides, etc | direct |
| air_PM_concen | * TextValue |
Concentration of substances that remain suspended in the air, and comprise mi... | direct |
| air_temp | 0..1 QuantityValue |
Temperature of the air at the time of sampling | direct |
| air_temp_regm | * TextValue |
Information about treatment involving an exposure to varying temperatures; sh... | direct |
| al_sat | 0..1 QuantityValue |
The relative abundance of aluminum in the sample | direct |
| al_sat_meth | 0..1 TextValue |
Reference or method used in determining Aluminum saturation | direct |
| alkalinity | 0..1 QuantityValue |
Alkalinity, the ability of a solution to neutralize acids to the equivalence ... | direct |
| alkalinity_method | 0..1 TextValue |
Method used for alkalinity measurement | direct |
| alkyl_diethers | 0..1 QuantityValue |
Concentration of alkyl diethers | direct |
| alt | 0..1 QuantityValue |
Altitude is a term used to identify heights of objects such as airplanes, spa... | direct |
| aminopept_act | 0..1 QuantityValue |
Measurement of aminopeptidase activity | direct |
| ammonium | 0..1 QuantityValue |
Concentration of ammonium in the sample | direct |
| ammonium_nitrogen | 0..1 QuantityValue |
Concentration of ammonium nitrogen in the sample | direct |
| amount_light | 0..1 QuantityValue |
The unit of illuminance and luminous emittance, measuring luminous flux per u... | direct |
| ances_data | 0..1 TextValue |
Information about either pedigree or other ancestral information description ... | direct |
| annual_precpt | 0..1 QuantityValue |
The average of all annual precipitation values known, or an estimated equival... | direct |
| annual_temp | 0..1 QuantityValue |
Mean annual temperature | direct |
| antibiotic_regm | * TextValue |
Information about treatment involving antibiotic administration; should inclu... | direct |
| api | 0..1 QuantityValue |
API gravity is a measure of how heavy or light a petroleum liquid is compared... | direct |
| arch_struc | 0..1 ArchStrucEnum |
An architectural structure is a human-made, free-standing, immobile outdoor c... | direct |
| aromatics_pc | 0..1 TextValue |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | direct |
| asphaltenes_pc | 0..1 TextValue |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | direct |
| atmospheric_data | * TextValue |
Measurement of atmospheric data; can include multiple data | direct |
| avg_dew_point | 0..1 QuantityValue |
The average of dew point measures taken at the beginning of every hour over a... | direct |
| avg_occup | 0..1 TextValue |
Daily average occupancy of room | direct |
| avg_temp | 0..1 QuantityValue |
The average of temperatures taken at the beginning of every hour over a 24 ho... | direct |
| bac_prod | 0..1 QuantityValue |
Bacterial production in the water column measured by isotope uptake | direct |
| bac_resp | 0..1 QuantityValue |
Measurement of bacterial respiration in the water column | direct |
| bacteria_carb_prod | 0..1 QuantityValue |
Measurement of bacterial carbon production | direct |
| barometric_press | 0..1 QuantityValue |
Force per unit area exerted against a surface by the weight of air above that... | direct |
| basin | 0..1 TextValue |
Name of the basin (e | direct |
| bathroom_count | 0..1 TextValue |
The number of bathrooms in the building | direct |
| bedroom_count | 0..1 TextValue |
The number of bedrooms in the building | direct |
| benzene | 0..1 QuantityValue |
Concentration of benzene in the sample | direct |
| biochem_oxygen_dem | 0..1 QuantityValue |
Amount of dissolved oxygen needed by aerobic biological organisms in a body o... | direct |
| biocide | 0..1 TextValue |
List of biocides (commercial name of product and supplier) and date of admini... | direct |
| biocide_admin_method | 0..1 TextValue |
Method of biocide administration (dose, frequency, duration, time elapsed bet... | direct |
| biol_stat | 0..1 BiolStatEnum |
The level of genome modification | direct |
| biomass | * TextValue |
Amount of biomass; should include the name for the part of biomass measured, ... | direct |
| biotic_regm | 0..1 TextValue |
Information about treatment(s) involving use of biotic factors, such as bacte... | direct |
| biotic_relationship | 0..1 BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... | direct |
| bishomohopanol | 0..1 QuantityValue |
Concentration of bishomohopanol | direct |
| blood_press_diast | 0..1 QuantityValue |
Resting diastolic blood pressure, measured as mm mercury | direct |
| blood_press_syst | 0..1 QuantityValue |
Resting systolic blood pressure, measured as mm mercury | direct |
| bromide | 0..1 QuantityValue |
Concentration of bromide | direct |
| build_docs | 0..1 BuildDocsEnum |
The building design, construction and operation documents | direct |
| build_occup_type | * BuildOccupTypeEnum |
The primary function for which a building or discrete part of a building is i... | direct |
| building_setting | 0..1 BuildingSettingEnum |
A location (geography) where a building is set | direct |
| built_struc_age | 0..1 QuantityValue |
The age of the built structure since construction | direct |
| built_struc_set | 0..1 TextValue |
The characterization of the location of the built structure as high or low hu... | direct |
| built_struc_type | 0..1 TextValue |
A physical structure that is a body or assemblage of bodies in space to form ... | direct |
| calcium | 0..1 QuantityValue |
Concentration of calcium in the sample | direct |
| carb_dioxide | 0..1 QuantityValue |
Carbon dioxide (gas) amount or concentration at the time of sampling | direct |
| carb_monoxide | 0..1 QuantityValue |
Carbon monoxide (gas) amount or concentration at the time of sampling | direct |
| carb_nitro_ratio | 0..1 QuantityValue |
Ratio of amount or concentrations of carbon to nitrogen | direct |
| ceil_area | 0..1 QuantityValue |
The area of the ceiling space within the room | direct |
| ceil_cond | 0..1 CeilCondEnum |
The physical condition of the ceiling at the time of sampling; photos or vide... | direct |
| ceil_finish_mat | 0..1 CeilFinishMatEnum |
The type of material used to finish a ceiling | direct |
| ceil_struc | 0..1 TextValue |
The construction format of the ceiling | direct |
| ceil_texture | 0..1 CeilTextureEnum |
The feel, appearance, or consistency of a ceiling surface | direct |
| ceil_thermal_mass | 0..1 QuantityValue |
The ability of the ceiling to provide inertia against temperature fluctuation... | direct |
| ceil_type | 0..1 CeilTypeEnum |
The type of ceiling according to the ceiling's appearance or construction | direct |
| ceil_water_mold | 0..1 TextValue |
Signs of the presence of mold or mildew on the ceiling | direct |
| chem_administration | * ControlledTermValue |
List of chemical compounds administered to the host or site where sampling oc... | direct |
| chem_mutagen | * TextValue |
Treatment involving use of mutagens; should include the name of mutagen, amou... | direct |
| chem_oxygen_dem | 0..1 QuantityValue |
A measure of the capacity of water to consume oxygen during the decomposition... | direct |
| chem_treat_method | 0..1 String |
Method of chemical administration(dose, frequency, duration, time elapsed bet... | direct |
| chem_treatment | 0..1 TextValue |
List of chemical compounds administered upstream the sampling location where ... | direct |
| chloride | 0..1 QuantityValue |
Concentration of chloride in the sample | direct |
| chlorophyll | 0..1 QuantityValue |
Concentration of chlorophyll | direct |
| climate_environment | * TextValue |
Treatment involving an exposure to a particular climate; treatment regimen in... | direct |
| collection_date | 0..1 TimestampValue |
The time of sampling, either as an instance (single point in time) or interva... | direct |
| conduc | 0..1 QuantityValue |
Electrical conductivity of water | direct |
| cool_syst_id | 0..1 TextValue |
The cooling system identifier | direct |
| core_field | 0..1 String |
basic fields | direct |
| crop_rotation | 0..1 TextValue |
Whether or not crop is rotated, and if yes, rotation schedule | direct |
| cult_root_med | 0..1 TextValue |
Name or reference for the hydroponic or in vitro culture rooting medium; can ... | direct |
| cur_land_use | 0..1 CurLandUseEnum |
Present state of sample site | direct |
| cur_vegetation | 0..1 TextValue |
Vegetation classification from one or more standard classification systems, o... | direct |
| cur_vegetation_meth | 0..1 TextValue |
Reference or method used in vegetation classification | direct |
| date_last_rain | 0..1 TimestampValue |
The date of the last time it rained | direct |
| density | 0..1 QuantityValue |
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 QuantityValue |
The vertical distance below local surface, e | direct |
| dew_point | 0..1 QuantityValue |
The temperature to which a given parcel of humid air must be cooled, at const... | direct |
| diether_lipids | * TextValue |
Concentration of diether lipids; can include multiple types of diether lipids | direct |
| diss_carb_dioxide | 0..1 QuantityValue |
Concentration of dissolved carbon dioxide in the sample or liquid portion of ... | direct |
| diss_hydrogen | 0..1 QuantityValue |
Concentration of dissolved hydrogen | direct |
| diss_inorg_carb | 0..1 QuantityValue |
Dissolved inorganic carbon concentration in the sample, typically measured af... | direct |
| diss_inorg_nitro | 0..1 QuantityValue |
Concentration of dissolved inorganic nitrogen | direct |
| diss_inorg_phosp | 0..1 QuantityValue |
Concentration of dissolved inorganic phosphorus in the sample | direct |
| diss_iron | 0..1 QuantityValue |
Concentration of dissolved iron in the sample | direct |
| diss_org_carb | 0..1 QuantityValue |
Concentration of dissolved organic carbon in the sample, liquid portion of th... | direct |
| diss_org_nitro | 0..1 QuantityValue |
Dissolved organic nitrogen concentration measured as; total dissolved nitroge... | direct |
| diss_oxygen | 0..1 QuantityValue |
Concentration of dissolved oxygen | direct |
| diss_oxygen_fluid | 0..1 QuantityValue |
Concentration of dissolved oxygen in the oil field produced fluids as it cont... | direct |
| dna_cont_well | 0..1 recommended String |
direct | |
| door_comp_type | 0..1 DoorCompTypeEnum |
The composite type of the door | direct |
| door_cond | 0..1 DoorCondEnum |
The phsical condition of the door | direct |
| door_direct | 0..1 DoorDirectEnum |
The direction the door opens | direct |
| door_loc | 0..1 DoorLocEnum |
The relative location of the door in the room | direct |
| door_mat | 0..1 DoorMatEnum |
The material the door is composed of | direct |
| door_move | 0..1 DoorMoveEnum |
The type of movement of the door | direct |
| door_size | 0..1 QuantityValue |
The size of the door | direct |
| door_type | 0..1 DoorTypeEnum |
The type of door material | direct |
| door_type_metal | 0..1 DoorTypeMetalEnum |
The type of metal door | direct |
| door_type_wood | 0..1 DoorTypeWoodEnum |
The type of wood door | direct |
| door_water_mold | 0..1 TextValue |
Signs of the presence of mold or mildew on a door | direct |
| down_par | 0..1 QuantityValue |
Visible waveband radiance and irradiance measurements in the water column | direct |
| drainage_class | 0..1 DrainageClassEnum |
Drainage classification from a standard system such as the USDA system | direct |
| drawings | 0..1 DrawingsEnum |
The buildings architectural drawings; if design is chosen, indicate phase-con... | direct |
| ecosystem | 0..1 String |
An ecosystem is a combination of a physical environment (abiotic factors) and... | direct |
| ecosystem_category | 0..1 String |
Ecosystem categories represent divisions within the ecosystem based on specif... | direct |
| ecosystem_subtype | 0..1 String |
Ecosystem subtypes represent further subdivision of Ecosystem types into more... | direct |
| ecosystem_type | 0..1 String |
Ecosystem types represent things having common characteristics within the Eco... | direct |
| efficiency_percent | 0..1 QuantityValue |
Percentage of volatile solids removed from the anaerobic digestor | direct |
| elev | 0..1 Float |
Elevation of the sampling site is its height above a fixed reference point, m... | direct |
| elevator | 0..1 TextValue |
The number of elevators within the built structure | direct |
| emulsions | * TextValue |
Amount or concentration of substances such as paints, adhesives, mayonnaise, ... | direct |
| env_broad_scale | 1 ControlledIdentifiedTermValue |
Report the major environmental system the sample or specimen came from | direct |
| env_local_scale | 1 ControlledIdentifiedTermValue |
Report the entity or entities which are in the sample or specimen’s local vic... | direct |
| env_medium | 1 ControlledIdentifiedTermValue |
Report the environmental material(s) immediately surrounding the sample or sp... | direct |
| env_package | 0..1 TextValue |
MIxS extension for reporting of measurements and observations obtained from o... | direct |
| environment_field | 0..1 String |
field describing environmental aspect of a sample | direct |
| escalator | 0..1 TextValue |
The number of escalators within the built structure | direct |
| ethylbenzene | 0..1 QuantityValue |
Concentration of ethylbenzene in the sample | direct |
| exp_duct | 0..1 QuantityValue |
The amount of exposed ductwork in the room | direct |
| exp_pipe | 0..1 QuantityValue |
The number of exposed pipes in the room | direct |
| experimental_factor | 0..1 ControlledTermValue |
Experimental factors are essentially the variable aspects of an experiment de... | direct |
| ext_door | 0..1 TextValue |
The number of exterior doors in the built structure | direct |
| ext_wall_orient | 0..1 ExtWallOrientEnum |
The orientation of the exterior wall | direct |
| ext_window_orient | 0..1 ExtWindowOrientEnum |
The compass direction the exterior window of the room is facing | direct |
| extreme_event | 0..1 String |
Unusual physical events that may have affected microbial populations | direct |
| fao_class | 0..1 FaoClassEnum |
Soil classification from the FAO World Reference Database for Soil Resources | direct |
| fertilizer_regm | * TextValue |
Information about treatment involving the use of fertilizers; should include ... | direct |
| field | 0..1 TextValue |
Name of the hydrocarbon field (e | direct |
| filter_type | * FilterTypeEnum |
A device which removes solid particulates or airborne molecular contaminants | direct |
| fire | 0..1 String |
Historical and/or physical evidence of fire | direct |
| fireplace_type | 0..1 TextValue |
A firebox with chimney | direct |
| flooding | 0..1 String |
Historical and/or physical evidence of flooding | direct |
| floor_age | 0..1 QuantityValue |
The time period since installment of the carpet or flooring | direct |
| floor_area | 0..1 QuantityValue |
The area of the floor space within the room | direct |
| floor_cond | 0..1 FloorCondEnum |
The physical condition of the floor at the time of sampling; photos or video ... | direct |
| floor_count | 0..1 TextValue |
The number of floors in the building, including basements and mechanical pent... | direct |
| floor_finish_mat | 0..1 FloorFinishMatEnum |
The floor covering type; the finished surface that is walked on | direct |
| floor_struc | 0..1 FloorStrucEnum |
Refers to the structural elements and subfloor upon which the finish flooring... | direct |
| floor_thermal_mass | 0..1 QuantityValue |
The ability of the floor to provide inertia against temperature fluctuations | direct |
| floor_water_mold | 0..1 FloorWaterMoldEnum |
Signs of the presence of mold or mildew in a room | direct |
| fluor | 0..1 QuantityValue |
Raw or converted fluorescence of water | direct |
| freq_clean | 0..1 QuantityValue |
The number of times the sample location is cleaned | direct |
| freq_cook | 0..1 QuantityValue |
The number of times a meal is cooked per week | direct |
| fungicide_regm | * TextValue |
Information about treatment involving use of fungicides; should include the n... | direct |
| furniture | 0..1 FurnitureEnum |
The types of furniture present in the sampled room | direct |
| gaseous_environment | * TextValue |
Use of conditions with differing gaseous environments; should include the nam... | direct |
| gaseous_substances | * TextValue |
Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... | direct |
| gender_restroom | 0..1 GenderRestroomEnum |
The gender type of the restroom | direct |
| genetic_mod | 0..1 TextValue |
Genetic modifications of the genome of an organism, which may occur naturally... | direct |
| geo_loc_name | 0..1 TextValue |
The geographical origin of the sample as defined by the country or sea name f... | direct |
| glucosidase_act | 0..1 QuantityValue |
Measurement of glucosidase activity | direct |
| gravidity | 0..1 TextValue |
Whether or not subject is gravid, and if yes date due or date post-conception... | direct |
| gravity | * TextValue |
Information about treatment involving use of gravity factor to study various ... | direct |
| growth_facil | 0..1 ControlledTermValue |
Type of facility where the sampled plant was grown; controlled vocabulary: gr... | direct |
| growth_habit | 0..1 GrowthHabitEnum |
Characteristic shape, appearance or growth form of a plant species | direct |
| growth_hormone_regm | * TextValue |
Information about treatment involving use of growth hormones; should include ... | direct |
| hall_count | 0..1 TextValue |
The total count of hallways and cooridors in the built structure | direct |
| handidness | 0..1 HandidnessEnum |
The handidness of the individual sampled | 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 QuantityValue |
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 TextValue |
Original pressure of the hydrocarbon resource | direct |
| hcr_temp | 0..1 TextValue |
Original temperature of the hydrocarbon resource | direct |
| heat_cool_type | * HeatCoolTypeEnum |
Methods of conditioning or heating a room or building | direct |
| heat_deliv_loc | 0..1 HeatDelivLocEnum |
The location of heat delivery within the room | direct |
| heat_sys_deliv_meth | 0..1 String |
The method by which the heat is delivered through the system | direct |
| heat_system_id | 0..1 TextValue |
The heating system identifier | direct |
| heavy_metals | * TextValue |
Heavy metals present in the sample and their concentrations | direct |
| heavy_metals_meth | * TextValue |
Reference or method used in determining heavy metals | direct |
| height_carper_fiber | 0..1 QuantityValue |
The average carpet fiber height in the indoor environment | direct |
| herbicide_regm | * TextValue |
Information about treatment involving use of herbicides; information about tr... | direct |
| horizon_meth | 0..1 TextValue |
Reference or method used in determining the horizon | direct |
| host_age | 0..1 QuantityValue |
Age of host at the time of sampling; relevant scale depends on species and st... | direct |
| host_body_habitat | 0..1 TextValue |
Original body habitat where the sample was obtained from | direct |
| host_body_product | 0..1 ControlledTermValue |
Substance produced by the body, e | direct |
| host_body_site | 0..1 ControlledTermValue |
Name of body site where the sample was obtained from, such as a specific orga... | direct |
| host_body_temp | 0..1 QuantityValue |
Core body temperature of the host when sample was collected | direct |
| host_color | 0..1 TextValue |
The color of host | direct |
| host_common_name | 0..1 TextValue |
Common name of the host | direct |
| host_diet | * TextValue |
Type of diet depending on the host, for animals omnivore, herbivore etc | direct |
| host_dry_mass | 0..1 QuantityValue |
Measurement of dry mass | direct |
| host_family_relation | * String |
Familial relationships to other hosts in the same study; can include multiple... | direct |
| host_genotype | 0..1 TextValue |
Observed genotype | direct |
| host_growth_cond | 0..1 TextValue |
Literature reference giving growth conditions of the host | direct |
| host_height | 0..1 QuantityValue |
The height of subject | direct |
| host_last_meal | * TextValue |
Content of last meal and time since feeding; can include multiple values | direct |
| host_length | 0..1 QuantityValue |
The length of subject | direct |
| host_life_stage | 0..1 TextValue |
Description of life stage of host | direct |
| host_phenotype | 0..1 ControlledTermValue |
Phenotype of human or other host | direct |
| host_sex | 0..1 HostSexEnum |
Gender or physical sex of the host | direct |
| host_shape | 0..1 TextValue |
Morphological shape of host | direct |
| host_subject_id | 0..1 TextValue |
A unique identifier by which each subject can be referred to, de-identified | direct |
| host_subspecf_genlin | * String |
Information about the genetic distinctness of the host organism below the sub... | direct |
| host_substrate | 0..1 TextValue |
The growth substrate of the host | direct |
| host_symbiont | * String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... | direct |
| host_taxid | 0..1 ControlledIdentifiedTermValue |
NCBI taxon id of the host, e | direct |
| host_tot_mass | 0..1 QuantityValue |
Total mass of the host at collection, the unit depends on host | direct |
| host_wet_mass | 0..1 QuantityValue |
Measurement of wet mass | direct |
| humidity | 0..1 QuantityValue |
Amount of water vapour in the air, at the time of sampling | direct |
| humidity_regm | * TextValue |
Information about treatment involving an exposure to varying degree of humidi... | direct |
| indoor_space | 0..1 IndoorSpaceEnum |
A distinguishable space within a structure, the purpose for which discrete ar... | direct |
| indoor_surf | 0..1 IndoorSurfEnum |
Type of indoor surface | direct |
| indust_eff_percent | 0..1 QuantityValue |
Percentage of industrial effluents received by wastewater treatment plant | direct |
| inorg_particles | * TextValue |
Concentration of particles such as sand, grit, metal particles, ceramics, etc | direct |
| inside_lux | 0..1 QuantityValue |
The recorded value at sampling time (power density) | direct |
| int_wall_cond | 0..1 IntWallCondEnum |
The physical condition of the wall at the time of sampling; photos or video p... | direct |
| investigation_field | 0..1 String |
field describing aspect of the investigation/study to which the sample belong... | direct |
| iw_bt_date_well | 0..1 TimestampValue |
Injection water breakthrough date per well following a secondary and/or terti... | direct |
| iwf | 0..1 QuantityValue |
Proportion of the produced fluids derived from injected water at the time of ... | direct |
| last_clean | 0..1 TimestampValue |
The last time the floor was cleaned (swept, mopped, vacuumed) | direct |
| lat_lon | 0..1 GeolocationValue |
The geographical origin of the sample as defined by latitude and longitude | direct |
| lbc_thirty | 0..1 QuantityValue |
lime buffer capacity, determined after 30 minute incubation | direct |
| lbceq | 0..1 QuantityValue |
lime buffer capacity, determined at equilibrium after 5 day incubation | direct |
| light_intensity | 0..1 QuantityValue |
Measurement of light intensity | direct |
| light_regm | 0..1 TextValue |
Information about treatment(s) involving exposure to light, including both li... | direct |
| light_type | * LightTypeEnum |
Application of light to achieve some practical or aesthetic effect | direct |
| link_addit_analys | 0..1 TextValue |
Link to additional analysis results performed on the sample | direct |
| link_class_info | 0..1 TextValue |
Link to digitized soil maps or other soil classification information | direct |
| link_climate_info | 0..1 TextValue |
Link to climate resource | direct |
| lithology | 0..1 LithologyEnum |
Hydrocarbon resource main lithology (Additional information: http://petrowiki | direct |
| local_class | 0..1 TextValue |
Soil classification based on local soil classification system | direct |
| local_class_meth | 0..1 TextValue |
Reference or method used in determining the local soil classification | direct |
| magnesium | 0..1 QuantityValue |
Concentration of magnesium in the sample | direct |
| manganese | 0..1 QuantityValue |
Concentration of manganese in the sample | direct |
| max_occup | 0..1 QuantityValue |
The maximum amount of people allowed in the indoor environment | direct |
| mean_frict_vel | 0..1 QuantityValue |
Measurement of mean friction velocity | direct |
| mean_peak_frict_vel | 0..1 QuantityValue |
Measurement of mean peak friction velocity | direct |
| mech_struc | 0..1 MechStrucEnum |
mechanical structure: a moving structure | direct |
| mechanical_damage | * TextValue |
Information about any mechanical damage exerted on the plant; can include mul... | direct |
| methane | 0..1 QuantityValue |
Methane (gas) amount or concentration at the time of sampling | direct |
| micro_biomass_meth | 0..1 String |
Reference or method used in determining microbial biomass | direct |
| microbial_biomass | 0..1 QuantityValue |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
| mineral_nutr_regm | * TextValue |
Information about treatment involving the use of mineral supplements; should ... | direct |
| misc_param | * TextValue |
Any other measurement performed or parameter collected, that is not listed he... | direct |
| n_alkanes | * TextValue |
Concentration of n-alkanes; can include multiple n-alkanes | direct |
| nitrate | 0..1 QuantityValue |
Concentration of nitrate in the sample | direct |
| nitrate_nitrogen | 0..1 QuantityValue |
Concentration of nitrate nitrogen in the sample | direct |
| nitrite | 0..1 QuantityValue |
Concentration of nitrite in the sample | direct |
| nitrite_nitrogen | 0..1 QuantityValue |
Concentration of nitrite nitrogen in the sample | direct |
| nitro | 0..1 QuantityValue |
Concentration of nitrogen (total) | direct |
| non_min_nutr_regm | * String |
Information about treatment involving the exposure of plant to non-mineral nu... | direct |
| nucleic_acid_sequence_source_field | 0..1 String |
direct | |
| number_pets | 0..1 QuantityValue |
The number of pets residing in the sampled space | direct |
| number_plants | 0..1 QuantityValue |
The number of plant(s) in the sampling space | direct |
| number_resident | 0..1 QuantityValue |
The number of individuals currently occupying in the sampling location | direct |
| occup_density_samp | 0..1 QuantityValue |
Average number of occupants at time of sampling per square footage | direct |
| occup_document | 0..1 OccupDocumentEnum |
The type of documentation of occupancy | direct |
| occup_samp | 0..1 QuantityValue |
Number of occupants present at time of sample within the given space | direct |
| org_carb | 0..1 QuantityValue |
Concentration of organic carbon | direct |
| org_count_qpcr_info | 0..1 String |
If qpcr was used for the cell count, the target gene name, the primer sequenc... | direct |
| org_matter | 0..1 QuantityValue |
Concentration of organic matter | direct |
| org_nitro | 0..1 QuantityValue |
Concentration of organic nitrogen | direct |
| org_particles | * TextValue |
Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... | direct |
| organism_count | * QuantityValue |
Total cell count of any organism (or group of organisms) per gram, volume or ... | direct |
| owc_tvdss | 0..1 QuantityValue |
Depth of the original oil water contact (OWC) zone (average) (m TVDSS) | direct |
| oxy_stat_samp | 0..1 OxyStatSampEnum |
Oxygenation status of sample | direct |
| oxygen | 0..1 QuantityValue |
Oxygen (gas) amount or concentration at the time of sampling | direct |
| part_org_carb | 0..1 QuantityValue |
Concentration of particulate organic carbon | direct |
| part_org_nitro | 0..1 QuantityValue |
Concentration of particulate organic nitrogen | direct |
| particle_class | * TextValue |
Particles are classified, based on their size, into six general categories:cl... | direct |
| permeability | 0..1 TextValue |
Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... | direct |
| perturbation | * TextValue |
Type of perturbation, e | direct |
| pesticide_regm | * TextValue |
Information about treatment involving use of insecticides; should include the... | direct |
| petroleum_hydrocarb | 0..1 QuantityValue |
Concentration of petroleum hydrocarbon | direct |
| ph | 0..1 Double |
Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... | direct |
| ph_meth | 0..1 TextValue |
Reference or method used in determining ph | direct |
| ph_regm | * TextValue |
Information about treatment involving exposure of plants to varying levels of... | direct |
| phaeopigments | * TextValue |
Concentration of phaeopigments; can include multiple phaeopigments | direct |
| phosphate | 0..1 QuantityValue |
Concentration of phosphate | direct |
| phosplipid_fatt_acid | * TextValue |
Concentration of phospholipid fatty acids; can include multiple values | direct |
| photon_flux | 0..1 QuantityValue |
Measurement of photon flux | direct |
| plant_growth_med | 0..1 ControlledTermValue |
Specification of the media for growing the plants or tissue cultured samples,... | direct |
| plant_product | 0..1 TextValue |
Substance produced by the plant, where the sample was obtained from | direct |
| plant_sex | 0..1 PlantSexEnum |
Sex of the reproductive parts on the whole plant, e | direct |
| plant_struc | 0..1 ControlledTermValue |
Name of plant structure the sample was obtained from; for Plant Ontology (PO)... | direct |
| pollutants | * TextValue |
Pollutant types and, amount or concentrations measured at the time of samplin... | direct |
| porosity | 0..1 TextValue |
Porosity of deposited sediment is volume of voids divided by the total volume... | direct |
| potassium | 0..1 QuantityValue |
Concentration of potassium in the sample | direct |
| pour_point | 0..1 QuantityValue |
Temperature at which a liquid becomes semi solid and loses its flow character... | direct |
| pre_treatment | 0..1 TextValue |
The process of pre-treatment removes materials that can be easily collected f... | direct |
| pres_animal_insect | 0..1 String |
The type and number of animals or insects present in the sampling space | direct |
| pressure | 0..1 QuantityValue |
Pressure to which the sample is subject to, in atmospheres | direct |
| prev_land_use_meth | 0..1 String |
Reference or method used in determining previous land use and dates | direct |
| previous_land_use | 0..1 TextValue |
Previous land use and dates | direct |
| primary_prod | 0..1 QuantityValue |
Measurement of primary production, generally measured as isotope uptake | direct |
| primary_treatment | 0..1 TextValue |
The process to produce both a generally homogeneous liquid capable of being t... | direct |
| prod_rate | 0..1 QuantityValue |
Oil and/or gas production rates per well (e | direct |
| prod_start_date | 0..1 TimestampValue |
Date of field's first production | direct |
| profile_position | 0..1 ProfilePositionEnum |
Cross-sectional position in the hillslope where sample was collected | direct |
| quad_pos | 0..1 QuadPosEnum |
The quadrant position of the sampling room within the building | direct |
| radiation_regm | * TextValue |
Information about treatment involving exposure of plant or a plant part to a ... | direct |
| rainfall_regm | * TextValue |
Information about treatment involving an exposure to a given amount of rainfa... | direct |
| reactor_type | 0..1 TextValue |
Anaerobic digesters can be designed and engineered to operate using a number ... | direct |
| redox_potential | 0..1 QuantityValue |
Redox potential, measured relative to a hydrogen cell, indicating oxidation o... | direct |
| rel_air_humidity | 0..1 QuantityValue |
Partial vapor and air pressure, density of the vapor and air, or by the actua... | direct |
| rel_humidity_out | 0..1 QuantityValue |
The recorded outside relative humidity value at the time of sampling | direct |
| rel_samp_loc | 0..1 RelSampLocEnum |
The sampling location within the train car | direct |
| reservoir | 0..1 TextValue |
Name of the reservoir (e | direct |
| resins_pc | 0..1 TextValue |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | direct |
| room_air_exch_rate | 0..1 QuantityValue |
The rate at which outside air replaces indoor air in a given space | direct |
| room_architec_elem | 0..1 String |
The unique details and component parts that, together, form the architecture ... | direct |
| room_condt | 0..1 RoomCondtEnum |
The condition of the room at the time of sampling | direct |
| room_connected | 0..1 RoomConnectedEnum |
List of rooms connected to the sampling room by a doorway | direct |
| room_count | 0..1 TextValue |
The total count of rooms in the built structure including all room types | direct |
| room_dim | 0..1 TextValue |
The length, width and height of sampling room | direct |
| room_door_dist | 0..1 TextValue |
Distance between doors (meters) in the hallway between the sampling room and ... | direct |
| room_door_share | 0..1 TextValue |
List of room(s) (room number, room name) sharing a door with the sampling roo... | direct |
| room_hallway | 0..1 TextValue |
List of room(s) (room number, room name) located in the same hallway as sampl... | direct |
| room_loc | 0..1 RoomLocEnum |
The position of the room within the building | direct |
| room_moist_dam_hist | 0..1 Integer |
The history of moisture damage or mold in the past 12 months | direct |
| room_net_area | 0..1 TextValue |
The net floor area of sampling room | direct |
| room_occup | 0..1 QuantityValue |
Count of room occupancy at time of sampling | direct |
| room_samp_pos | 0..1 RoomSampPosEnum |
The horizontal sampling position in the room relative to architectural elemen... | direct |
| room_type | 0..1 RoomTypeEnum |
The main purpose or activity of the sampling room | direct |
| room_vol | 0..1 TextValue |
Volume of sampling room | direct |
| room_wall_share | 0..1 TextValue |
List of room(s) (room number, room name) sharing a wall with the sampling roo... | direct |
| room_window_count | 0..1 Integer |
Number of windows in the room | direct |
| root_cond | 0..1 TextValue |
Relevant rooting conditions such as field plot size, sowing density, containe... | direct |
| root_med_carbon | 0..1 TextValue |
Source of organic carbon in the culture rooting medium; e | direct |
| root_med_macronutr | 0..1 TextValue |
Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... | direct |
| root_med_micronutr | 0..1 TextValue |
Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... | direct |
| root_med_ph | 0..1 QuantityValue |
pH measurement of the culture rooting medium; e | direct |
| root_med_regl | 0..1 TextValue |
Growth regulators in the culture rooting medium such as cytokinins, auxins, g... | direct |
| root_med_solid | 0..1 TextValue |
Specification of the solidifying agent in the culture rooting medium; e | direct |
| root_med_suppl | 0..1 TextValue |
Organic supplements of the culture rooting medium, such as vitamins, amino ac... | direct |
| salinity | 0..1 QuantityValue |
The total concentration of all dissolved salts in a liquid or solid sample | direct |
| salinity_meth | 0..1 TextValue |
Reference or method used in determining salinity | direct |
| salt_regm | * TextValue |
Information about treatment involving use of salts as supplement to liquid an... | direct |
| samp_capt_status | 0..1 SampCaptStatusEnum |
Reason for the sample | direct |
| samp_collec_device | 0..1 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_dis_stage | 0..1 SampDisStageEnum |
Stage of the disease at the time of sample collection, e | direct |
| samp_floor | 0..1 SampFloorEnum |
The floor of the building, where the sampling room is located | direct |
| samp_loc_corr_rate | 0..1 TextValue |
Metal corrosion rate is the speed of metal deterioration due to environmental... | direct |
| samp_mat_process | 0..1 ControlledTermValue |
A brief description of any processing applied to the sample during or after r... | direct |
| samp_md | 0..1 QuantityValue |
In non deviated well, measured depth is equal to the true vertical depth, TVD... | direct |
| samp_name | 0..1 String |
A local identifier or name that for the material sample used for extracting n... | direct |
| samp_preserv | 0..1 TextValue |
Preservative added to the sample (e | direct |
| samp_room_id | 0..1 TextValue |
Sampling room number | direct |
| samp_size | 0..1 QuantityValue |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | direct |
| samp_sort_meth | * TextValue |
Method by which samples are sorted; open face filter collecting total suspend... | direct |
| samp_store_dur | 0..1 TextValue |
Duration for which the sample was stored | direct |
| samp_store_loc | 0..1 TextValue |
Location at which sample was stored, usually name of a specific freezer/room | direct |
| samp_store_temp | 0..1 QuantityValue |
Temperature at which sample was stored, e | direct |
| samp_subtype | 0..1 SampSubtypeEnum |
Name of sample sub-type | direct |
| samp_taxon_id | 0..1 ControlledIdentifiedTermValue |
NCBI taxon id of the sample | direct |
| samp_time_out | 0..1 TextValue |
The recent and long term history of outside sampling | direct |
| samp_transport_cond | 0..1 TextValue |
Sample transport duration (in days or hrs) and temperature the sample was exp... | direct |
| samp_tvdss | 0..1 TextValue |
Depth of the sample i | direct |
| samp_type | 0..1 TextValue |
The type of material from which the sample was obtained | direct |
| samp_weather | 0..1 SampWeatherEnum |
The weather on the sampling day | direct |
| samp_well_name | 0..1 TextValue |
Name of the well (e | direct |
| saturates_pc | 0..1 TextValue |
Saturate, Aromatic, Resin and Asphaltene (SARA) is an analysis method that d... | direct |
| season | 0..1 TextValue |
The season when sampling occurred | direct |
| season_environment | * TextValue |
Treatment involving an exposure to a particular season (e | direct |
| season_precpt | 0..1 QuantityValue |
The average of all seasonal precipitation values known, or an estimated equiv... | direct |
| season_temp | 0..1 QuantityValue |
Mean seasonal temperature | direct |
| season_use | 0..1 SeasonUseEnum |
The seasons the space is occupied | direct |
| secondary_treatment | 0..1 TextValue |
The process for substantially degrading the biological content of the sewage | direct |
| sediment_type | 0..1 SedimentTypeEnum |
Information about the sediment type based on major constituents | direct |
| sequencing_field | 0..1 String |
direct | |
| sewage_type | 0..1 TextValue |
Type of wastewater treatment plant as municipial or industrial | direct |
| shad_dev_water_mold | 0..1 String |
Signs of the presence of mold or mildew on the shading device | direct |
| shading_device_cond | 0..1 ShadingDeviceCondEnum |
The physical condition of the shading device at the time of sampling | direct |
| shading_device_loc | 0..1 TextValue |
The location of the shading device in relation to the built structure | direct |
| shading_device_mat | 0..1 TextValue |
The material the shading device is composed of | direct |
| shading_device_type | 0..1 ShadingDeviceTypeEnum |
The type of shading device | direct |
| sieving | 0..1 TextValue |
Collection design of pooled samples and/or sieve size and amount of sample si... | direct |
| silicate | 0..1 QuantityValue |
Concentration of silicate | direct |
| size_frac | 0..1 TextValue |
Filtering pore size used in sample preparation | direct |
| size_frac_low | 0..1 QuantityValue |
Refers to the mesh/pore size used to pre-filter/pre-sort the sample | direct |
| size_frac_up | 0..1 QuantityValue |
Refers to the mesh/pore size used to retain the sample | direct |
| slope_aspect | 0..1 QuantityValue |
The direction a slope faces | direct |
| slope_gradient | 0..1 QuantityValue |
Commonly called 'slope' | direct |
| sludge_retent_time | 0..1 QuantityValue |
The time activated sludge remains in reactor | direct |
| sodium | 0..1 QuantityValue |
Sodium concentration in the sample | direct |
| soil_horizon | 0..1 SoilHorizonEnum |
Specific layer in the land area which measures parallel to the soil surface a... | direct |
| soil_text_measure | 0..1 QuantityValue |
The relative proportion of different grain sizes of mineral particles in a so... | direct |
| soil_texture_meth | 0..1 String |
Reference or method used in determining soil texture | direct |
| soil_type | 0..1 TextValue |
Description of the soil type or classification | direct |
| soil_type_meth | 0..1 TextValue |
Reference or method used in determining soil series name or other lower-level... | direct |
| solar_irradiance | 0..1 QuantityValue |
The amount of solar energy that arrives at a specific area of a surface durin... | direct |
| soluble_inorg_mat | * TextValue |
Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... | direct |
| soluble_org_mat | * TextValue |
Concentration of substances such as urea, fruit sugars, soluble proteins, dru... | direct |
| soluble_react_phosp | 0..1 QuantityValue |
Concentration of soluble reactive phosphorus | direct |
| source_mat_id | 0..1 TextValue |
A globally unique identifier assigned to the biological sample | direct |
| space_typ_state | 0..1 TextValue |
Customary or normal state of the space | direct |
| specific | 0..1 SpecificEnum |
The building specifications | direct |
| specific_ecosystem | 0..1 String |
Specific ecosystems represent specific features of the environment like aphot... | direct |
| specific_humidity | 0..1 QuantityValue |
The mass of water vapour in a unit mass of moist air, usually expressed as gr... | direct |
| sr_dep_env | 0..1 SrDepEnvEnum |
Source rock depositional environment (https://en | direct |
| sr_geol_age | 0..1 SrGeolAgeEnum |
Geological age of source rock (Additional info: https://en | direct |
| sr_kerog_type | 0..1 SrKerogTypeEnum |
Origin of kerogen | direct |
| sr_lithology | 0..1 SrLithologyEnum |
Lithology of source rock (https://en | direct |
| standing_water_regm | * TextValue |
Treatment involving an exposure to standing water during a plant's life span,... | direct |
| store_cond | 0..1 TextValue |
Explain how and for how long the soil sample was stored before DNA extraction... | direct |
| substructure_type | * SubstructureTypeEnum |
The substructure or under building is that largely hidden section of the buil... | direct |
| sulfate | 0..1 QuantityValue |
Concentration of sulfate in the sample | direct |
| sulfate_fw | 0..1 QuantityValue |
Original sulfate concentration in the hydrocarbon resource | direct |
| sulfide | 0..1 QuantityValue |
Concentration of sulfide in the sample | direct |
| surf_air_cont | * SurfAirContEnum |
Contaminant identified on surface | direct |
| surf_humidity | 0..1 QuantityValue |
Surfaces: water activity as a function of air and material moisture | direct |
| surf_material | 0..1 SurfMaterialEnum |
Surface materials at the point of sampling | direct |
| surf_moisture | 0..1 QuantityValue |
Water held on a surface | direct |
| surf_moisture_ph | 0..1 Double |
ph measurement of surface | direct |
| surf_temp | 0..1 QuantityValue |
Temperature of the surface at the time of sampling | direct |
| suspend_part_matter | 0..1 QuantityValue |
Concentration of suspended particulate matter | direct |
| suspend_solids | * TextValue |
Concentration of substances including a wide variety of material, such as sil... | direct |
| tan | 0..1 QuantityValue |
Total Acid Number (TAN) is a measurement of acidity that is determined by th... | direct |
| temp | 0..1 QuantityValue |
Temperature of the sample at the time of sampling | direct |
| temp_out | 0..1 QuantityValue |
The recorded temperature value at sampling time outside | direct |
| tertiary_treatment | 0..1 TextValue |
The process providing a final treatment stage to raise the effluent quality b... | direct |
| tidal_stage | 0..1 TidalStageEnum |
Stage of tide | direct |
| tillage | * TillageEnum |
Note method(s) used for tilling | direct |
| tiss_cult_growth_med | 0..1 TextValue |
Description of plant tissue culture growth media used | direct |
| toluene | 0..1 QuantityValue |
Concentration of toluene in the sample | direct |
| tot_carb | 0..1 QuantityValue |
Total carbon content | direct |
| tot_depth_water_col | 0..1 QuantityValue |
Measurement of total depth of water column | direct |
| tot_diss_nitro | 0..1 QuantityValue |
Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... | direct |
| tot_inorg_nitro | 0..1 QuantityValue |
Total inorganic nitrogen content | direct |
| tot_iron | 0..1 QuantityValue |
Concentration of total iron in the sample | direct |
| tot_nitro | 0..1 QuantityValue |
Total nitrogen concentration of water samples, calculated by: total nitrogen ... | direct |
| tot_nitro_cont_meth | 0..1 String |
Reference or method used in determining the total nitrogen | direct |
| tot_nitro_content | 0..1 QuantityValue |
Total nitrogen content of the sample | direct |
| tot_org_c_meth | 0..1 TextValue |
Reference or method used in determining total organic carbon | direct |
| tot_org_carb | 0..1 QuantityValue |
Definition for soil: total organic carbon content of the soil, definition oth... | direct |
| tot_part_carb | 0..1 QuantityValue |
Total particulate carbon content | direct |
| tot_phosp | 0..1 QuantityValue |
Total phosphorus concentration in the sample, calculated by: total phosphorus... | direct |
| tot_phosphate | 0..1 QuantityValue |
Total amount or concentration of phosphate | direct |
| tot_sulfur | 0..1 QuantityValue |
Concentration of total sulfur in the sample | direct |
| train_line | 0..1 TrainLineEnum |
The subway line name | direct |
| train_stat_loc | 0..1 TrainStatLocEnum |
The train station collection location | direct |
| train_stop_loc | 0..1 TrainStopLocEnum |
The train stop collection location | direct |
| turbidity | 0..1 QuantityValue |
Measure of the amount of cloudiness or haziness in water caused by individual... | direct |
| tvdss_of_hcr_press | 0..1 QuantityValue |
True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... | direct |
| tvdss_of_hcr_temp | 0..1 QuantityValue |
True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... | direct |
| typ_occup_density | 0..1 Double |
Customary or normal density of occupants | direct |
| ventilation_rate | 0..1 QuantityValue |
Ventilation rate of the system in the sampled premises | direct |
| ventilation_type | 0..1 TextValue |
Ventilation system used in the sampled premises | direct |
| vfa | 0..1 QuantityValue |
Concentration of Volatile Fatty Acids in the sample | direct |
| vfa_fw | 0..1 QuantityValue |
Original volatile fatty acid concentration in the hydrocarbon resource | direct |
| vis_media | 0..1 VisMediaEnum |
The building visual media | direct |
| viscosity | 0..1 TextValue |
A measure of oil's resistance to gradual deformation by shear stress or t... | direct |
| volatile_org_comp | * TextValue |
Concentration of carbon-based chemicals that easily evaporate at room tempera... | direct |
| wall_area | 0..1 QuantityValue |
The total area of the sampled room's walls | direct |
| wall_const_type | 0..1 WallConstTypeEnum |
The building class of the wall defined by the composition of the building ele... | direct |
| wall_finish_mat | 0..1 WallFinishMatEnum |
The material utilized to finish the outer most layer of the wall | direct |
| wall_height | 0..1 QuantityValue |
The average height of the walls in the sampled room | direct |
| wall_loc | 0..1 WallLocEnum |
The relative location of the wall within the room | direct |
| wall_surf_treatment | 0..1 WallSurfTreatmentEnum |
The surface treatment of interior wall | direct |
| wall_texture | 0..1 WallTextureEnum |
The feel, appearance, or consistency of a wall surface | direct |
| wall_thermal_mass | 0..1 QuantityValue |
The ability of the wall to provide inertia against temperature fluctuations | direct |
| wall_water_mold | 0..1 TextValue |
Signs of the presence of mold or mildew on a wall | direct |
| wastewater_type | 0..1 TextValue |
The origin of wastewater such as human waste, rainfall, storm drains, etc | direct |
| water_cont_soil_meth | 0..1 String |
Reference or method used in determining the water content of soil | direct |
| water_content | * String |
Water content measurement | direct |
| water_current | 0..1 QuantityValue |
Measurement of magnitude and direction of flow within a fluid | direct |
| water_cut | 0..1 QuantityValue |
Current amount of water (%) in a produced fluid stream; or the average of the... | direct |
| water_feat_size | 0..1 QuantityValue |
The size of the water feature | direct |
| water_feat_type | 0..1 WaterFeatTypeEnum |
The type of water feature present within the building being sampled | direct |
| water_prod_rate | 0..1 QuantityValue |
Water production rates per well (e | direct |
| water_temp_regm | * TextValue |
Information about treatment involving an exposure to water with varying degre... | direct |
| watering_regm | * TextValue |
Information about treatment involving an exposure to watering frequencies, tr... | direct |
| weekday | 0..1 WeekdayEnum |
The day of the week when sampling occurred | direct |
| win | 0..1 TextValue |
A unique identifier of a well or wellbore | direct |
| wind_direction | 0..1 TextValue |
Wind direction is the direction from which a wind originates | direct |
| wind_speed | 0..1 QuantityValue |
Speed of wind measured at the time of sampling | direct |
| window_cond | 0..1 WindowCondEnum |
The physical condition of the window at the time of sampling | direct |
| window_cover | 0..1 WindowCoverEnum |
The type of window covering | direct |
| window_horiz_pos | 0..1 WindowHorizPosEnum |
The horizontal position of the window on the wall | direct |
| window_loc | 0..1 WindowLocEnum |
The relative location of the window within the room | direct |
| window_mat | 0..1 WindowMatEnum |
The type of material used to finish a window | direct |
| window_open_freq | 0..1 TextValue |
The number of times windows are opened per week | direct |
| window_size | 0..1 TextValue |
The window's length and width | direct |
| window_status | 0..1 TextValue |
Defines whether the windows were open or closed during environmental testing | direct |
| window_type | 0..1 WindowTypeEnum |
The type of windows | direct |
| window_vert_pos | 0..1 WindowVertPosEnum |
The vertical position of the window on the wall | direct |
| window_water_mold | 0..1 TextValue |
Signs of the presence of mold or mildew on the window | direct |
| xylene | 0..1 QuantityValue |
Concentration of xylene in the sample | direct |
| zinc | 0..1 QuantityValue |
Concentration of zinc in the sample | direct |
| ecosystem | 0..1 String |
An ecosystem is a combination of a physical environment (abiotic factors) and... | direct |
| ecosystem_category | 0..1 String |
Ecosystem categories represent divisions within the ecosystem based on specif... | direct |
| ecosystem_type | 0..1 String |
Ecosystem types represent things having common characteristics within the Eco... | direct |
| ecosystem_subtype | 0..1 String |
Ecosystem subtypes represent further subdivision of Ecosystem types into more... | direct |
| specific_ecosystem | 0..1 String |
Specific ecosystems represent specific features of the environment like aphot... | direct |
| add_date | 0..1 String |
The date on which the information was added to the database | direct |
| community | 0..1 String |
direct | |
| habitat | 0..1 String |
direct | |
| host_name | 0..1 String |
direct | |
| location | 0..1 String |
direct | |
| mod_date | 0..1 String |
The last date on which the database information was modified | direct |
| ncbi_taxonomy_name | 0..1 String |
direct | |
| proport_woa_temperature | 0..1 String |
direct | |
| salinity_category | 0..1 String |
Categorical description of the sample's salinity | direct |
| sample_collection_site | 0..1 String |
direct | |
| soluble_iron_micromol | 0..1 String |
direct | |
| subsurface_depth | 0..1 QuantityValue |
direct | |
| air_temp_regm | * TextValue |
Information about treatment involving an exposure to varying temperatures; sh... | direct |
| biotic_regm | 0..1 TextValue |
Information about treatment(s) involving use of biotic factors, such as bacte... | direct |
| biotic_relationship | 0..1 BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... | direct |
| climate_environment | * TextValue |
Treatment involving an exposure to a particular climate; treatment regimen in... | direct |
| experimental_factor | 0..1 ControlledTermValue |
Experimental factors are essentially the variable aspects of an experiment de... | direct |
| gaseous_environment | * TextValue |
Use of conditions with differing gaseous environments; should include the nam... | direct |
| growth_facil | 0..1 ControlledTermValue |
Type of facility where the sampled plant was grown; controlled vocabulary: gr... | direct |
| humidity_regm | * TextValue |
Information about treatment involving an exposure to varying degree of humidi... | direct |
| light_regm | 0..1 TextValue |
Information about treatment(s) involving exposure to light, including both li... | direct |
| phosphate | 0..1 QuantityValue |
Concentration of phosphate | direct |
| samp_collec_method | 0..1 String |
The method employed for collecting the sample | direct |
| samp_size | 0..1 QuantityValue |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | direct |
| source_mat_id | 0..1 TextValue |
A globally unique identifier assigned to the biological sample | direct |
| watering_regm | * TextValue |
Information about treatment involving an exposure to watering frequencies, tr... | direct |
| dna_absorb1 | 0..1 recommended Float |
260/280 measurement of DNA sample purity | direct |
| dna_absorb2 | 0..1 recommended Float |
260/230 measurement of DNA sample purity | direct |
| dna_collect_site | 0..1 recommended String |
Provide information on the site your DNA sample was collected from | direct |
| dna_concentration | 0..1 recommended Float |
direct | |
| dna_cont_type | 0..1 recommended JgiContTypeEnum |
Tube or plate (96-well) | direct |
| dna_cont_well | 0..1 recommended String |
direct | |
| dna_container_id | 0..1 recommended String |
direct | |
| dna_dnase | 0..1 recommended YesNoEnum |
direct | |
| dna_isolate_meth | 0..1 recommended String |
Describe the method/protocol/kit used to extract DNA/RNA | direct |
| dna_organisms | 0..1 recommended String |
List any organisms known or suspected to grow in co-culture, as well as estim... | direct |
| dna_project_contact | 0..1 recommended String |
direct | |
| dna_samp_id | 0..1 recommended String |
direct | |
| dna_sample_format | 0..1 recommended DNASampleFormatEnum |
Solution in which the DNA sample has been suspended | direct |
| dna_sample_name | 0..1 recommended String |
Give the DNA sample a name that is meaningful to you | direct |
| dna_seq_project | 0..1 recommended String |
direct | |
| dna_seq_project_pi | 0..1 recommended String |
direct | |
| dna_seq_project_name | 0..1 recommended String |
direct | |
| dna_volume | 0..1 recommended Float |
direct | |
| proposal_dna | 0..1 recommended String |
direct | |
| dnase_rna | 0..1 recommended YesNoEnum |
direct | |
| proposal_rna | 0..1 recommended String |
direct | |
| rna_absorb1 | 0..1 recommended Float |
260/280 measurement of RNA sample purity | direct |
| rna_absorb2 | 0..1 recommended Float |
260/230 measurement of RNA sample purity | direct |
| rna_collect_site | 0..1 recommended String |
Provide information on the site your RNA sample was collected from | direct |
| rna_concentration | 0..1 recommended Float |
direct | |
| rna_cont_type | 0..1 recommended JgiContTypeEnum |
Tube or plate (96-well) | direct |
| rna_cont_well | 0..1 recommended String |
direct | |
| rna_container_id | 0..1 recommended String |
direct | |
| rna_isolate_meth | 0..1 recommended String |
Describe the method/protocol/kit used to extract DNA/RNA | direct |
| rna_organisms | 0..1 recommended String |
List any organisms known or suspected to grow in co-culture, as well as estim... | direct |
| rna_project_contact | 0..1 recommended String |
direct | |
| rna_samp_id | 0..1 recommended String |
direct | |
| rna_sample_format | 0..1 recommended RNASampleFormatEnum |
Solution in which the RNA sample has been suspended | direct |
| rna_sample_name | 0..1 recommended String |
Give the RNA sample a name that is meaningful to you | direct |
| rna_seq_project | 0..1 recommended String |
direct | |
| rna_seq_project_pi | 0..1 recommended String |
direct | |
| rna_seq_project_name | 0..1 recommended String |
direct | |
| rna_volume | 0..1 recommended Float |
direct | |
| collection_date_inc | 0..1 recommended String |
Date the incubation was harvested/collected/ended | direct |
| collection_time | 0..1 recommended String |
The time of sampling, either as an instance (single point) or interval | direct |
| collection_time_inc | 0..1 recommended String |
Time the incubation was harvested/collected/ended | direct |
| experimental_factor_other | 0..1 recommended String |
Other details about your sample that you feel can't be accurately represented... | direct |
| filter_method | 0..1 recommended String |
Type of filter used or how the sample was filtered | direct |
| isotope_exposure | 0..1 recommended String |
List isotope exposure or addition applied to your sample | direct |
| micro_biomass_c_meth | 0..1 recommended String |
Reference or method used in determining microbial biomass carbon | direct |
| micro_biomass_n_meth | 0..1 String |
Reference or method used in determining microbial biomass nitrogen | direct |
| microbial_biomass_c | 0..1 String |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
| microbial_biomass_n | 0..1 String |
The part of the organic matter in the soil that constitutes living microorgan... | direct |
| non_microb_biomass | 0..1 String |
Amount of biomass; should include the name for the part of biomass measured, ... | direct |
| non_microb_biomass_method | 0..1 String |
Reference or method used in determining biomass | direct |
| org_nitro_method | 0..1 String |
Method used for obtaining organic nitrogen | direct |
| other_treatment | 0..1 recommended String |
Other treatments applied to your samples that are not applicable to the provi... | direct |
| start_date_inc | 0..1 recommended String |
Date the incubation was started | direct |
| start_time_inc | 0..1 recommended String |
Time the incubation was started | direct |
| project_id | 0..1 recommended String |
Proposal IDs or names associated with dataset | direct |
| replicate_number | 0..1 recommended String |
If sending biological replicates, indicate the rep number here | direct |
| sample_shipped | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... | direct |
| sample_type | 0..1 recommended SampleTypeEnum |
Type of sample being submitted | direct |
| technical_reps | 0..1 recommended String |
If sending technical replicates of the same sample, indicate the replicate co... | direct |
| analysis_type | * recommended AnalysisTypeEnum |
Select all the data types associated or available for this biosample | direct |
| sample_link | * recommended String |
A unique identifier to assign parent-child, subsample, or sibling samples | direct |
| bulk_elect_conductivity | 0..1 QuantityValue |
Electrical conductivity is a measure of the ability to carry electric current... | direct |
| infiltrations | * String |
The amount of time it takes to complete each infiltration activity | direct |
| zinc | 0..1 QuantityValue |
Concentration of zinc in the sample | direct |
| manganese | 0..1 QuantityValue |
Concentration of manganese in the sample | direct |
| ammonium_nitrogen | 0..1 QuantityValue |
Concentration of ammonium nitrogen in the sample | direct |
| nitrate_nitrogen | 0..1 QuantityValue |
Concentration of nitrate nitrogen in the sample | direct |
| nitrite_nitrogen | 0..1 QuantityValue |
Concentration of nitrite nitrogen in the sample | direct |
| lbc_thirty | 0..1 QuantityValue |
lime buffer capacity, determined after 30 minute incubation | direct |
| lbceq | 0..1 QuantityValue |
lime buffer capacity, determined at equilibrium after 5 day incubation | direct |
| id | 1 Uriorcurie |
An NMDC assigned unique identifier for a biosample submitted to NMDC | NamedThing |
| name | 0..1 String |
A human readable label for an entity | NamedThing |
| description | 0..1 String |
a human-readable description of a thing | NamedThing |
| alternative_identifiers | * Uriorcurie |
Unique identifier for a biosample submitted to additional resources | NamedThing |
| type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | NamedThing |
Usages
| used by | used in | type | used |
|---|---|---|---|
| NucleotideSequencing | has_input | any_of[range] | Biosample |
| MassSpectrometry | has_input | any_of[range] | Biosample |
| Database | biosample_set | range | Biosample |
| Pooling | has_input | any_of[range] | Biosample |
| Extraction | has_input | any_of[range] | Biosample |
| LibraryPreparation | has_input | any_of[range] | Biosample |
| CollectingBiosamplesFromSite | has_output | range | Biosample |
| SubSamplingProcess | has_input | any_of[range] | Biosample |
| MixingProcess | has_input | any_of[range] | Biosample |
| FiltrationProcess | has_input | any_of[range] | Biosample |
| ChromatographicSeparationProcess | has_input | any_of[range] | Biosample |
| DissolvingProcess | has_input | any_of[range] | Biosample |
| ChemicalConversionProcess | has_input | any_of[range] | Biosample |
| MaterialProcessing | has_input | any_of[range] | Biosample |
| DataGeneration | has_input | any_of[range] | Biosample |
Aliases
- sample
- material sample
- specimen
- biospecimen
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | nmdc:Biosample |
| native | nmdc:Biosample |
| exact | OBI:0000747, NCIT:C43412, http://purl.obolibrary.org/obo/FBcv_0003024 |
LinkML Source
Direct
name: Biosample
description: Biological source material which can be characterized by an experiment.
alt_descriptions:
embl.ena:
source: embl.ena
description: A sample contains information about the sequenced source material.
Samples are associated with checklists, which define the fields used to annotate
the samples. Samples are always associated with a taxon.
notes:
- could add GOLD and EBI's biosample definitions to the alt_descriptions?
in_subset:
- sample subset
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample
- material sample
- specimen
- biospecimen
exact_mappings:
- OBI:0000747
- NCIT:C43412
- http://purl.obolibrary.org/obo/FBcv_0003024
is_a: MaterialEntity
slots:
- associated_studies
- biosample_categories
- collected_from
- embargoed
- host_disease_stat
- host_taxid
- img_identifiers
- neon_biosample_identifiers
- samp_name
- gold_biosample_identifiers
- insdc_biosample_identifiers
- emsl_biosample_identifiers
- igsn_biosample_identifiers
- abs_air_humidity
- add_recov_method
- additional_info
- address
- adj_room
- aero_struc
- agrochem_addition
- air_PM_concen
- air_temp
- air_temp_regm
- al_sat
- al_sat_meth
- alkalinity
- alkalinity_method
- alkyl_diethers
- alt
- aminopept_act
- ammonium
- ammonium_nitrogen
- amount_light
- ances_data
- annual_precpt
- annual_temp
- antibiotic_regm
- api
- arch_struc
- aromatics_pc
- asphaltenes_pc
- atmospheric_data
- avg_dew_point
- avg_occup
- avg_temp
- bac_prod
- bac_resp
- bacteria_carb_prod
- barometric_press
- basin
- bathroom_count
- bedroom_count
- benzene
- biochem_oxygen_dem
- biocide
- biocide_admin_method
- biol_stat
- biomass
- biotic_regm
- biotic_relationship
- bishomohopanol
- blood_press_diast
- blood_press_syst
- bromide
- build_docs
- build_occup_type
- building_setting
- built_struc_age
- built_struc_set
- built_struc_type
- calcium
- carb_dioxide
- carb_monoxide
- carb_nitro_ratio
- ceil_area
- ceil_cond
- ceil_finish_mat
- ceil_struc
- ceil_texture
- ceil_thermal_mass
- ceil_type
- ceil_water_mold
- chem_administration
- chem_mutagen
- chem_oxygen_dem
- chem_treat_method
- chem_treatment
- chloride
- chlorophyll
- climate_environment
- collection_date
- conduc
- cool_syst_id
- core field
- crop_rotation
- cult_root_med
- cur_land_use
- cur_vegetation
- cur_vegetation_meth
- date_last_rain
- density
- depos_env
- depth
- dew_point
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_inorg_nitro
- diss_inorg_phosp
- diss_iron
- diss_org_carb
- diss_org_nitro
- diss_oxygen
- diss_oxygen_fluid
- dna_cont_well
- door_comp_type
- door_cond
- door_direct
- door_loc
- door_mat
- door_move
- door_size
- door_type
- door_type_metal
- door_type_wood
- door_water_mold
- down_par
- drainage_class
- drawings
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- efficiency_percent
- elev
- elevator
- emulsions
- env_broad_scale
- env_local_scale
- env_medium
- env_package
- environment field
- escalator
- ethylbenzene
- exp_duct
- exp_pipe
- experimental_factor
- ext_door
- ext_wall_orient
- ext_window_orient
- extreme_event
- fao_class
- fertilizer_regm
- field
- filter_type
- fire
- fireplace_type
- flooding
- floor_age
- floor_area
- floor_cond
- floor_count
- floor_finish_mat
- floor_struc
- floor_thermal_mass
- floor_water_mold
- fluor
- freq_clean
- freq_cook
- fungicide_regm
- furniture
- gaseous_environment
- gaseous_substances
- gender_restroom
- genetic_mod
- geo_loc_name
- glucosidase_act
- gravidity
- gravity
- growth_facil
- growth_habit
- growth_hormone_regm
- hall_count
- handidness
- hc_produced
- hcr
- hcr_fw_salinity
- hcr_geol_age
- hcr_pressure
- hcr_temp
- heat_cool_type
- heat_deliv_loc
- heat_sys_deliv_meth
- heat_system_id
- heavy_metals
- heavy_metals_meth
- height_carper_fiber
- herbicide_regm
- horizon_meth
- host_age
- host_body_habitat
- host_body_product
- host_body_site
- host_body_temp
- host_color
- host_common_name
- host_diet
- host_dry_mass
- host_family_relation
- host_genotype
- host_growth_cond
- host_height
- host_last_meal
- host_length
- host_life_stage
- host_phenotype
- host_sex
- host_shape
- host_subject_id
- host_subspecf_genlin
- host_substrate
- host_symbiont
- host_taxid
- host_tot_mass
- host_wet_mass
- humidity
- humidity_regm
- indoor_space
- indoor_surf
- indust_eff_percent
- inorg_particles
- inside_lux
- int_wall_cond
- investigation field
- iw_bt_date_well
- iwf
- last_clean
- lat_lon
- lbc_thirty
- lbceq
- light_intensity
- light_regm
- light_type
- link_addit_analys
- link_class_info
- link_climate_info
- lithology
- local_class
- local_class_meth
- magnesium
- manganese
- max_occup
- mean_frict_vel
- mean_peak_frict_vel
- mech_struc
- mechanical_damage
- methane
- micro_biomass_meth
- microbial_biomass
- mineral_nutr_regm
- misc_param
- n_alkanes
- nitrate
- nitrate_nitrogen
- nitrite
- nitrite_nitrogen
- nitro
- non_min_nutr_regm
- nucleic acid sequence source field
- number_pets
- number_plants
- number_resident
- occup_density_samp
- occup_document
- occup_samp
- org_carb
- org_count_qpcr_info
- org_matter
- org_nitro
- org_particles
- organism_count
- owc_tvdss
- oxy_stat_samp
- oxygen
- part_org_carb
- part_org_nitro
- particle_class
- permeability
- perturbation
- pesticide_regm
- petroleum_hydrocarb
- ph
- ph_meth
- ph_regm
- phaeopigments
- phosphate
- phosplipid_fatt_acid
- photon_flux
- plant_growth_med
- plant_product
- plant_sex
- plant_struc
- pollutants
- porosity
- potassium
- pour_point
- pre_treatment
- pres_animal_insect
- pressure
- prev_land_use_meth
- previous_land_use
- primary_prod
- primary_treatment
- prod_rate
- prod_start_date
- profile_position
- quad_pos
- radiation_regm
- rainfall_regm
- reactor_type
- redox_potential
- rel_air_humidity
- rel_humidity_out
- rel_samp_loc
- reservoir
- resins_pc
- room_air_exch_rate
- room_architec_elem
- room_condt
- room_connected
- room_count
- room_dim
- room_door_dist
- room_door_share
- room_hallway
- room_loc
- room_moist_dam_hist
- room_net_area
- room_occup
- room_samp_pos
- room_type
- room_vol
- room_wall_share
- room_window_count
- root_cond
- root_med_carbon
- root_med_macronutr
- root_med_micronutr
- root_med_ph
- root_med_regl
- root_med_solid
- root_med_suppl
- salinity
- salinity_meth
- salt_regm
- samp_capt_status
- samp_collec_device
- samp_collec_method
- samp_collect_point
- samp_dis_stage
- samp_floor
- samp_loc_corr_rate
- samp_mat_process
- samp_md
- samp_name
- samp_preserv
- samp_room_id
- samp_size
- samp_sort_meth
- samp_store_dur
- samp_store_loc
- samp_store_temp
- samp_subtype
- samp_taxon_id
- samp_time_out
- samp_transport_cond
- samp_tvdss
- samp_type
- samp_weather
- samp_well_name
- saturates_pc
- season
- season_environment
- season_precpt
- season_temp
- season_use
- secondary_treatment
- sediment_type
- sequencing field
- sewage_type
- shad_dev_water_mold
- shading_device_cond
- shading_device_loc
- shading_device_mat
- shading_device_type
- sieving
- silicate
- size_frac
- size_frac_low
- size_frac_up
- slope_aspect
- slope_gradient
- sludge_retent_time
- sodium
- soil_horizon
- soil_text_measure
- soil_texture_meth
- soil_type
- soil_type_meth
- solar_irradiance
- soluble_inorg_mat
- soluble_org_mat
- soluble_react_phosp
- source_mat_id
- space_typ_state
- specific
- specific_ecosystem
- specific_humidity
- sr_dep_env
- sr_geol_age
- sr_kerog_type
- sr_lithology
- standing_water_regm
- store_cond
- substructure_type
- sulfate
- sulfate_fw
- sulfide
- surf_air_cont
- surf_humidity
- surf_material
- surf_moisture
- surf_moisture_ph
- surf_temp
- suspend_part_matter
- suspend_solids
- tan
- temp
- temp_out
- tertiary_treatment
- tidal_stage
- tillage
- tiss_cult_growth_med
- toluene
- tot_carb
- tot_depth_water_col
- tot_diss_nitro
- tot_inorg_nitro
- tot_iron
- tot_nitro
- tot_nitro_cont_meth
- tot_nitro_content
- tot_org_c_meth
- tot_org_carb
- tot_part_carb
- tot_phosp
- tot_phosphate
- tot_sulfur
- train_line
- train_stat_loc
- train_stop_loc
- turbidity
- tvdss_of_hcr_press
- tvdss_of_hcr_temp
- typ_occup_density
- ventilation_rate
- ventilation_type
- vfa
- vfa_fw
- vis_media
- viscosity
- volatile_org_comp
- wall_area
- wall_const_type
- wall_finish_mat
- wall_height
- wall_loc
- wall_surf_treatment
- wall_texture
- wall_thermal_mass
- wall_water_mold
- wastewater_type
- water_cont_soil_meth
- water_content
- water_current
- water_cut
- water_feat_size
- water_feat_type
- water_prod_rate
- water_temp_regm
- watering_regm
- weekday
- win
- wind_direction
- wind_speed
- window_cond
- window_cover
- window_horiz_pos
- window_loc
- window_mat
- window_open_freq
- window_size
- window_status
- window_type
- window_vert_pos
- window_water_mold
- xylene
- zinc
- ecosystem
- ecosystem_category
- ecosystem_type
- ecosystem_subtype
- specific_ecosystem
- add_date
- community
- habitat
- host_name
- location
- mod_date
- ncbi_taxonomy_name
- proport_woa_temperature
- salinity_category
- sample_collection_site
- soluble_iron_micromol
- subsurface_depth
- air_temp_regm
- biotic_regm
- biotic_relationship
- climate_environment
- experimental_factor
- gaseous_environment
- growth_facil
- humidity_regm
- light_regm
- phosphate
- samp_collec_method
- samp_size
- source_mat_id
- watering_regm
- dna_absorb1
- dna_absorb2
- dna_collect_site
- dna_concentration
- dna_cont_type
- dna_cont_well
- dna_container_id
- dna_dnase
- dna_isolate_meth
- dna_organisms
- dna_project_contact
- dna_samp_id
- dna_sample_format
- dna_sample_name
- dna_seq_project
- dna_seq_project_pi
- dna_seq_project_name
- dna_volume
- proposal_dna
- dnase_rna
- proposal_rna
- rna_absorb1
- rna_absorb2
- rna_collect_site
- rna_concentration
- rna_cont_type
- rna_cont_well
- rna_container_id
- rna_isolate_meth
- rna_organisms
- rna_project_contact
- rna_samp_id
- rna_sample_format
- rna_sample_name
- rna_seq_project
- rna_seq_project_pi
- rna_seq_project_name
- rna_volume
- collection_date_inc
- collection_time
- collection_time_inc
- experimental_factor_other
- filter_method
- isotope_exposure
- micro_biomass_c_meth
- micro_biomass_n_meth
- microbial_biomass_c
- microbial_biomass_n
- non_microb_biomass
- non_microb_biomass_method
- org_nitro_method
- other_treatment
- start_date_inc
- start_time_inc
- project_id
- replicate_number
- sample_shipped
- sample_type
- technical_reps
- analysis_type
- sample_link
- bulk_elect_conductivity
- infiltrations
- zinc
- manganese
- ammonium_nitrogen
- nitrate_nitrogen
- nitrite_nitrogen
- lbc_thirty
- lbceq
slot_usage:
collected_from:
name: collected_from
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
elev:
name: elev
title: elevation, meters
comments:
- All elevations must be reported in meters. Provide the numerical portion only.
- Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
if needed, to help estimate the elevation based on latitude and longitude coordinates.
examples:
- value: '100'
range: float
id:
name: id
description: An NMDC assigned unique identifier for a biosample submitted to NMDC.
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'
interpolated: true
gold_biosample_identifiers:
name: gold_biosample_identifiers
annotations:
tooltip:
tag: tooltip
value: Provide the GOLD biosample IDs associated with this biosample.
description: Unique identifier for a biosample submitted to GOLD that matches
the NMDC submitted biosample
comments:
- This is the ID provided by GOLD that starts with 'GB'
alternative_identifiers:
name: alternative_identifiers
description: Unique identifier for a biosample submitted to additional resources.
Matches the entity that has been submitted to NMDC
lat_lon:
name: lat_lon
notes:
- This is currently a required field but it's not clear if this should be required
for human hosts
env_broad_scale:
name: env_broad_scale
required: true
env_local_scale:
name: env_local_scale
required: true
env_medium:
name: env_medium
required: true
associated_studies:
name: associated_studies
range: Study
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'
interpolated: true
fire:
name: fire
annotations:
expected_value:
tag: expected_value
value: date string
todos:
- is "to" acceptable? Is there a better way to request that be written?
comments:
- Provide the date the fire occurred. If extended burning occurred provide the
date range.
examples:
- value: '1871-10-10'
- value: 1871-10-01 to 1871-10-31
range: string
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?(\s+to\s+[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)?$
flooding:
name: flooding
annotations:
expected_value:
tag: expected_value
value: date string
todos:
- is "to" acceptable? Is there a better way to request that be written?
- What about if the "day" isn't known? Is this ok?
comments:
- Provide the date the flood occurred. If extended flooding occurred provide the
date range.
examples:
- value: '1927-04-15'
- value: 1927-04 to 1927-05
range: string
extreme_event:
name: extreme_event
annotations:
expected_value:
tag: expected_value
value: date, string
examples:
- value: 1980-05-18, volcanic eruption
range: string
slope_aspect:
name: slope_aspect
description: The direction a slope faces. While looking down a slope use a compass
to record the direction you are facing (direction or degrees). This measure
provides an indication of sun and wind exposure that will influence soil temperature
and evapotranspiration.
comments:
- Aspect is the orientation of slope, measured clockwise in degrees from 0 to
360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270
is west-facing.
examples:
- value: '35'
slope_gradient:
name: slope_gradient
todos:
- Slope is a percent. How does the validation work? Check to correct examples
examples:
- value: 10%
- value: 10 %
- value: '0.10'
al_sat:
name: al_sat
description: The relative abundance of aluminum in the sample
title: aluminum saturation/ extreme unusual properties
todos:
- Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
validate?
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
I would argue this isn't an extreme unusual property. It's just a biogeochemical
measurement.
notes:
- Aluminum saturation is the percentage of the CEC occupies by aluminum. Like
all cations, aluminum held by the cation exchange complex is in equilibrium
with aluminum in the soil solution.
examples:
- value: 27%
al_sat_meth:
name: al_sat_meth
description: Reference or method used in determining Aluminum saturation
title: aluminum saturation method/ extreme unusual properties
todos:
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
comments:
- Required when aluminum saturation is provided.
examples:
- value: https://doi.org/10.1371/journal.pone.0176357
annual_precpt:
name: annual_precpt
examples:
- value: 8.94 inch
cur_vegetation:
name: cur_vegetation
description: Vegetation classification from one or more standard classification
systems, or agricultural crop
todos:
- Recommend changing this from text value to some king of ontology?
comments:
- Values provided here can be specific species of vegetation or vegetation regions
- See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region
examples:
- value: deciduous forest
- value: forest
- value: Bauhinia variegata
cur_vegetation_meth:
name: cur_vegetation_meth
todos:
- I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
out how they accomplish this if provided.
comments:
- Required when current vegetation is provided.
examples:
- value: https://doi.org/10.1111/j.1654-109X.2011.01154.x
heavy_metals:
name: heavy_metals
description: Heavy metals present in the sample and their concentrations.
title: heavy metals/ extreme unusual properties
todos:
- Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
validate?
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
I would argue this isn't an extreme unusual property. It's just a biogeochemical
measurement.
comments:
- For multiple heavy metals and concentrations, separate by ;
examples:
- value: mercury 0.09 micrograms per gram
- value: mercury 0.09 ug/g; chromium 0.03 ug/g
heavy_metals_meth:
name: heavy_metals_meth
title: heavy metals method/ extreme unusual properties
comments:
- Required when heavy metals are provided
- If different methods are used for multiple metals, indicate the metal and method.
Separate metals by ;
examples:
- value: https://doi.org/10.3390/ijms9040434
- value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8
multivalued: true
season_precpt:
name: season_precpt
title: average seasonal precipitation
todos:
- check validation & examples. always mm? so value only? Or value + unit
notes:
- mean and average are the same thing, but it seems like bad practice to not be
consistent. Changed mean to average
comments:
- Seasons are defined as spring (March, April, May), summer (June, July, August),
autumn (September, October, November) and winter (December, January, February).
examples:
- value: 0.4 inch
- value: 10.16 mm
water_cont_soil_meth:
name: water_cont_soil_meth
todos:
- Why is it soil water content method in the name but not the title? Is this slot
used in other samples?
- Soil water content can be measure MANY ways and often, multiple ways are used
in one experiment (gravimetric water content and water holding capacity and
water filled pore space, to name a few).
- Should this be multi valued? How to we manage and validate this?
comments:
- Required if providing water content
examples:
- value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503
- value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm
water_content:
name: water_content
annotations:
expected_value:
tag: expected_value
value: string
preferred_unit:
tag: preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
todos:
- value in preferred unit is too limiting. need to change this
- check and correct validation so examples are accepted
- how to manage multiple water content methods?
examples:
- value: 0.75 g water/g dry soil
- value: 75% water holding capacity
- value: 1.1 g fresh weight/ dry weight
- value: 10% water filled pore space
range: string
multivalued: true
ph_meth:
name: ph_meth
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
tot_carb:
name: tot_carb
todos:
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
examples:
- value: 1 ug/L
tot_nitro_cont_meth:
name: tot_nitro_cont_meth
examples:
- value: https://doi.org/10.2134/agronmonogr9.2.c32
- value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
tot_nitro_content:
name: tot_nitro_content
examples:
- value: 5 mg N/ L
tot_org_c_meth:
name: tot_org_c_meth
examples:
- value: https://doi.org/10.1080/07352680902776556
tot_org_carb:
name: tot_org_carb
todos:
- check description. How are they different?
examples:
- value: 5 mg N/ L
salinity_meth:
name: salinity_meth
examples:
- value: https://doi.org/10.1007/978-1-61779-986-0_28
sieving:
name: sieving
todos:
- check validation and examples
comments:
- Describe how samples were composited or sieved.
- Use 'sample link' to indicate which samples were combined.
examples:
- value: combined 2 cores | 4mm sieved
- value: 4 mm sieved and homogenized
- value: 50 g | 5 cores | 2 mm sieved
climate_environment:
name: climate_environment
todos:
- description says "can include multiple climates" but multivalued is set to false
- add examples, i need to see some examples to add correctly formatted example.
gaseous_environment:
name: gaseous_environment
todos:
- would like to see usage examples for this slot. Requiring micromole/L seems
too limiting and doesn't match expected_value value
- did I do this right? keep the example that's provided and add another? so as
to not override
examples:
- value: CO2; 500ppm above ambient; constant
- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
watering_regm:
name: watering_regm
examples:
- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
- value: 75% water holding capacity; constant
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.
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/).
examples:
- value: IGSN:AU1243
- value: UUID:24f1467a-40f4-11ed-b878-0242ac120002
class_uri: nmdc:Biosample
unique_keys:
samp_name_unique_key:
unique_key_name: samp_name_unique_key
unique_key_slots:
- samp_name
rules:
- preconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: .+
postconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
description: DNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: dna_well_requires_plate
- preconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
postconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: DNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case. Waiting for value_present
validation to be added to runtime
title: dna_plate_requires_well
- preconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: .+
postconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
description: RNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: rna_well_requires_plate
- preconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
postconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: RNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case. Waiting for value_present
validation to be added to runtime
title: rna_plate_requires_well
Induced
name: Biosample
description: Biological source material which can be characterized by an experiment.
alt_descriptions:
embl.ena:
source: embl.ena
description: A sample contains information about the sequenced source material.
Samples are associated with checklists, which define the fields used to annotate
the samples. Samples are always associated with a taxon.
notes:
- could add GOLD and EBI's biosample definitions to the alt_descriptions?
in_subset:
- sample subset
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample
- material sample
- specimen
- biospecimen
exact_mappings:
- OBI:0000747
- NCIT:C43412
- http://purl.obolibrary.org/obo/FBcv_0003024
is_a: MaterialEntity
slot_usage:
collected_from:
name: collected_from
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
elev:
name: elev
title: elevation, meters
comments:
- All elevations must be reported in meters. Provide the numerical portion only.
- Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,
if needed, to help estimate the elevation based on latitude and longitude coordinates.
examples:
- value: '100'
range: float
id:
name: id
description: An NMDC assigned unique identifier for a biosample submitted to NMDC.
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'
interpolated: true
gold_biosample_identifiers:
name: gold_biosample_identifiers
annotations:
tooltip:
tag: tooltip
value: Provide the GOLD biosample IDs associated with this biosample.
description: Unique identifier for a biosample submitted to GOLD that matches
the NMDC submitted biosample
comments:
- This is the ID provided by GOLD that starts with 'GB'
alternative_identifiers:
name: alternative_identifiers
description: Unique identifier for a biosample submitted to additional resources.
Matches the entity that has been submitted to NMDC
lat_lon:
name: lat_lon
notes:
- This is currently a required field but it's not clear if this should be required
for human hosts
env_broad_scale:
name: env_broad_scale
required: true
env_local_scale:
name: env_local_scale
required: true
env_medium:
name: env_medium
required: true
associated_studies:
name: associated_studies
range: Study
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'
interpolated: true
fire:
name: fire
annotations:
expected_value:
tag: expected_value
value: date string
todos:
- is "to" acceptable? Is there a better way to request that be written?
comments:
- Provide the date the fire occurred. If extended burning occurred provide the
date range.
examples:
- value: '1871-10-10'
- value: 1871-10-01 to 1871-10-31
range: string
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?(\s+to\s+[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)?$
flooding:
name: flooding
annotations:
expected_value:
tag: expected_value
value: date string
todos:
- is "to" acceptable? Is there a better way to request that be written?
- What about if the "day" isn't known? Is this ok?
comments:
- Provide the date the flood occurred. If extended flooding occurred provide the
date range.
examples:
- value: '1927-04-15'
- value: 1927-04 to 1927-05
range: string
extreme_event:
name: extreme_event
annotations:
expected_value:
tag: expected_value
value: date, string
examples:
- value: 1980-05-18, volcanic eruption
range: string
slope_aspect:
name: slope_aspect
description: The direction a slope faces. While looking down a slope use a compass
to record the direction you are facing (direction or degrees). This measure
provides an indication of sun and wind exposure that will influence soil temperature
and evapotranspiration.
comments:
- Aspect is the orientation of slope, measured clockwise in degrees from 0 to
360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270
is west-facing.
examples:
- value: '35'
slope_gradient:
name: slope_gradient
todos:
- Slope is a percent. How does the validation work? Check to correct examples
examples:
- value: 10%
- value: 10 %
- value: '0.10'
al_sat:
name: al_sat
description: The relative abundance of aluminum in the sample
title: aluminum saturation/ extreme unusual properties
todos:
- Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
validate?
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
I would argue this isn't an extreme unusual property. It's just a biogeochemical
measurement.
notes:
- Aluminum saturation is the percentage of the CEC occupies by aluminum. Like
all cations, aluminum held by the cation exchange complex is in equilibrium
with aluminum in the soil solution.
examples:
- value: 27%
al_sat_meth:
name: al_sat_meth
description: Reference or method used in determining Aluminum saturation
title: aluminum saturation method/ extreme unusual properties
todos:
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
comments:
- Required when aluminum saturation is provided.
examples:
- value: https://doi.org/10.1371/journal.pone.0176357
annual_precpt:
name: annual_precpt
examples:
- value: 8.94 inch
cur_vegetation:
name: cur_vegetation
description: Vegetation classification from one or more standard classification
systems, or agricultural crop
todos:
- Recommend changing this from text value to some king of ontology?
comments:
- Values provided here can be specific species of vegetation or vegetation regions
- See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region
examples:
- value: deciduous forest
- value: forest
- value: Bauhinia variegata
cur_vegetation_meth:
name: cur_vegetation_meth
todos:
- I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
out how they accomplish this if provided.
comments:
- Required when current vegetation is provided.
examples:
- value: https://doi.org/10.1111/j.1654-109X.2011.01154.x
heavy_metals:
name: heavy_metals
description: Heavy metals present in the sample and their concentrations.
title: heavy metals/ extreme unusual properties
todos:
- Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
validate?
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
I would argue this isn't an extreme unusual property. It's just a biogeochemical
measurement.
comments:
- For multiple heavy metals and concentrations, separate by ;
examples:
- value: mercury 0.09 micrograms per gram
- value: mercury 0.09 ug/g; chromium 0.03 ug/g
heavy_metals_meth:
name: heavy_metals_meth
title: heavy metals method/ extreme unusual properties
comments:
- Required when heavy metals are provided
- If different methods are used for multiple metals, indicate the metal and method.
Separate metals by ;
examples:
- value: https://doi.org/10.3390/ijms9040434
- value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8
multivalued: true
season_precpt:
name: season_precpt
title: average seasonal precipitation
todos:
- check validation & examples. always mm? so value only? Or value + unit
notes:
- mean and average are the same thing, but it seems like bad practice to not be
consistent. Changed mean to average
comments:
- Seasons are defined as spring (March, April, May), summer (June, July, August),
autumn (September, October, November) and winter (December, January, February).
examples:
- value: 0.4 inch
- value: 10.16 mm
water_cont_soil_meth:
name: water_cont_soil_meth
todos:
- Why is it soil water content method in the name but not the title? Is this slot
used in other samples?
- Soil water content can be measure MANY ways and often, multiple ways are used
in one experiment (gravimetric water content and water holding capacity and
water filled pore space, to name a few).
- Should this be multi valued? How to we manage and validate this?
comments:
- Required if providing water content
examples:
- value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503
- value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm
water_content:
name: water_content
annotations:
expected_value:
tag: expected_value
value: string
preferred_unit:
tag: preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
todos:
- value in preferred unit is too limiting. need to change this
- check and correct validation so examples are accepted
- how to manage multiple water content methods?
examples:
- value: 0.75 g water/g dry soil
- value: 75% water holding capacity
- value: 1.1 g fresh weight/ dry weight
- value: 10% water filled pore space
range: string
multivalued: true
ph_meth:
name: ph_meth
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
tot_carb:
name: tot_carb
todos:
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
examples:
- value: 1 ug/L
tot_nitro_cont_meth:
name: tot_nitro_cont_meth
examples:
- value: https://doi.org/10.2134/agronmonogr9.2.c32
- value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
tot_nitro_content:
name: tot_nitro_content
examples:
- value: 5 mg N/ L
tot_org_c_meth:
name: tot_org_c_meth
examples:
- value: https://doi.org/10.1080/07352680902776556
tot_org_carb:
name: tot_org_carb
todos:
- check description. How are they different?
examples:
- value: 5 mg N/ L
salinity_meth:
name: salinity_meth
examples:
- value: https://doi.org/10.1007/978-1-61779-986-0_28
sieving:
name: sieving
todos:
- check validation and examples
comments:
- Describe how samples were composited or sieved.
- Use 'sample link' to indicate which samples were combined.
examples:
- value: combined 2 cores | 4mm sieved
- value: 4 mm sieved and homogenized
- value: 50 g | 5 cores | 2 mm sieved
climate_environment:
name: climate_environment
todos:
- description says "can include multiple climates" but multivalued is set to false
- add examples, i need to see some examples to add correctly formatted example.
gaseous_environment:
name: gaseous_environment
todos:
- would like to see usage examples for this slot. Requiring micromole/L seems
too limiting and doesn't match expected_value value
- did I do this right? keep the example that's provided and add another? so as
to not override
examples:
- value: CO2; 500ppm above ambient; constant
- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
watering_regm:
name: watering_regm
examples:
- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
- value: 75% water holding capacity; constant
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.
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/).
examples:
- value: IGSN:AU1243
- value: UUID:24f1467a-40f4-11ed-b878-0242ac120002
attributes:
associated_studies:
name: associated_studies
description: The study associated with a resource.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: associated_studies
owner: Biosample
domain_of:
- Biosample
- DataGeneration
range: Study
required: true
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'
interpolated: true
biosample_categories:
name: biosample_categories
title: Categories the biosample belongs to
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: biosample_categories
owner: Biosample
domain_of:
- Biosample
range: BiosampleCategoryEnum
multivalued: true
collected_from:
name: collected_from
description: The Site from which a Biosample was collected
todos:
- add an OBO slot_uri ?
comments:
- this illustrates implementing a Biosample relation with a (binary) slot
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: collected_from
owner: Biosample
domain_of:
- Biosample
range: FieldResearchSite
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
embargoed:
name: embargoed
description: If true, the data are embargoed and not available for public access.
todos:
- make this required?
- first apply to Biosample
- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?
- applying to a Study may not be granular enough
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: embargoed
owner: Biosample
domain_of:
- Biosample
range: boolean
recommended: true
host_disease_stat:
name: host_disease_stat
annotations:
expected_value:
tag: expected_value
value: disease name or Disease Ontology term
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: rabies [DOID:11260]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host disease status
rank: 1000
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000031
alias: host_disease_stat
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_taxid:
name: host_taxid
annotations:
expected_value:
tag: expected_value
value: NCBI taxon identifier
occurrence:
tag: occurrence
value: '1'
description: NCBI taxon id of the host, e.g. 9606
title: host taxid
comments:
- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host taxid
rank: 1000
is_a: core field
slot_uri: MIXS:0000250
alias: host_taxid
owner: Biosample
domain_of:
- Biosample
range: ControlledIdentifiedTermValue
multivalued: false
img_identifiers:
name: img_identifiers
description: A list of identifiers that relate the biosample to records in the
IMG database.
title: IMG Identifiers
todos:
- add is_a or mixin modeling, like other external_database_identifiers
- what class would IMG records belong to?! Are they Studies, Biosamples, or something
else?
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: external_database_identifiers
alias: img_identifiers
owner: Biosample
domain_of:
- MetagenomeAnnotation
- Biosample
- MetatranscriptomeAnnotation
- MetatranscriptomeExpressionAnalysis
- MagsAnalysis
range: external_identifier
multivalued: true
pattern: ^img\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\/\.]*$
neon_biosample_identifiers:
name: neon_biosample_identifiers
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: biosample_identifiers
mixins:
- neon_identifiers
alias: neon_biosample_identifiers
owner: Biosample
domain_of:
- Biosample
range: external_identifier
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
samp_name:
name: samp_name
annotations:
expected_value:
tag: expected_value
value: text
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name.
title: sample name
examples:
- value: ISDsoil1
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample name
rank: 1000
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0001107
alias: samp_name
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
gold_biosample_identifiers:
name: gold_biosample_identifiers
annotations:
tooltip:
tag: tooltip
value: Provide the GOLD biosample IDs associated with this biosample.
description: Unique identifier for a biosample submitted to GOLD that matches
the NMDC submitted biosample
comments:
- This is the ID provided by GOLD that starts with 'GB'
examples:
- value: https://bioregistry.io/gold:Gb0312930
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: biosample_identifiers
mixins:
- gold_identifiers
alias: gold_biosample_identifiers
owner: Biosample
domain_of:
- Biosample
range: uriorcurie
multivalued: true
pattern: ^gold:Gb[0-9]+$
insdc_biosample_identifiers:
name: insdc_biosample_identifiers
description: identifiers for corresponding sample in INSDC
examples:
- value: https://bioregistry.io/biosample:SAMEA5989477
- value: https://bioregistry.io/biosample:SAMD00212331
description: I13_N_5-10 sample from Soil fungal diversity along elevational
gradients
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/bioregistry/bioregistry/issues/108
- https://www.ebi.ac.uk/biosamples/
- https://www.ncbi.nlm.nih.gov/biosample
- https://www.ddbj.nig.ac.jp/biosample/index-e.html
aliases:
- EBI biosample identifiers
- NCBI biosample identifiers
- DDBJ biosample identifiers
rank: 1000
is_a: biosample_identifiers
mixins:
- insdc_identifiers
alias: insdc_biosample_identifiers
owner: Biosample
domain_of:
- Biosample
range: external_identifier
multivalued: true
pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$
emsl_biosample_identifiers:
name: emsl_biosample_identifiers
description: A list of identifiers for the biosample from the EMSL database. This
is used to link the biosample, as modeled by NMDC, to the biosample in the planned
EMSL NEXUS database.
title: EMSL Biosample Identifiers
todos:
- removed "planned" once NEXUS is online
- determine real expansion for emsl prefix
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: biosample_identifiers
mixins:
- emsl_identifiers
alias: emsl_biosample_identifiers
owner: Biosample
domain_of:
- Biosample
range: external_identifier
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
igsn_biosample_identifiers:
name: igsn_biosample_identifiers
description: A list of identifiers for the biosample from the IGSN database.
title: IGSN Biosample Identifiers
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: biosample_identifiers
mixins:
- igsn_identifiers
alias: igsn_biosample_identifiers
owner: Biosample
domain_of:
- Biosample
range: external_identifier
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
abs_air_humidity:
name: abs_air_humidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per gram, kilogram per kilogram, kilogram, pound
occurrence:
tag: occurrence
value: '1'
description: Actual mass of water vapor - mh20 - present in the air water vapor
mixture
title: absolute air humidity
examples:
- value: 9 gram per gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- absolute air humidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000122
alias: abs_air_humidity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0001009
alias: add_recov_method
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000300
alias: additional_info
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
address:
name: address
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The street name and building number where the sampling occurred.
title: address
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- address
rank: 1000
is_a: core field
string_serialization: '{integer}{text}'
slot_uri: MIXS:0000218
alias: address
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
adj_room:
name: adj_room
annotations:
expected_value:
tag: expected_value
value: room name;room number
occurrence:
tag: occurrence
value: '1'
description: List of rooms (room number, room name) immediately adjacent to the
sampling room
title: adjacent rooms
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- adjacent rooms
rank: 1000
is_a: core field
string_serialization: '{text};{integer}'
slot_uri: MIXS:0000219
alias: adj_room
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
aero_struc:
name: aero_struc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Aerospace structures typically consist of thin plates with stiffeners
for the external surfaces, bulkheads and frames to support the shape and fasteners
such as welds, rivets, screws and bolts to hold the components together
title: aerospace structure
examples:
- value: plane
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aerospace structure
rank: 1000
is_a: core field
string_serialization: '[plane|glider]'
slot_uri: MIXS:0000773
alias: aero_struc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
agrochem_addition:
name: agrochem_addition
annotations:
expected_value:
tag: expected_value
value: agrochemical name;agrochemical amount;timestamp
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Addition of fertilizers, pesticides, etc. - amount and time of applications
title: history/agrochemical additions
examples:
- value: roundup;5 milligram per liter;2018-06-21
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/agrochemical additions
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{timestamp}'
slot_uri: MIXS:0000639
alias: agrochem_addition
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
air_PM_concen:
name: air_PM_concen
annotations:
expected_value:
tag: expected_value
value: particulate matter name;measurement value
preferred_unit:
tag: preferred_unit
value: micrograms per cubic meter
occurrence:
tag: occurrence
value: m
description: Concentration of substances that remain suspended in the air, and
comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can
report multiple PM's by entering numeric values preceded by name of PM
title: air particulate matter concentration
examples:
- value: PM2.5;10 microgram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- air particulate matter concentration
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000108
alias: air_PM_concen
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
air_temp:
name: air_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 of the air at the time of sampling
title: air temperature
examples:
- value: 20 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- air temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000124
alias: air_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
air_temp_regm:
name: air_temp_regm
annotations:
expected_value:
tag: expected_value
value: temperature value;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving an exposure to varying temperatures;
should include the temperature, treatment regimen including how many times the
treatment was repeated, how long each treatment lasted, and the start and end
time of the entire treatment; can include different temperature regimens
title: air temperature regimen
examples:
- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- air temperature regimen
rank: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000551
alias: air_temp_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
al_sat:
name: al_sat
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percentage
occurrence:
tag: occurrence
value: '1'
description: The relative abundance of aluminum in the sample
title: aluminum saturation/ extreme unusual properties
todos:
- Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
validate?
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
I would argue this isn't an extreme unusual property. It's just a biogeochemical
measurement.
notes:
- Aluminum saturation is the percentage of the CEC occupies by aluminum. Like
all cations, aluminum held by the cation exchange complex is in equilibrium
with aluminum in the soil solution.
examples:
- value: 27%
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- extreme_unusual_properties/Al saturation
rank: 1000
is_a: core field
slot_uri: MIXS:0000607
alias: al_sat
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
al_sat_meth:
name: al_sat_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or URL
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining Aluminum saturation
title: aluminum saturation method/ extreme unusual properties
todos:
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
comments:
- Required when aluminum saturation is provided.
examples:
- value: https://doi.org/10.1371/journal.pone.0176357
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- extreme_unusual_properties/Al saturation method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000324
alias: al_sat_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000421
alias: alkalinity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000298
alias: alkalinity_method
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
alkyl_diethers:
name: alkyl_diethers
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of alkyl diethers
title: alkyl diethers
examples:
- value: 0.005 mole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- alkyl diethers
rank: 1000
is_a: core field
slot_uri: MIXS:0000490
alias: alkyl_diethers
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
alt:
name: alt
annotations:
expected_value:
tag: expected_value
value: measurement value
description: Altitude is a term used to identify heights of objects such as airplanes,
space shuttles, rockets, atmospheric balloons and heights of places such as
atmospheric layers and clouds. It is used to measure the height of an object
which is above the earth's surface. In this context, the altitude measurement
is the vertical distance between the earth's surface above sea level and the
sampled position in the air
title: altitude
examples:
- value: 100 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- altitude
rank: 1000
is_a: environment field
slot_uri: MIXS:0000094
alias: alt
owner: Biosample
domain_of:
- agriculture
- air
- built environment
- core
- food-animal and animal feed
- food-farm environment
- food-food production facility
- food-human foods
- host-associated
- human-associated
- human-gut
- human-oral
- human-skin
- human-vaginal
- hydrocarbon resources-cores
- hydrocarbon resources-fluids_swabs
- microbial mat_biofilm
- miscellaneous natural or artificial environment
- plant-associated
- sediment
- soil
- symbiont-associated
- wastewater_sludge
- water
- Biosample
range: QuantityValue
multivalued: false
aminopept_act:
name: aminopept_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of aminopeptidase activity
title: aminopeptidase activity
examples:
- value: 0.269 mole per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- aminopeptidase activity
rank: 1000
is_a: core field
slot_uri: MIXS:0000172
alias: aminopept_act
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000427
alias: ammonium
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
ammonium_nitrogen:
name: ammonium_nitrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mg/kg
occurrence:
tag: occurrence
value: '1'
description: Concentration of ammonium nitrogen in the sample
title: ammonium nitrogen
examples:
- value: 2.3 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
aliases:
- ammonium_nitrogen
- NH4-N
rank: 1000
alias: ammonium_nitrogen
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
amount_light:
name: amount_light
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: lux, lumens per square meter
occurrence:
tag: occurrence
value: '1'
description: The unit of illuminance and luminous emittance, measuring luminous
flux per unit area
title: amount of light
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- amount of light
rank: 1000
is_a: core field
slot_uri: MIXS:0000140
alias: amount_light
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
ances_data:
name: ances_data
annotations:
expected_value:
tag: expected_value
value: free text
occurrence:
tag: occurrence
value: '1'
description: Information about either pedigree or other ancestral information
description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
(meaning [(A x B) x B] x B)
title: ancestral data
examples:
- value: A/3*B
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ancestral data
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000247
alias: ances_data
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
annual_precpt:
name: annual_precpt
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millimeter
occurrence:
tag: occurrence
value: '1'
description: The average of all annual precipitation values known, or an estimated
equivalent value derived by such methods as regional indexes or Isohyetal maps.
title: mean annual precipitation
examples:
- value: 8.94 inch
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean annual precipitation
rank: 1000
is_a: core field
slot_uri: MIXS:0000644
alias: annual_precpt
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
annual_temp:
name: annual_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Mean annual temperature
title: mean annual temperature
examples:
- value: 12.5 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean annual temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000642
alias: annual_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
antibiotic_regm:
name: antibiotic_regm
annotations:
expected_value:
tag: expected_value
value: antibiotic name;antibiotic amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: milligram
occurrence:
tag: occurrence
value: m
description: Information about treatment involving antibiotic administration;
should include the name of antibiotic, amount administered, treatment regimen
including how many times the treatment was repeated, how long each treatment
lasted, and the start and end time of the entire treatment; can include multiple
antibiotic regimens
title: antibiotic regimen
examples:
- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- antibiotic regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000553
alias: antibiotic_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
slot_uri: MIXS:0000157
alias: api
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
arch_struc:
name: arch_struc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: An architectural structure is a human-made, free-standing, immobile
outdoor construction
title: architectural structure
examples:
- value: shed
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- architectural structure
rank: 1000
is_a: core field
slot_uri: MIXS:0000774
alias: arch_struc
owner: Biosample
domain_of:
- Biosample
range: arch_struc_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000133
alias: aromatics_pc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000135
alias: asphaltenes_pc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
atmospheric_data:
name: atmospheric_data
annotations:
expected_value:
tag: expected_value
value: atmospheric data name;measurement value
occurrence:
tag: occurrence
value: m
description: Measurement of atmospheric data; can include multiple data
title: atmospheric data
examples:
- value: wind speed;9 knots
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- atmospheric data
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0001097
alias: atmospheric_data
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
avg_dew_point:
name: avg_dew_point
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The average of dew point measures taken at the beginning of every
hour over a 24 hour period on the sampling day
title: average dew point
examples:
- value: 25.5 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- average dew point
rank: 1000
is_a: core field
slot_uri: MIXS:0000141
alias: avg_dew_point
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
avg_occup:
name: avg_occup
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: Daily average occupancy of room. Indicate the number of person(s)
daily occupying the sampling room.
title: average daily occupancy
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- average daily occupancy
rank: 1000
is_a: core field
slot_uri: MIXS:0000775
alias: avg_occup
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
avg_temp:
name: avg_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The average of temperatures taken at the beginning of every hour
over a 24 hour period on the sampling day
title: average temperature
examples:
- value: 12.5 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- average temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000142
alias: avg_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
bac_prod:
name: bac_prod
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter per day
occurrence:
tag: occurrence
value: '1'
description: Bacterial production in the water column measured by isotope uptake
title: bacterial production
examples:
- value: 5 milligram per cubic meter per day
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bacterial production
rank: 1000
is_a: core field
slot_uri: MIXS:0000683
alias: bac_prod
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
bac_resp:
name: bac_resp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter per day, micromole oxygen per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of bacterial respiration in the water column
title: bacterial respiration
examples:
- value: 300 micromole oxygen per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bacterial respiration
rank: 1000
is_a: core field
slot_uri: MIXS:0000684
alias: bac_resp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
bacteria_carb_prod:
name: bacteria_carb_prod
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of bacterial carbon production
title: bacterial carbon production
examples:
- value: 2.53 microgram per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bacterial carbon production
rank: 1000
is_a: core field
slot_uri: MIXS:0000173
alias: bacteria_carb_prod
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
barometric_press:
name: barometric_press
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millibar
occurrence:
tag: occurrence
value: '1'
description: Force per unit area exerted against a surface by the weight of air
above that surface
title: barometric pressure
examples:
- value: 5 millibar
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- barometric pressure
rank: 1000
is_a: core field
slot_uri: MIXS:0000096
alias: barometric_press
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000290
alias: basin
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
bathroom_count:
name: bathroom_count
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of bathrooms in the building
title: bathroom count
examples:
- value: '1'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bathroom count
rank: 1000
is_a: core field
slot_uri: MIXS:0000776
alias: bathroom_count
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
bedroom_count:
name: bedroom_count
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of bedrooms in the building
title: bedroom count
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bedroom count
rank: 1000
is_a: core field
slot_uri: MIXS:0000777
alias: bedroom_count
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000153
alias: benzene
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
biochem_oxygen_dem:
name: biochem_oxygen_dem
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Amount of dissolved oxygen needed by aerobic biological organisms
in a body of water to break down organic material present in a given water sample
at certain temperature over a specific time period
title: biochemical oxygen demand
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biochemical oxygen demand
rank: 1000
is_a: core field
slot_uri: MIXS:0000653
alias: biochem_oxygen_dem
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001011
alias: biocide
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'
slot_uri: MIXS:0000456
alias: biocide_admin_method
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
biol_stat:
name: biol_stat
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The level of genome modification.
title: biological status
examples:
- value: natural
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biological status
rank: 1000
is_a: core field
slot_uri: MIXS:0000858
alias: biol_stat
owner: Biosample
domain_of:
- Biosample
range: biol_stat_enum
multivalued: false
biomass:
name: biomass
annotations:
expected_value:
tag: expected_value
value: biomass type;measurement value
preferred_unit:
tag: preferred_unit
value: ton, kilogram, gram
occurrence:
tag: occurrence
value: m
description: Amount of biomass; should include the name for the part of biomass
measured, e.g. Microbial, total. Can include multiple measurements
title: biomass
examples:
- value: total;20 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biomass
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000174
alias: biomass
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
biotic_regm:
name: biotic_regm
annotations:
expected_value:
tag: expected_value
value: free text
occurrence:
tag: occurrence
value: '1'
description: Information about treatment(s) involving use of biotic factors, such
as bacteria, viruses or fungi.
title: biotic regimen
examples:
- value: sample inoculated with Rhizobium spp. Culture
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- biotic regimen
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001038
alias: biotic_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
biotic_relationship:
name: biotic_relationship
annotations:
expected_value:
tag: expected_value
value: enumeration
description: Description of relationship(s) between the subject organism and other
organism(s) it is associated with. E.g., parasite on species X; mutualist with
species Y. The target organism is the subject of the relationship, and the other
organism(s) is the object
title: observed biotic relationship
examples:
- value: free living
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- observed biotic relationship
rank: 1000
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000028
alias: biotic_relationship
owner: Biosample
domain_of:
- Biosample
range: biotic_relationship_enum
multivalued: false
bishomohopanol:
name: bishomohopanol
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, microgram per gram
occurrence:
tag: occurrence
value: '1'
description: Concentration of bishomohopanol
title: bishomohopanol
examples:
- value: 14 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bishomohopanol
rank: 1000
is_a: core field
slot_uri: MIXS:0000175
alias: bishomohopanol
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
blood_press_diast:
name: blood_press_diast
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millimeter mercury
occurrence:
tag: occurrence
value: '1'
description: Resting diastolic blood pressure, measured as mm mercury
title: host blood pressure diastolic
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host blood pressure diastolic
rank: 1000
is_a: core field
slot_uri: MIXS:0000258
alias: blood_press_diast
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
blood_press_syst:
name: blood_press_syst
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millimeter mercury
occurrence:
tag: occurrence
value: '1'
description: Resting systolic blood pressure, measured as mm mercury
title: host blood pressure systolic
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host blood pressure systolic
rank: 1000
is_a: core field
slot_uri: MIXS:0000259
alias: blood_press_syst
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
bromide:
name: bromide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: parts per million
occurrence:
tag: occurrence
value: '1'
description: Concentration of bromide
title: bromide
examples:
- value: 0.05 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- bromide
rank: 1000
is_a: core field
slot_uri: MIXS:0000176
alias: bromide
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
build_docs:
name: build_docs
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The building design, construction and operation documents
title: design, construction, and operation documents
examples:
- value: maintenance plans
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- design, construction, and operation documents
rank: 1000
is_a: core field
slot_uri: MIXS:0000787
alias: build_docs
owner: Biosample
domain_of:
- Biosample
range: build_docs_enum
multivalued: false
build_occup_type:
name: build_occup_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: The primary function for which a building or discrete part of a building
is intended to be used
title: building occupancy type
examples:
- value: market
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- building occupancy type
rank: 1000
is_a: core field
slot_uri: MIXS:0000761
alias: build_occup_type
owner: Biosample
domain_of:
- Biosample
range: build_occup_type_enum
multivalued: true
building_setting:
name: building_setting
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: A location (geography) where a building is set
title: building setting
examples:
- value: rural
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- building setting
rank: 1000
is_a: core field
slot_uri: MIXS:0000768
alias: building_setting
owner: Biosample
domain_of:
- Biosample
range: building_setting_enum
multivalued: false
built_struc_age:
name: built_struc_age
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: year
occurrence:
tag: occurrence
value: '1'
description: The age of the built structure since construction
title: built structure age
examples:
- value: '15'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- built structure age
rank: 1000
is_a: core field
slot_uri: MIXS:0000145
alias: built_struc_age
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
built_struc_set:
name: built_struc_set
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The characterization of the location of the built structure as high
or low human density
title: built structure setting
examples:
- value: rural
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- built structure setting
rank: 1000
is_a: core field
string_serialization: '[urban|rural]'
slot_uri: MIXS:0000778
alias: built_struc_set
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
built_struc_type:
name: built_struc_type
annotations:
expected_value:
tag: expected_value
value: free text
occurrence:
tag: occurrence
value: '1'
description: A physical structure that is a body or assemblage of bodies in space
to form a system capable of supporting loads
title: built structure type
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- built structure type
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000721
alias: built_struc_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000432
alias: calcium
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
carb_dioxide:
name: carb_dioxide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Carbon dioxide (gas) amount or concentration at the time of sampling
title: carbon dioxide
examples:
- value: 410 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- carbon dioxide
rank: 1000
is_a: core field
slot_uri: MIXS:0000097
alias: carb_dioxide
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
carb_monoxide:
name: carb_monoxide
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, parts per million
occurrence:
tag: occurrence
value: '1'
description: Carbon monoxide (gas) amount or concentration at the time of sampling
title: carbon monoxide
examples:
- value: 0.1 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- carbon monoxide
rank: 1000
is_a: core field
slot_uri: MIXS:0000098
alias: carb_monoxide
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
carb_nitro_ratio:
name: carb_nitro_ratio
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Ratio of amount or concentrations of carbon to nitrogen
title: carbon/nitrogen ratio
examples:
- value: '0.417361111'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- carbon/nitrogen ratio
rank: 1000
is_a: core field
slot_uri: MIXS:0000310
alias: carb_nitro_ratio
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
ceil_area:
name: ceil_area
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square meter
occurrence:
tag: occurrence
value: '1'
description: The area of the ceiling space within the room
title: ceiling area
examples:
- value: 25 square meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling area
rank: 1000
is_a: core field
slot_uri: MIXS:0000148
alias: ceil_area
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
ceil_cond:
name: ceil_cond
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The physical condition of the ceiling at the time of sampling; photos
or video preferred; use drawings to indicate location of damaged areas
title: ceiling condition
examples:
- value: damaged
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000779
alias: ceil_cond
owner: Biosample
domain_of:
- Biosample
range: ceil_cond_enum
multivalued: false
ceil_finish_mat:
name: ceil_finish_mat
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of material used to finish a ceiling
title: ceiling finish material
examples:
- value: stucco
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling finish material
rank: 1000
is_a: core field
slot_uri: MIXS:0000780
alias: ceil_finish_mat
owner: Biosample
domain_of:
- Biosample
range: ceil_finish_mat_enum
multivalued: false
ceil_struc:
name: ceil_struc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The construction format of the ceiling
title: ceiling structure
examples:
- value: concrete
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling structure
rank: 1000
is_a: core field
string_serialization: '[wood frame|concrete]'
slot_uri: MIXS:0000782
alias: ceil_struc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
ceil_texture:
name: ceil_texture
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The feel, appearance, or consistency of a ceiling surface
title: ceiling texture
examples:
- value: popcorn
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling texture
rank: 1000
is_a: core field
slot_uri: MIXS:0000783
alias: ceil_texture
owner: Biosample
domain_of:
- Biosample
range: ceil_texture_enum
multivalued: false
ceil_thermal_mass:
name: ceil_thermal_mass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: joule per degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The ability of the ceiling to provide inertia against temperature
fluctuations. Generally this means concrete that is exposed. A metal deck that
supports a concrete slab will act thermally as long as it is exposed to room
air flow
title: ceiling thermal mass
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling thermal mass
rank: 1000
is_a: core field
slot_uri: MIXS:0000143
alias: ceil_thermal_mass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
ceil_type:
name: ceil_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of ceiling according to the ceiling's appearance or construction
title: ceiling type
examples:
- value: coffered
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling type
rank: 1000
is_a: core field
slot_uri: MIXS:0000784
alias: ceil_type
owner: Biosample
domain_of:
- Biosample
range: ceil_type_enum
multivalued: false
ceil_water_mold:
name: ceil_water_mold
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Signs of the presence of mold or mildew on the ceiling
title: ceiling signs of water/mold
examples:
- value: presence of mold visible
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ceiling signs of water/mold
rank: 1000
is_a: core field
string_serialization: '[presence of mold visible|no presence of mold visible]'
slot_uri: MIXS:0000781
alias: ceil_water_mold
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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];2018-05-11T20:00Z
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical administration
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
alias: chem_administration
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: true
inlined: true
inlined_as_list: true
chem_mutagen:
name: chem_mutagen
annotations:
expected_value:
tag: expected_value
value: mutagen name;mutagen amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: m
description: Treatment involving use of mutagens; should include the name of mutagen,
amount administered, treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment; can include multiple mutagen regimens
title: chemical mutagen
examples:
- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical mutagen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000555
alias: chem_mutagen
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
chem_oxygen_dem:
name: chem_oxygen_dem
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: A measure of the capacity of water to consume oxygen during the decomposition
of organic matter and the oxidation of inorganic chemicals such as ammonia and
nitrite
title: chemical oxygen demand
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chemical oxygen demand
rank: 1000
is_a: core field
slot_uri: MIXS:0000656
alias: chem_oxygen_dem
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'
slot_uri: MIXS:0000457
alias: chem_treat_method
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{text};{timestamp}'
slot_uri: MIXS:0001012
alias: chem_treatment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000429
alias: chloride
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
chlorophyll:
name: chlorophyll
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter, microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of chlorophyll
title: chlorophyll
examples:
- value: 5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- chlorophyll
rank: 1000
is_a: core field
slot_uri: MIXS:0000177
alias: chlorophyll
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
climate_environment:
name: climate_environment
annotations:
expected_value:
tag: expected_value
value: climate name;treatment interval and duration
occurrence:
tag: occurrence
value: m
description: Treatment involving an exposure to a particular climate; treatment
regimen including how many times the treatment was repeated, how long each treatment
lasted, and the start and end time of the entire treatment; can include multiple
climates
title: climate environment
todos:
- description says "can include multiple climates" but multivalued is set to false
- add examples, i need to see some examples to add correctly formatted example.
examples:
- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- climate environment
rank: 1000
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001040
alias: climate_environment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
collection_date:
name: collection_date
annotations:
expected_value:
tag: expected_value
value: date and time
description: 'The time of sampling, either as an instance (single point in time)
or interval. In case no exact time is available, the date/time can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: collection date
examples:
- value: 2018-05-11T10:00:00+01:00; 2018-05-11
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- collection date
rank: 1000
is_a: environment field
slot_uri: MIXS:0000011
alias: collection_date
owner: Biosample
domain_of:
- Biosample
range: TimestampValue
multivalued: false
conduc:
name: conduc
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milliSiemens per centimeter
occurrence:
tag: occurrence
value: '1'
description: Electrical conductivity of water
title: conductivity
examples:
- value: 10 milliSiemens per centimeter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- conductivity
rank: 1000
is_a: core field
slot_uri: MIXS:0000692
alias: conduc
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
cool_syst_id:
name: cool_syst_id
annotations:
expected_value:
tag: expected_value
value: unique identifier
occurrence:
tag: occurrence
value: '1'
description: The cooling system identifier
title: cooling system identifier
examples:
- value: '12345'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- cooling system identifier
rank: 1000
is_a: core field
slot_uri: MIXS:0000785
alias: cool_syst_id
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
core field:
name: core field
description: basic fields
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
abstract: true
alias: core_field
owner: Biosample
domain_of:
- Biosample
range: string
crop_rotation:
name: crop_rotation
annotations:
expected_value:
tag: expected_value
value: crop rotation status;schedule
occurrence:
tag: occurrence
value: '1'
description: Whether or not crop is rotated, and if yes, rotation schedule
title: history/crop rotation
examples:
- value: yes;R2/2017-01-01/2018-12-31/P6M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/crop rotation
rank: 1000
is_a: core field
string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000318
alias: crop_rotation
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
cult_root_med:
name: cult_root_med
annotations:
expected_value:
tag: expected_value
value: name, PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Name or reference for the hydroponic or in vitro culture rooting
medium; can be the name of a commonly used medium or reference to a specific
medium, e.g. Murashige and Skoog medium. If the medium has not been formally
published, use the rooting medium descriptors.
title: culture rooting medium
examples:
- value: http://himedialabs.com/TD/PT158.pdf
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- culture rooting medium
rank: 1000
is_a: core field
string_serialization: '{text}|{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0001041
alias: cult_root_med
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
cur_land_use:
name: cur_land_use
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Present state of sample site
title: current land use
examples:
- value: conifers
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- current land use
rank: 1000
is_a: core field
slot_uri: MIXS:0001080
alias: cur_land_use
owner: Biosample
domain_of:
- Biosample
range: cur_land_use_enum
multivalued: false
cur_vegetation:
name: cur_vegetation
annotations:
expected_value:
tag: expected_value
value: current vegetation type
occurrence:
tag: occurrence
value: '1'
description: Vegetation classification from one or more standard classification
systems, or agricultural crop
title: current vegetation
todos:
- Recommend changing this from text value to some king of ontology?
comments:
- Values provided here can be specific species of vegetation or vegetation regions
- See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region
examples:
- value: deciduous forest
- value: forest
- value: Bauhinia variegata
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- current vegetation
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000312
alias: cur_vegetation
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
cur_vegetation_meth:
name: cur_vegetation_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in vegetation classification
title: current vegetation method
todos:
- I'm not sure this is a DOI, PMID, or URI. Should pool the community and find
out how they accomplish this if provided.
comments:
- Required when current vegetation is provided.
examples:
- value: https://doi.org/10.1111/j.1654-109X.2011.01154.x
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- current vegetation method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000314
alias: cur_vegetation_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
date_last_rain:
name: date_last_rain
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: The date of the last time it rained
title: date last rain
examples:
- value: 2018-05-11:T14:30Z
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- date last rain
rank: 1000
is_a: core field
slot_uri: MIXS:0000786
alias: date_last_rain
owner: Biosample
domain_of:
- Biosample
range: TimestampValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000435
alias: density
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000992
alias: depos_env
owner: Biosample
domain_of:
- Biosample
range: depos_env_enum
multivalued: false
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
examples:
- value: 10 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- depth
rank: 1000
is_a: environment field
slot_uri: MIXS:0000018
alias: depth
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
dew_point:
name: dew_point
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The temperature to which a given parcel of humid air must be cooled,
at constant barometric pressure, for water vapor to condense into water.
title: dew point
examples:
- value: 22 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dew point
rank: 1000
is_a: core field
slot_uri: MIXS:0000129
alias: dew_point
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
diether_lipids:
name: diether_lipids
annotations:
expected_value:
tag: expected_value
value: diether lipid name;measurement value
preferred_unit:
tag: preferred_unit
value: nanogram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of diether lipids; can include multiple types of diether
lipids
title: diether lipids
examples:
- value: 0.2 nanogram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- diether lipids
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000178
alias: diether_lipids
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
slot_uri: MIXS:0000436
alias: diss_carb_dioxide
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
diss_hydrogen:
name: diss_hydrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved hydrogen
title: dissolved hydrogen
examples:
- value: 0.3 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved hydrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000179
alias: diss_hydrogen
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000434
alias: diss_inorg_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
diss_inorg_nitro:
name: diss_inorg_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved inorganic nitrogen
title: dissolved inorganic nitrogen
examples:
- value: 761 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved inorganic nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000698
alias: diss_inorg_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000106
alias: diss_inorg_phosp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000139
alias: diss_iron
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000433
alias: diss_org_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
diss_org_nitro:
name: diss_org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Dissolved organic nitrogen concentration measured as; total dissolved
nitrogen - NH4 - NO3 - NO2
title: dissolved organic nitrogen
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved organic nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000162
alias: diss_org_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
diss_oxygen:
name: diss_oxygen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per kilogram, milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of dissolved oxygen
title: dissolved oxygen
examples:
- value: 175 micromole per kilogram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- dissolved oxygen
rank: 1000
is_a: core field
slot_uri: MIXS:0000119
alias: diss_oxygen
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000438
alias: diss_oxygen_fluid
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
dna_cont_well:
name: dna_cont_well
title: DNA plate position
comments:
- Required when 'plate' is selected for container type.
- Leave blank if the sample will be shipped in a tube.
- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not
pass validation.
- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).
examples:
- value: B2
from_schema: https://w3id.org/nmdc/nmdc
rank: 11
string_serialization: '{96 well plate pos}'
alias: dna_cont_well
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
door_comp_type:
name: door_comp_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The composite type of the door
title: door type, composite
examples:
- value: revolving
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door type, composite
rank: 1000
is_a: core field
slot_uri: MIXS:0000795
alias: door_comp_type
owner: Biosample
domain_of:
- Biosample
range: door_comp_type_enum
multivalued: false
door_cond:
name: door_cond
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The phsical condition of the door
title: door condition
examples:
- value: new
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000788
alias: door_cond
owner: Biosample
domain_of:
- Biosample
range: door_cond_enum
multivalued: false
door_direct:
name: door_direct
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The direction the door opens
title: door direction of opening
examples:
- value: inward
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door direction of opening
rank: 1000
is_a: core field
slot_uri: MIXS:0000789
alias: door_direct
owner: Biosample
domain_of:
- Biosample
range: door_direct_enum
multivalued: false
door_loc:
name: door_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The relative location of the door in the room
title: door location
examples:
- value: north
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door location
rank: 1000
is_a: core field
slot_uri: MIXS:0000790
alias: door_loc
owner: Biosample
domain_of:
- Biosample
range: door_loc_enum
multivalued: false
door_mat:
name: door_mat
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The material the door is composed of
title: door material
examples:
- value: wood
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door material
rank: 1000
is_a: core field
slot_uri: MIXS:0000791
alias: door_mat
owner: Biosample
domain_of:
- Biosample
range: door_mat_enum
multivalued: false
door_move:
name: door_move
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of movement of the door
title: door movement
examples:
- value: swinging
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door movement
rank: 1000
is_a: core field
slot_uri: MIXS:0000792
alias: door_move
owner: Biosample
domain_of:
- Biosample
range: door_move_enum
multivalued: false
door_size:
name: door_size
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square meter
occurrence:
tag: occurrence
value: '1'
description: The size of the door
title: door area or size
examples:
- value: 2.5 square meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door area or size
rank: 1000
is_a: core field
slot_uri: MIXS:0000158
alias: door_size
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
door_type:
name: door_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of door material
title: door type
examples:
- value: wooden
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door type
rank: 1000
is_a: core field
slot_uri: MIXS:0000794
alias: door_type
owner: Biosample
domain_of:
- Biosample
range: door_type_enum
multivalued: false
door_type_metal:
name: door_type_metal
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of metal door
title: door type, metal
examples:
- value: hollow
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door type, metal
rank: 1000
is_a: core field
slot_uri: MIXS:0000796
alias: door_type_metal
owner: Biosample
domain_of:
- Biosample
range: door_type_metal_enum
multivalued: false
door_type_wood:
name: door_type_wood
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of wood door
title: door type, wood
examples:
- value: battened
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door type, wood
rank: 1000
is_a: core field
slot_uri: MIXS:0000797
alias: door_type_wood
owner: Biosample
domain_of:
- Biosample
range: door_type_wood_enum
multivalued: false
door_water_mold:
name: door_water_mold
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Signs of the presence of mold or mildew on a door
title: door signs of water/mold
examples:
- value: presence of mold visible
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- door signs of water/mold
rank: 1000
is_a: core field
string_serialization: '[presence of mold visible|no presence of mold visible]'
slot_uri: MIXS:0000793
alias: door_water_mold
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
down_par:
name: down_par
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microEinstein per square meter per second, microEinstein per square
centimeter per second
occurrence:
tag: occurrence
value: '1'
description: Visible waveband radiance and irradiance measurements in the water
column
title: downward PAR
examples:
- value: 28.71 microEinstein per square meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- downward PAR
rank: 1000
is_a: core field
slot_uri: MIXS:0000703
alias: down_par
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
drainage_class:
name: drainage_class
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Drainage classification from a standard system such as the USDA system
title: drainage classification
examples:
- value: well
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- drainage classification
rank: 1000
is_a: core field
slot_uri: MIXS:0001085
alias: drainage_class
owner: Biosample
domain_of:
- Biosample
range: drainage_class_enum
multivalued: false
drawings:
name: drawings
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The buildings architectural drawings; if design is chosen, indicate
phase-conceptual, schematic, design development, and construction documents
title: drawings
examples:
- value: sketch
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- drawings
rank: 1000
is_a: core field
slot_uri: MIXS:0000798
alias: drawings
owner: Biosample
domain_of:
- Biosample
range: drawings_enum
multivalued: false
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: 1000
is_a: gold_path_field
alias: ecosystem
owner: Biosample
domain_of:
- Biosample
- Study
range: string
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: 1000
is_a: gold_path_field
alias: ecosystem_category
owner: Biosample
domain_of:
- Biosample
- Study
range: string
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: 1000
is_a: gold_path_field
alias: ecosystem_subtype
owner: Biosample
domain_of:
- Biosample
- Study
range: string
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: 1000
is_a: gold_path_field
alias: ecosystem_type
owner: Biosample
domain_of:
- Biosample
- Study
range: string
efficiency_percent:
name: efficiency_percent
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Percentage of volatile solids removed from the anaerobic digestor
title: efficiency percent
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- efficiency percent
rank: 1000
is_a: core field
slot_uri: MIXS:0000657
alias: efficiency_percent
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
elev:
name: elev
annotations:
expected_value:
tag: expected_value
value: measurement value
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: '100'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- elevation
rank: 1000
is_a: environment field
slot_uri: MIXS:0000093
alias: elev
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: float
multivalued: false
elevator:
name: elevator
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of elevators within the built structure
title: elevator count
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- elevator count
rank: 1000
is_a: core field
slot_uri: MIXS:0000799
alias: elevator
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
emulsions:
name: emulsions
annotations:
expected_value:
tag: expected_value
value: emulsion name;measurement value
preferred_unit:
tag: preferred_unit
value: gram per liter
occurrence:
tag: occurrence
value: m
description: Amount or concentration of substances such as paints, adhesives,
mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion
types
title: emulsions
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- emulsions
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000660
alias: emulsions
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
env_broad_scale:
name: env_broad_scale
annotations:
expected_value:
tag: expected_value
value: The major environment type(s) where the sample was collected. Recommend
subclasses of biome [ENVO:00000428]. Multiple terms can be separated by
one or more pipes.
tooltip:
tag: tooltip
value: The biome or major environmental system where the sample or specimen
originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]
in the Environment Ontology (ENVO). For host-associated or plant-associated
samples, use terms from the UBERON or Plant Ontology to describe the broad
anatomical or morphological context
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
sample from the photic zone in middle of the Atlantic Ocean
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- broad-scale environmental context
rank: 1000
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
alias: env_broad_scale
owner: Biosample
domain_of:
- Biosample
range: ControlledIdentifiedTermValue
required: true
multivalued: false
env_local_scale:
name: env_local_scale
annotations:
expected_value:
tag: expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling.
tooltip:
tag: tooltip
value: The specific environmental entities or features near the sample or
specimen that significantly influence its characteristics or composition.
These entities are typically smaller in scale than the broad environmental
context. Values for this field should be countable, material nouns and must
be chosen from subclasses of BFO:0000040 (material entity) that appear in
the Environment Ontology (ENVO). For host-associated or plant-associated
samples, use terms from the UBERON or Plant Ontology to describe specific
anatomical structures or plant parts.
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
examples:
- value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from
various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb
and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub
layer [ENVO:01000336].'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- local environmental context
rank: 1000
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
alias: env_local_scale
owner: Biosample
domain_of:
- Biosample
range: ControlledIdentifiedTermValue
required: true
multivalued: false
env_medium:
name: env_medium
annotations:
expected_value:
tag: expected_value
value: The material displaced by the entity at time of sampling. Recommend
subclasses of environmental material [ENVO:00010483].
tooltip:
tag: tooltip
value: The predominant environmental material or substrate that directly surrounds
or hosts the sample or specimen at the time of sampling. Choose values from
subclasses of the 'environmental material' class [ENVO:00010483] in the
Environment Ontology (ENVO). Values for this field should be measurable
or mass material nouns, representing continuous environmental materials.
For host-associated or plant-associated samples, use terms from the UBERON
or Plant Ontology to indicate a tissue, organ, or plant structure
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
examples:
- value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m
of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating
a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- environmental medium
rank: 1000
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000014
alias: env_medium
owner: Biosample
domain_of:
- Biosample
range: ControlledIdentifiedTermValue
required: true
multivalued: false
env_package:
name: env_package
description: MIxS extension for reporting of measurements and observations obtained
from one or more of the environments where the sample was obtained. All environmental
packages listed here are further defined in separate subtables. By giving the
name of the environmental package, a selection of fields can be made from the
subtables and can be reported
notes:
- no longer in MIxS as of 6.0?
in_subset:
- mixs extension
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- environmental package
rank: 1000
alias: env_package
owner: Biosample
domain_of:
- Biosample
range: TextValue
environment field:
name: environment field
description: field describing environmental aspect of a sample
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
abstract: true
alias: environment_field
owner: Biosample
domain_of:
- Biosample
range: string
escalator:
name: escalator
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of escalators within the built structure
title: escalator count
examples:
- value: '4'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- escalator count
rank: 1000
is_a: core field
slot_uri: MIXS:0000800
alias: escalator
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000155
alias: ethylbenzene
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
exp_duct:
name: exp_duct
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square meter
occurrence:
tag: occurrence
value: '1'
description: The amount of exposed ductwork in the room
title: exposed ductwork
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- exposed ductwork
rank: 1000
is_a: core field
slot_uri: MIXS:0000144
alias: exp_duct
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
exp_pipe:
name: exp_pipe
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The number of exposed pipes in the room
title: exposed pipes
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- exposed pipes
rank: 1000
is_a: core field
slot_uri: MIXS:0000220
alias: exp_pipe
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: investigation field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000008
alias: experimental_factor
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
ext_door:
name: ext_door
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of exterior doors in the built structure
title: exterior door count
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- exterior door count
rank: 1000
is_a: core field
slot_uri: MIXS:0000170
alias: ext_door
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
ext_wall_orient:
name: ext_wall_orient
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The orientation of the exterior wall
title: orientations of exterior wall
examples:
- value: northwest
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- orientations of exterior wall
rank: 1000
is_a: core field
slot_uri: MIXS:0000817
alias: ext_wall_orient
owner: Biosample
domain_of:
- Biosample
range: ext_wall_orient_enum
multivalued: false
ext_window_orient:
name: ext_window_orient
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The compass direction the exterior window of the room is facing
title: orientations of exterior window
examples:
- value: southwest
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- orientations of exterior window
rank: 1000
is_a: core field
slot_uri: MIXS:0000818
alias: ext_window_orient
owner: Biosample
domain_of:
- Biosample
range: ext_window_orient_enum
multivalued: false
extreme_event:
name: extreme_event
annotations:
expected_value:
tag: expected_value
value: date, string
description: Unusual physical events that may have affected microbial populations
title: history/extreme events
examples:
- value: 1980-05-18, volcanic eruption
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/extreme events
rank: 1000
is_a: core field
slot_uri: MIXS:0000320
alias: extreme_event
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
fao_class:
name: fao_class
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Soil classification from the FAO World Reference Database for Soil
Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
title: soil_taxonomic/FAO classification
examples:
- value: Luvisols
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil_taxonomic/FAO classification
rank: 1000
is_a: core field
slot_uri: MIXS:0001083
alias: fao_class
owner: Biosample
domain_of:
- Biosample
range: fao_class_enum
multivalued: false
fertilizer_regm:
name: fertilizer_regm
annotations:
expected_value:
tag: expected_value
value: fertilizer name;fertilizer amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving the use of fertilizers; should
include the name of fertilizer, amount administered, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple fertilizer
regimens
title: fertilizer regimen
examples:
- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- fertilizer regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000556
alias: fertilizer_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000291
alias: field
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
filter_type:
name: filter_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: A device which removes solid particulates or airborne molecular contaminants
title: filter type
examples:
- value: HEPA
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- filter type
rank: 1000
is_a: core field
slot_uri: MIXS:0000765
alias: filter_type
owner: Biosample
domain_of:
- Biosample
range: filter_type_enum
multivalued: true
fire:
name: fire
annotations:
expected_value:
tag: expected_value
value: date string
description: Historical and/or physical evidence of fire
title: history/fire
todos:
- is "to" acceptable? Is there a better way to request that be written?
comments:
- Provide the date the fire occurred. If extended burning occurred provide the
date range.
examples:
- value: '1871-10-10'
- value: 1871-10-01 to 1871-10-31
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/fire
rank: 1000
is_a: core field
slot_uri: MIXS:0001086
alias: fire
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?(\s+to\s+[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)?$
fireplace_type:
name: fireplace_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: A firebox with chimney
title: fireplace type
examples:
- value: wood burning
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- fireplace type
rank: 1000
is_a: core field
string_serialization: '[gas burning|wood burning]'
slot_uri: MIXS:0000802
alias: fireplace_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
flooding:
name: flooding
annotations:
expected_value:
tag: expected_value
value: date string
description: Historical and/or physical evidence of flooding
title: history/flooding
todos:
- is "to" acceptable? Is there a better way to request that be written?
- What about if the "day" isn't known? Is this ok?
comments:
- Provide the date the flood occurred. If extended flooding occurred provide the
date range.
examples:
- value: '1927-04-15'
- value: 1927-04 to 1927-05
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/flooding
rank: 1000
is_a: core field
slot_uri: MIXS:0000319
alias: flooding
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
floor_age:
name: floor_age
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: years, weeks, days
occurrence:
tag: occurrence
value: '1'
description: The time period since installment of the carpet or flooring
title: floor age
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor age
rank: 1000
is_a: core field
slot_uri: MIXS:0000164
alias: floor_age
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
floor_area:
name: floor_area
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square meter
occurrence:
tag: occurrence
value: '1'
description: The area of the floor space within the room
title: floor area
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor area
rank: 1000
is_a: core field
slot_uri: MIXS:0000165
alias: floor_area
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
floor_cond:
name: floor_cond
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The physical condition of the floor at the time of sampling; photos
or video preferred; use drawings to indicate location of damaged areas
title: floor condition
examples:
- value: new
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000803
alias: floor_cond
owner: Biosample
domain_of:
- Biosample
range: floor_cond_enum
multivalued: false
floor_count:
name: floor_count
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of floors in the building, including basements and mechanical
penthouse
title: floor count
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor count
rank: 1000
is_a: core field
slot_uri: MIXS:0000225
alias: floor_count
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
floor_finish_mat:
name: floor_finish_mat
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The floor covering type; the finished surface that is walked on
title: floor finish material
examples:
- value: carpet
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor finish material
rank: 1000
is_a: core field
slot_uri: MIXS:0000804
alias: floor_finish_mat
owner: Biosample
domain_of:
- Biosample
range: floor_finish_mat_enum
multivalued: false
floor_struc:
name: floor_struc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Refers to the structural elements and subfloor upon which the finish
flooring is installed
title: floor structure
examples:
- value: concrete
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor structure
rank: 1000
is_a: core field
slot_uri: MIXS:0000806
alias: floor_struc
owner: Biosample
domain_of:
- Biosample
range: floor_struc_enum
multivalued: false
floor_thermal_mass:
name: floor_thermal_mass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: joule per degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The ability of the floor to provide inertia against temperature fluctuations
title: floor thermal mass
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor thermal mass
rank: 1000
is_a: core field
slot_uri: MIXS:0000166
alias: floor_thermal_mass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
floor_water_mold:
name: floor_water_mold
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Signs of the presence of mold or mildew in a room
title: floor signs of water/mold
examples:
- value: ceiling discoloration
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- floor signs of water/mold
rank: 1000
is_a: core field
slot_uri: MIXS:0000805
alias: floor_water_mold
owner: Biosample
domain_of:
- Biosample
range: floor_water_mold_enum
multivalued: false
fluor:
name: fluor
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram chlorophyll a per cubic meter, volts
occurrence:
tag: occurrence
value: '1'
description: Raw or converted fluorescence of water
title: fluorescence
examples:
- value: 2.5 volts
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- fluorescence
rank: 1000
is_a: core field
slot_uri: MIXS:0000704
alias: fluor
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
freq_clean:
name: freq_clean
annotations:
expected_value:
tag: expected_value
value: enumeration or {text}
occurrence:
tag: occurrence
value: '1'
description: The number of times the sample location is cleaned. Frequency of
cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
title: frequency of cleaning
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- frequency of cleaning
rank: 1000
is_a: core field
slot_uri: MIXS:0000226
alias: freq_clean
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
freq_cook:
name: freq_cook
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The number of times a meal is cooked per week
title: frequency of cooking
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- frequency of cooking
rank: 1000
is_a: core field
slot_uri: MIXS:0000227
alias: freq_cook
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
fungicide_regm:
name: fungicide_regm
annotations:
expected_value:
tag: expected_value
value: fungicide name;fungicide amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving use of fungicides; should include
the name of fungicide, amount administered, treatment regimen including how
many times the treatment was repeated, how long each treatment lasted, and the
start and end time of the entire treatment; can include multiple fungicide regimens
title: fungicide regimen
examples:
- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- fungicide regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000557
alias: fungicide_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
furniture:
name: furniture
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The types of furniture present in the sampled room
title: furniture
examples:
- value: chair
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- furniture
rank: 1000
is_a: core field
slot_uri: MIXS:0000807
alias: furniture
owner: Biosample
domain_of:
- Biosample
range: furniture_enum
multivalued: false
gaseous_environment:
name: gaseous_environment
annotations:
expected_value:
tag: expected_value
value: gaseous compound name;gaseous compound amount;treatment interval and
duration
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: m
description: Use of conditions with differing gaseous environments; should include
the name of gaseous compound, amount administered, treatment duration, interval
and total experimental duration; can include multiple gaseous environment regimens
title: gaseous environment
todos:
- would like to see usage examples for this slot. Requiring micromole/L seems
too limiting and doesn't match expected_value value
- did I do this right? keep the example that's provided and add another? so as
to not override
examples:
- value: CO2; 500ppm above ambient; constant
- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- gaseous environment
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000558
alias: gaseous_environment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
gaseous_substances:
name: gaseous_substances
annotations:
expected_value:
tag: expected_value
value: gaseous substance name;measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: m
description: Amount or concentration of substances such as hydrogen sulfide, carbon
dioxide, methane, etc.; can include multiple substances
title: gaseous substances
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- gaseous substances
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000661
alias: gaseous_substances
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
gender_restroom:
name: gender_restroom
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The gender type of the restroom
title: gender of restroom
examples:
- value: male
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- gender of restroom
rank: 1000
is_a: core field
slot_uri: MIXS:0000808
alias: gender_restroom
owner: Biosample
domain_of:
- Biosample
range: gender_restroom_enum
multivalued: false
genetic_mod:
name: genetic_mod
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url or free text
occurrence:
tag: occurrence
value: '1'
description: Genetic modifications of the genome of an organism, which may occur
naturally by spontaneous mutation, or be introduced by some experimental means,
e.g. specification of a transgene or the gene knocked-out or details of transient
transfection
title: genetic modification
examples:
- value: aox1A transgenic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- genetic modification
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0000859
alias: genetic_mod
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
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: 1000
is_a: environment field
string_serialization: '{term}: {term}, {text}'
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
glucosidase_act:
name: glucosidase_act
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mol per liter per hour
occurrence:
tag: occurrence
value: '1'
description: Measurement of glucosidase activity
title: glucosidase activity
examples:
- value: 5 mol per liter per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- glucosidase activity
rank: 1000
is_a: core field
slot_uri: MIXS:0000137
alias: glucosidase_act
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
gravidity:
name: gravidity
annotations:
expected_value:
tag: expected_value
value: gravidity status;timestamp
occurrence:
tag: occurrence
value: '1'
description: Whether or not subject is gravid, and if yes date due or date post-conception,
specifying which is used
title: gravidity
examples:
- value: yes;due date:2018-05-11
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- gravidity
rank: 1000
is_a: core field
string_serialization: '{boolean};{timestamp}'
slot_uri: MIXS:0000875
alias: gravidity
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
gravity:
name: gravity
annotations:
expected_value:
tag: expected_value
value: gravity factor value;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: meter per square second, g
occurrence:
tag: occurrence
value: m
description: Information about treatment involving use of gravity factor to study
various types of responses in presence, absence or modified levels of gravity;
treatment regimen including how many times the treatment was repeated, how long
each treatment lasted, and the start and end time of the entire treatment; can
include multiple treatments
title: gravity
examples:
- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- gravity
rank: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000559
alias: gravity
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
growth_facil:
name: growth_facil
annotations:
expected_value:
tag: expected_value
value: free text or CO
occurrence:
tag: occurrence
value: '1'
description: 'Type of facility where the sampled plant was grown; controlled vocabulary:
growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively
use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'
title: growth facility
examples:
- value: Growth chamber [CO_715:0000189]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- growth facility
rank: 1000
is_a: core field
string_serialization: '{text}|{termLabel} {[termID]}'
slot_uri: MIXS:0001043
alias: growth_facil
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
growth_habit:
name: growth_habit
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Characteristic shape, appearance or growth form of a plant species
title: growth habit
examples:
- value: spreading
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- growth habit
rank: 1000
is_a: core field
slot_uri: MIXS:0001044
alias: growth_habit
owner: Biosample
domain_of:
- Biosample
range: growth_habit_enum
multivalued: false
growth_hormone_regm:
name: growth_hormone_regm
annotations:
expected_value:
tag: expected_value
value: growth hormone name;growth hormone amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving use of growth hormones; should
include the name of growth hormone, amount administered, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple growth
hormone regimens
title: growth hormone regimen
examples:
- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- growth hormone regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000560
alias: growth_hormone_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
hall_count:
name: hall_count
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The total count of hallways and cooridors in the built structure
title: hallway/corridor count
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- hallway/corridor count
rank: 1000
is_a: core field
slot_uri: MIXS:0000228
alias: hall_count
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
handidness:
name: handidness
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The handidness of the individual sampled
title: handidness
examples:
- value: right handedness
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- handidness
rank: 1000
is_a: core field
slot_uri: MIXS:0000809
alias: handidness
owner: Biosample
domain_of:
- Biosample
range: handidness_enum
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000989
alias: hc_produced
owner: Biosample
domain_of:
- Biosample
range: hc_produced_enum
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000988
alias: hcr
owner: Biosample
domain_of:
- Biosample
range: hcr_enum
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000406
alias: hcr_fw_salinity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000993
alias: hcr_geol_age
owner: Biosample
domain_of:
- Biosample
range: hcr_geol_age_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000395
alias: hcr_pressure
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000393
alias: hcr_temp
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
heat_cool_type:
name: heat_cool_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: Methods of conditioning or heating a room or building
title: heating and cooling system type
examples:
- value: heat pump
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- heating and cooling system type
rank: 1000
is_a: core field
slot_uri: MIXS:0000766
alias: heat_cool_type
owner: Biosample
domain_of:
- Biosample
range: heat_cool_type_enum
multivalued: true
heat_deliv_loc:
name: heat_deliv_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The location of heat delivery within the room
title: heating delivery locations
examples:
- value: north
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- heating delivery locations
rank: 1000
is_a: core field
slot_uri: MIXS:0000810
alias: heat_deliv_loc
owner: Biosample
domain_of:
- Biosample
range: heat_deliv_loc_enum
multivalued: false
heat_sys_deliv_meth:
name: heat_sys_deliv_meth
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The method by which the heat is delivered through the system
title: heating system delivery method
examples:
- value: radiant
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- heating system delivery method
rank: 1000
is_a: core field
string_serialization: '[conductive|radiant]'
slot_uri: MIXS:0000812
alias: heat_sys_deliv_meth
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
heat_system_id:
name: heat_system_id
annotations:
expected_value:
tag: expected_value
value: unique identifier
occurrence:
tag: occurrence
value: '1'
description: The heating system identifier
title: heating system identifier
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- heating system identifier
rank: 1000
is_a: core field
slot_uri: MIXS:0000833
alias: heat_system_id
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
heavy_metals:
name: heavy_metals
annotations:
expected_value:
tag: expected_value
value: heavy metal name;measurement value unit
preferred_unit:
tag: preferred_unit
value: microgram per gram
occurrence:
tag: occurrence
value: m
description: Heavy metals present in the sample and their concentrations.
title: heavy metals/ extreme unusual properties
todos:
- Example & validation. Can we configure things so that 27% & 27 % & 0.27 will
validate?
- I think it's weird the way GSC writes the title. I recommend this change. Thoughts?
I would argue this isn't an extreme unusual property. It's just a biogeochemical
measurement.
comments:
- For multiple heavy metals and concentrations, separate by ;
examples:
- value: mercury 0.09 micrograms per gram
- value: mercury 0.09 ug/g; chromium 0.03 ug/g
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- extreme_unusual_properties/heavy metals
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000652
alias: heavy_metals
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
heavy_metals_meth:
name: heavy_metals_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining heavy metals
title: heavy metals method/ extreme unusual properties
comments:
- Required when heavy metals are provided
- If different methods are used for multiple metals, indicate the metal and method.
Separate metals by ;
examples:
- value: https://doi.org/10.3390/ijms9040434
- value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- extreme_unusual_properties/heavy metals method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000343
alias: heavy_metals_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
height_carper_fiber:
name: height_carper_fiber
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: centimeter
occurrence:
tag: occurrence
value: '1'
description: The average carpet fiber height in the indoor environment
title: height carpet fiber mat
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- height carpet fiber mat
rank: 1000
is_a: core field
slot_uri: MIXS:0000167
alias: height_carper_fiber
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
herbicide_regm:
name: herbicide_regm
annotations:
expected_value:
tag: expected_value
value: herbicide name;herbicide amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving use of herbicides; information
about treatment involving use of growth hormones; should include the name of
herbicide, amount administered, treatment regimen including how many times the
treatment was repeated, how long each treatment lasted, and the start and end
time of the entire treatment; can include multiple regimens
title: herbicide regimen
examples:
- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- herbicide regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000561
alias: herbicide_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
horizon_meth:
name: horizon_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining the horizon
title: soil horizon method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil horizon method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000321
alias: horizon_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_age:
name: host_age
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: year, day, hour
occurrence:
tag: occurrence
value: '1'
description: Age of host at the time of sampling; relevant scale depends on species
and study, e.g. Could be seconds for amoebae or centuries for trees
title: host age
examples:
- value: 10 days
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host age
rank: 1000
is_a: core field
slot_uri: MIXS:0000255
alias: host_age
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
host_body_habitat:
name: host_body_habitat
annotations:
expected_value:
tag: expected_value
value: free text
occurrence:
tag: occurrence
value: '1'
description: Original body habitat where the sample was obtained from
title: host body habitat
examples:
- value: nasopharynx
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host body habitat
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000866
alias: host_body_habitat
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_body_product:
name: host_body_product
annotations:
expected_value:
tag: expected_value
value: FMA or UBERON
occurrence:
tag: occurrence
value: '1'
description: Substance produced by the body, e.g. Stool, mucus, where the sample
was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
or https://www.ebi.ac.uk/ols/ontologies/uberon
title: host body product
examples:
- value: Portion of mucus [fma66938]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host body product
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000888
alias: host_body_product
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
host_body_site:
name: host_body_site
annotations:
expected_value:
tag: expected_value
value: FMA or UBERON
occurrence:
tag: occurrence
value: '1'
description: Name of body site where the sample was obtained from, such as a specific
organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology
(fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
title: host body site
examples:
- value: gill [UBERON:0002535]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host body site
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000867
alias: host_body_site
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
host_body_temp:
name: host_body_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Core body temperature of the host when sample was collected
title: host body temperature
examples:
- value: 15 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host body temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000274
alias: host_body_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
host_color:
name: host_color
annotations:
expected_value:
tag: expected_value
value: color
occurrence:
tag: occurrence
value: '1'
description: The color of host
title: host color
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host color
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000260
alias: host_color
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_common_name:
name: host_common_name
annotations:
expected_value:
tag: expected_value
value: common name
occurrence:
tag: occurrence
value: '1'
description: Common name of the host.
title: host common name
examples:
- value: human
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host common name
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000248
alias: host_common_name
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_diet:
name: host_diet
annotations:
expected_value:
tag: expected_value
value: diet type
occurrence:
tag: occurrence
value: m
description: Type of diet depending on the host, for animals omnivore, herbivore
etc., for humans high-fat, meditteranean etc.; can include multiple diet types
title: host diet
examples:
- value: herbivore
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host diet
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000869
alias: host_diet
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
host_dry_mass:
name: host_dry_mass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: kilogram, gram
occurrence:
tag: occurrence
value: '1'
description: Measurement of dry mass
title: host dry mass
examples:
- value: 500 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host dry mass
rank: 1000
is_a: core field
slot_uri: MIXS:0000257
alias: host_dry_mass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
host_family_relation:
name: host_family_relation
annotations:
expected_value:
tag: expected_value
value: relationship type;arbitrary identifier
occurrence:
tag: occurrence
value: m
description: Familial relationships to other hosts in the same study; can include
multiple relationships
title: host family relationship
examples:
- value: offspring;Mussel25
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host family relationship
rank: 1000
is_a: core field
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
alias: host_family_relation
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: true
host_genotype:
name: host_genotype
annotations:
expected_value:
tag: expected_value
value: genotype
occurrence:
tag: occurrence
value: '1'
description: Observed genotype
title: host genotype
examples:
- value: C57BL/6
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host genotype
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000365
alias: host_genotype
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_growth_cond:
name: host_growth_cond
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url or free text
occurrence:
tag: occurrence
value: '1'
description: Literature reference giving growth conditions of the host
title: host growth conditions
examples:
- value: https://academic.oup.com/icesjms/article/68/2/349/617247
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host growth conditions
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0000871
alias: host_growth_cond
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_height:
name: host_height
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: centimeter, millimeter, meter
occurrence:
tag: occurrence
value: '1'
description: The height of subject
title: host height
examples:
- value: 0.1 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host height
rank: 1000
is_a: core field
slot_uri: MIXS:0000264
alias: host_height
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
host_last_meal:
name: host_last_meal
annotations:
expected_value:
tag: expected_value
value: content;duration
occurrence:
tag: occurrence
value: m
description: Content of last meal and time since feeding; can include multiple
values
title: host last meal
examples:
- value: corn feed;P2H
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host last meal
rank: 1000
is_a: core field
string_serialization: '{text};{duration}'
slot_uri: MIXS:0000870
alias: host_last_meal
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
host_length:
name: host_length
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: centimeter, millimeter, meter
occurrence:
tag: occurrence
value: '1'
description: The length of subject
title: host length
examples:
- value: 1 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host length
rank: 1000
is_a: core field
slot_uri: MIXS:0000256
alias: host_length
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
host_life_stage:
name: host_life_stage
annotations:
expected_value:
tag: expected_value
value: stage
occurrence:
tag: occurrence
value: '1'
description: Description of life stage of host
title: host life stage
examples:
- value: adult
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host life stage
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000251
alias: host_life_stage
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_phenotype:
name: host_phenotype
annotations:
expected_value:
tag: expected_value
value: PATO or HP
occurrence:
tag: occurrence
value: '1'
description: Phenotype of human or other host. For phenotypic quality ontology
(pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
title: host phenotype
examples:
- value: elongated [PATO:0001154]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host phenotype
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000874
alias: host_phenotype
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
host_sex:
name: host_sex
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Gender or physical sex of the host.
title: host sex
examples:
- value: non-binary
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host sex
rank: 1000
is_a: core field
slot_uri: MIXS:0000811
alias: host_sex
owner: Biosample
domain_of:
- Biosample
range: host_sex_enum
multivalued: false
host_shape:
name: host_shape
annotations:
expected_value:
tag: expected_value
value: shape
occurrence:
tag: occurrence
value: '1'
description: Morphological shape of host
title: host shape
examples:
- value: round
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host shape
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000261
alias: host_shape
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_subject_id:
name: host_subject_id
annotations:
expected_value:
tag: expected_value
value: unique identifier
occurrence:
tag: occurrence
value: '1'
description: A unique identifier by which each subject can be referred to, de-identified.
title: host subject id
examples:
- value: MPI123
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host subject id
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000861
alias: host_subject_id
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_subspecf_genlin:
name: host_subspecf_genlin
annotations:
expected_value:
tag: expected_value
value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
e.g. serovar, biotype, ecotype, variety, cultivar.
occurrence:
tag: occurrence
value: m
description: Information about the genetic distinctness of the host organism below
the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
or any relevant genetic typing schemes like Group I plasmid. Subspecies should
not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
name and the lineage rank separated by a colon, e.g., biovar:abc123.
title: host subspecific genetic lineage
examples:
- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host subspecific genetic lineage
rank: 1000
is_a: core field
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0001318
alias: host_subspecf_genlin
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: true
host_substrate:
name: host_substrate
annotations:
expected_value:
tag: expected_value
value: substrate name
occurrence:
tag: occurrence
value: '1'
description: The growth substrate of the host.
title: host substrate
examples:
- value: rock
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host substrate
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000252
alias: host_substrate
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
host_symbiont:
name: host_symbiont
annotations:
expected_value:
tag: expected_value
value: species name or common name
occurrence:
tag: occurrence
value: m
description: The taxonomic name of the organism(s) found living in mutualistic,
commensalistic, or parasitic symbiosis with the specific host.
title: observed host symbionts
examples:
- value: flukeworms
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- observed host symbionts
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001298
alias: host_symbiont
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: true
host_tot_mass:
name: host_tot_mass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: kilogram, gram
occurrence:
tag: occurrence
value: '1'
description: Total mass of the host at collection, the unit depends on host
title: host total mass
examples:
- value: 2500 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host total mass
rank: 1000
is_a: core field
slot_uri: MIXS:0000263
alias: host_tot_mass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
host_wet_mass:
name: host_wet_mass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: kilogram, gram
occurrence:
tag: occurrence
value: '1'
description: Measurement of wet mass
title: host wet mass
examples:
- value: 1500 gram
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- host wet mass
rank: 1000
is_a: core field
slot_uri: MIXS:0000567
alias: host_wet_mass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
humidity:
name: humidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram per cubic meter
occurrence:
tag: occurrence
value: '1'
description: Amount of water vapour in the air, at the time of sampling
title: humidity
examples:
- value: 25 gram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- humidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000100
alias: humidity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
humidity_regm:
name: humidity_regm
annotations:
expected_value:
tag: expected_value
value: humidity value;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram per cubic meter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving an exposure to varying degree
of humidity; information about treatment involving use of growth hormones; should
include amount of humidity administered, treatment regimen including how many
times the treatment was repeated, how long each treatment lasted, and the start
and end time of the entire treatment; can include multiple regimens
title: humidity regimen
examples:
- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- humidity regimen
rank: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000568
alias: humidity_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
indoor_space:
name: indoor_space
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: A distinguishable space within a structure, the purpose for which
discrete areas of a building is used
title: indoor space
examples:
- value: foyer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- indoor space
rank: 1000
is_a: core field
slot_uri: MIXS:0000763
alias: indoor_space
owner: Biosample
domain_of:
- Biosample
range: indoor_space_enum
multivalued: false
indoor_surf:
name: indoor_surf
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Type of indoor surface
title: indoor surface
examples:
- value: wall
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- indoor surface
rank: 1000
is_a: core field
slot_uri: MIXS:0000764
alias: indoor_surf
owner: Biosample
domain_of:
- Biosample
range: indoor_surf_enum
multivalued: false
indust_eff_percent:
name: indust_eff_percent
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percentage
occurrence:
tag: occurrence
value: '1'
description: Percentage of industrial effluents received by wastewater treatment
plant
title: industrial effluent percent
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- industrial effluent percent
rank: 1000
is_a: core field
slot_uri: MIXS:0000662
alias: indust_eff_percent
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
inorg_particles:
name: inorg_particles
annotations:
expected_value:
tag: expected_value
value: inorganic particle name;measurement value
preferred_unit:
tag: preferred_unit
value: mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of particles such as sand, grit, metal particles, ceramics,
etc.; can include multiple particles
title: inorganic particles
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- inorganic particles
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000664
alias: inorg_particles
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
inside_lux:
name: inside_lux
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: kilowatt per square metre
occurrence:
tag: occurrence
value: '1'
description: The recorded value at sampling time (power density)
title: inside lux light
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- inside lux light
rank: 1000
is_a: core field
slot_uri: MIXS:0000168
alias: inside_lux
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
int_wall_cond:
name: int_wall_cond
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The physical condition of the wall at the time of sampling; photos
or video preferred; use drawings to indicate location of damaged areas
title: interior wall condition
examples:
- value: damaged
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- interior wall condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000813
alias: int_wall_cond
owner: Biosample
domain_of:
- Biosample
range: int_wall_cond_enum
multivalued: false
investigation field:
name: investigation field
description: field describing aspect of the investigation/study to which the sample
belongs
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
abstract: true
alias: investigation_field
owner: Biosample
domain_of:
- Biosample
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: 1000
is_a: core field
slot_uri: MIXS:0001010
alias: iw_bt_date_well
owner: Biosample
domain_of:
- Biosample
range: TimestampValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000455
alias: iwf
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
last_clean:
name: last_clean
annotations:
expected_value:
tag: expected_value
value: timestamp
occurrence:
tag: occurrence
value: '1'
description: The last time the floor was cleaned (swept, mopped, vacuumed)
title: last time swept/mopped/vacuumed
examples:
- value: 2018-05-11:T14:30Z
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- last time swept/mopped/vacuumed
rank: 1000
is_a: core field
slot_uri: MIXS:0000814
alias: last_clean
owner: Biosample
domain_of:
- Biosample
range: TimestampValue
multivalued: false
lat_lon:
name: lat_lon
annotations:
expected_value:
tag: expected_value
value: decimal degrees, limit to 8 decimal points
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
examples:
- value: 50.586825 6.408977
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- geographic location (latitude and longitude)
rank: 1000
is_a: environment field
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: GeolocationValue
multivalued: false
lbc_thirty:
name: lbc_thirty
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: ppm CaCO3/pH
occurrence:
tag: occurrence
value: '1'
description: lime buffer capacity, determined after 30 minute incubation
title: lime buffer capacity (at 30 minutes)
comments:
- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
one pH unit
examples:
- value: 543 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF
aliases:
- lbc_thirty
- lbc30
- lime buffer capacity (at 30 minutes)
rank: 1000
alias: lbc_thirty
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
lbceq:
name: lbceq
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: ppm CaCO3/pH
occurrence:
tag: occurrence
value: '1'
description: lime buffer capacity, determined at equilibrium after 5 day incubation
title: lime buffer capacity (after 5 day incubation)
comments:
- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by
one pH unit
examples:
- value: 1575 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
aliases:
- lbceq
- lime buffer capacity (at 5-day equilibrium)
rank: 1000
alias: lbceq
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
light_intensity:
name: light_intensity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: lux
occurrence:
tag: occurrence
value: '1'
description: Measurement of light intensity
title: light intensity
examples:
- value: 0.3 lux
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- light intensity
rank: 1000
is_a: core field
slot_uri: MIXS:0000706
alias: light_intensity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
light_regm:
name: light_regm
annotations:
expected_value:
tag: expected_value
value: exposure type;light intensity;light quality
preferred_unit:
tag: preferred_unit
value: lux; micrometer, nanometer, angstrom
occurrence:
tag: occurrence
value: '1'
description: Information about treatment(s) involving exposure to light, including
both light intensity and quality.
title: light regimen
examples:
- value: incandescant light;10 lux;450 nanometer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- light regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{float} {unit}'
slot_uri: MIXS:0000569
alias: light_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
light_type:
name: light_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: Application of light to achieve some practical or aesthetic effect.
Lighting includes the use of both artificial light sources such as lamps and
light fixtures, as well as natural illumination by capturing daylight. Can also
include absence of light
title: light type
examples:
- value: desk lamp
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- light type
rank: 1000
is_a: core field
slot_uri: MIXS:0000769
alias: light_type
owner: Biosample
domain_of:
- Biosample
range: light_type_enum
multivalued: true
link_addit_analys:
name: link_addit_analys
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Link to additional analysis results performed on the sample
title: links to additional analysis
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- links to additional analysis
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000340
alias: link_addit_analys
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
link_class_info:
name: link_class_info
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Link to digitized soil maps or other soil classification information
title: link to classification information
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- link to classification information
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000329
alias: link_class_info
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
link_climate_info:
name: link_climate_info
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Link to climate resource
title: link to climate information
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- link to climate information
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000328
alias: link_climate_info
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000990
alias: lithology
owner: Biosample
domain_of:
- Biosample
range: lithology_enum
multivalued: false
local_class:
name: local_class
annotations:
expected_value:
tag: expected_value
value: local classification name
occurrence:
tag: occurrence
value: '1'
description: Soil classification based on local soil classification system
title: soil_taxonomic/local classification
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil_taxonomic/local classification
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000330
alias: local_class
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
local_class_meth:
name: local_class_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining the local soil classification
title: soil_taxonomic/local classification method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil_taxonomic/local classification method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000331
alias: local_class_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000431
alias: magnesium
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
manganese:
name: manganese
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mg/kg (ppm)
occurrence:
tag: occurrence
value: '1'
description: Concentration of manganese in the sample
title: manganese
examples:
- value: 24.7 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
aliases:
- manganese
rank: 1000
alias: manganese
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
max_occup:
name: max_occup
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The maximum amount of people allowed in the indoor environment
title: maximum occupancy
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- maximum occupancy
rank: 1000
is_a: core field
slot_uri: MIXS:0000229
alias: max_occup
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
mean_frict_vel:
name: mean_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean friction velocity
title: mean friction velocity
examples:
- value: 0.5 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean friction velocity
rank: 1000
is_a: core field
slot_uri: MIXS:0000498
alias: mean_frict_vel
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
mean_peak_frict_vel:
name: mean_peak_frict_vel
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second
occurrence:
tag: occurrence
value: '1'
description: Measurement of mean peak friction velocity
title: mean peak friction velocity
examples:
- value: 1 meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean peak friction velocity
rank: 1000
is_a: core field
slot_uri: MIXS:0000502
alias: mean_peak_frict_vel
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
mech_struc:
name: mech_struc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'mechanical structure: a moving structure'
title: mechanical structure
examples:
- value: elevator
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mechanical structure
rank: 1000
is_a: core field
slot_uri: MIXS:0000815
alias: mech_struc
owner: Biosample
domain_of:
- Biosample
range: mech_struc_enum
multivalued: false
mechanical_damage:
name: mechanical_damage
annotations:
expected_value:
tag: expected_value
value: damage type;body site
occurrence:
tag: occurrence
value: m
description: Information about any mechanical damage exerted on the plant; can
include multiple damages and sites
title: mechanical damage
examples:
- value: pruning;bark
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mechanical damage
rank: 1000
is_a: core field
string_serialization: '{text};{text}'
slot_uri: MIXS:0001052
alias: mechanical_damage
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
methane:
name: methane
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter, parts per billion, parts per million
occurrence:
tag: occurrence
value: '1'
description: Methane (gas) amount or concentration at the time of sampling
title: methane
examples:
- value: 1800 parts per billion
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- methane
rank: 1000
is_a: core field
slot_uri: MIXS:0000101
alias: methane
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
micro_biomass_meth:
name: micro_biomass_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining microbial biomass
title: microbial biomass method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- microbial biomass method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000339
alias: micro_biomass_meth
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
microbial_biomass:
name: microbial_biomass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: ton, kilogram, gram per kilogram soil
occurrence:
tag: occurrence
value: '1'
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer. If you keep this, you would need
to have correction factors used for conversion to the final units
title: microbial biomass
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- microbial biomass
rank: 1000
is_a: core field
slot_uri: MIXS:0000650
alias: microbial_biomass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
mineral_nutr_regm:
name: mineral_nutr_regm
annotations:
expected_value:
tag: expected_value
value: mineral nutrient name;mineral nutrient amount;treatment interval and
duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving the use of mineral supplements;
should include the name of mineral nutrient, amount administered, treatment
regimen including how many times the treatment was repeated, how long each treatment
lasted, and the start and end time of the entire treatment; can include multiple
mineral nutrient regimens
title: mineral nutrient regimen
examples:
- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mineral nutrient regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000570
alias: mineral_nutr_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
alias: misc_param
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
n_alkanes:
name: n_alkanes
annotations:
expected_value:
tag: expected_value
value: n-alkane name;measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of n-alkanes; can include multiple n-alkanes
title: n-alkanes
examples:
- value: n-hexadecane;100 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- n-alkanes
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000503
alias: n_alkanes
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
slot_uri: MIXS:0000425
alias: nitrate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
nitrate_nitrogen:
name: nitrate_nitrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mg/kg
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrate nitrogen in the sample
title: nitrate_nitrogen
comments:
- often below some specified limit of detection
examples:
- value: 0.29 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
aliases:
- nitrate_nitrogen
- NO3-N
rank: 1000
alias: nitrate_nitrogen
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
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: 1000
is_a: core field
slot_uri: MIXS:0000426
alias: nitrite
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
nitrite_nitrogen:
name: nitrite_nitrogen
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mg/kg
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrite nitrogen in the sample
title: nitrite_nitrogen
examples:
- value: 1.2 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
aliases:
- nitrite_nitrogen
- NO2-N
rank: 1000
alias: nitrite_nitrogen
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
nitro:
name: nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of nitrogen (total)
title: nitrogen
examples:
- value: 4.2 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000504
alias: nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
non_min_nutr_regm:
name: non_min_nutr_regm
annotations:
expected_value:
tag: expected_value
value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval
and duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving the exposure of plant to non-mineral
nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
nutrient, amount administered, treatment regimen including how many times the
treatment was repeated, how long each treatment lasted, and the start and end
time of the entire treatment; can include multiple non-mineral nutrient regimens
title: non-mineral nutrient regimen
examples:
- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- non-mineral nutrient regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000571
alias: non_min_nutr_regm
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: true
nucleic acid sequence source field:
name: nucleic acid sequence source field
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
abstract: true
alias: nucleic_acid_sequence_source_field
owner: Biosample
domain_of:
- Biosample
range: string
number_pets:
name: number_pets
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The number of pets residing in the sampled space
title: number of pets
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- number of pets
rank: 1000
is_a: core field
slot_uri: MIXS:0000231
alias: number_pets
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
number_plants:
name: number_plants
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The number of plant(s) in the sampling space
title: number of houseplants
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- number of houseplants
rank: 1000
is_a: core field
slot_uri: MIXS:0000230
alias: number_plants
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
number_resident:
name: number_resident
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The number of individuals currently occupying in the sampling location
title: number of residents
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- number of residents
rank: 1000
is_a: core field
slot_uri: MIXS:0000232
alias: number_resident
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
occup_density_samp:
name: occup_density_samp
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Average number of occupants at time of sampling per square footage
title: occupant density at sampling
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- occupant density at sampling
rank: 1000
is_a: core field
slot_uri: MIXS:0000217
alias: occup_density_samp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
occup_document:
name: occup_document
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of documentation of occupancy
title: occupancy documentation
examples:
- value: estimate
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- occupancy documentation
rank: 1000
is_a: core field
slot_uri: MIXS:0000816
alias: occup_document
owner: Biosample
domain_of:
- Biosample
range: occup_document_enum
multivalued: false
occup_samp:
name: occup_samp
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Number of occupants present at time of sample within the given space
title: occupancy at sampling
examples:
- value: '10'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- occupancy at sampling
rank: 1000
is_a: core field
slot_uri: MIXS:0000772
alias: occup_samp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
org_carb:
name: org_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic carbon
title: organic carbon
examples:
- value: 1.5 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic carbon
rank: 1000
is_a: core field
slot_uri: MIXS:0000508
alias: org_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
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
alias: org_count_qpcr_info
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
org_matter:
name: org_matter
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic matter
title: organic matter
examples:
- value: 1.75 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic matter
rank: 1000
is_a: core field
slot_uri: MIXS:0000204
alias: org_matter
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
org_nitro:
name: org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of organic nitrogen
title: organic nitrogen
examples:
- value: 4 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000205
alias: org_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
org_particles:
name: org_particles
annotations:
expected_value:
tag: expected_value
value: particle name;measurement value
preferred_unit:
tag: preferred_unit
value: gram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of particles such as faeces, hairs, food, vomit, paper
fibers, plant material, humus, etc.
title: organic particles
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- organic particles
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000665
alias: org_particles
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
slot_uri: MIXS:0000103
alias: organism_count
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: true
inlined: true
inlined_as_list: true
owc_tvdss:
name: owc_tvdss
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)
title: oil water contact depth
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- oil water contact depth
rank: 1000
is_a: core field
slot_uri: MIXS:0000405
alias: owc_tvdss
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000753
alias: oxy_stat_samp
owner: Biosample
domain_of:
- Biosample
range: oxy_stat_samp_enum
multivalued: false
oxygen:
name: oxygen
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: Oxygen (gas) amount or concentration at the time of sampling
title: oxygen
examples:
- value: 600 parts per million
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- oxygen
rank: 1000
is_a: core field
slot_uri: MIXS:0000104
alias: oxygen
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
part_org_carb:
name: part_org_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of particulate organic carbon
title: particulate organic carbon
examples:
- value: 1.92 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- particulate organic carbon
rank: 1000
is_a: core field
slot_uri: MIXS:0000515
alias: part_org_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
part_org_nitro:
name: part_org_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of particulate organic nitrogen
title: particulate organic nitrogen
examples:
- value: 0.3 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- particulate organic nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000719
alias: part_org_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
particle_class:
name: particle_class
annotations:
expected_value:
tag: expected_value
value: particle name;measurement value
preferred_unit:
tag: preferred_unit
value: micrometer
occurrence:
tag: occurrence
value: m
description: Particles are classified, based on their size, into six general categories:clay,
silt, sand, gravel, cobbles, and boulders; should include amount of particle
preceded by the name of the particle type; can include multiple values
title: particle classification
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- particle classification
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000206
alias: particle_class
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
permeability:
name: permeability
annotations:
expected_value:
tag: expected_value
value: measurement value range
preferred_unit:
tag: preferred_unit
value: mD
occurrence:
tag: occurrence
value: '1'
description: 'Measure of the ability of a hydrocarbon resource to allow fluids
to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'
title: permeability
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- permeability
rank: 1000
is_a: core field
string_serialization: '{integer} - {integer} {unit}'
slot_uri: MIXS:0000404
alias: permeability
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
perturbation:
name: perturbation
annotations:
expected_value:
tag: expected_value
value: perturbation type name;perturbation interval and duration
occurrence:
tag: occurrence
value: m
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- perturbation
rank: 1000
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
alias: perturbation
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
pesticide_regm:
name: pesticide_regm
annotations:
expected_value:
tag: expected_value
value: pesticide name;pesticide amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving use of insecticides; should
include the name of pesticide, amount administered, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple pesticide
regimens
title: pesticide regimen
examples:
- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pesticide regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000573
alias: pesticide_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
petroleum_hydrocarb:
name: petroleum_hydrocarb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of petroleum hydrocarbon
title: petroleum hydrocarbon
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- petroleum hydrocarbon
rank: 1000
is_a: core field
slot_uri: MIXS:0000516
alias: petroleum_hydrocarb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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
examples:
- value: '7.2'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pH
rank: 1000
is_a: core field
slot_uri: MIXS:0001001
alias: ph
owner: Biosample
domain_of:
- Biosample
range: double
multivalued: false
ph_meth:
name: ph_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
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
aliases:
- pH method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0001106
alias: ph_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
ph_regm:
name: ph_regm
annotations:
expected_value:
tag: expected_value
value: measurement value;treatment interval and duration
occurrence:
tag: occurrence
value: m
description: Information about treatment involving exposure of plants to varying
levels of ph of the growth media, treatment regimen including how many times
the treatment was repeated, how long each treatment lasted, and the start and
end time of the entire treatment; can include multiple regimen
title: pH regimen
examples:
- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pH regimen
rank: 1000
is_a: core field
string_serialization: '{float};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001056
alias: ph_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
phaeopigments:
name: phaeopigments
annotations:
expected_value:
tag: expected_value
value: phaeopigment name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter
occurrence:
tag: occurrence
value: m
description: Concentration of phaeopigments; can include multiple phaeopigments
title: phaeopigments
examples:
- value: 2.5 milligram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phaeopigments
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000180
alias: phaeopigments
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
phosphate:
name: phosphate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of phosphate
title: phosphate
examples:
- value: 0.7 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phosphate
rank: 1000
is_a: core field
slot_uri: MIXS:0000505
alias: phosphate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
phosplipid_fatt_acid:
name: phosplipid_fatt_acid
annotations:
expected_value:
tag: expected_value
value: phospholipid fatty acid name;measurement value
preferred_unit:
tag: preferred_unit
value: mole per gram, mole per liter
occurrence:
tag: occurrence
value: m
description: Concentration of phospholipid fatty acids; can include multiple values
title: phospholipid fatty acid
examples:
- value: 2.98 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- phospholipid fatty acid
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000181
alias: phosplipid_fatt_acid
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
photon_flux:
name: photon_flux
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: number of photons per second per unit area
occurrence:
tag: occurrence
value: '1'
description: Measurement of photon flux
title: photon flux
examples:
- value: 3.926 micromole photons per second per square meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- photon flux
rank: 1000
is_a: core field
slot_uri: MIXS:0000725
alias: photon_flux
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
plant_growth_med:
name: plant_growth_med
annotations:
expected_value:
tag: expected_value
value: EO or enumeration
occurrence:
tag: occurrence
value: '1'
description: Specification of the media for growing the plants or tissue cultured
samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
vitro liquid culture medium. Recommended value is a specific value from EO:plant
growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
or other controlled vocabulary
title: plant growth medium
examples:
- value: hydroponic plant culture media [EO:0007067]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- plant growth medium
rank: 1000
is_a: core field
slot_uri: MIXS:0001057
alias: plant_growth_med
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
plant_product:
name: plant_product
annotations:
expected_value:
tag: expected_value
value: product name
occurrence:
tag: occurrence
value: '1'
description: Substance produced by the plant, where the sample was obtained from
title: plant product
examples:
- value: xylem sap [PO:0025539]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- plant product
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001058
alias: plant_product
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
plant_sex:
name: plant_sex
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Sex of the reproductive parts on the whole plant, e.g. pistillate,
staminate, monoecieous, hermaphrodite.
title: plant sex
examples:
- value: Hermaphroditic
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- plant sex
rank: 1000
is_a: core field
slot_uri: MIXS:0001059
alias: plant_sex
owner: Biosample
domain_of:
- Biosample
range: plant_sex_enum
multivalued: false
plant_struc:
name: plant_struc
annotations:
expected_value:
tag: expected_value
value: PO
occurrence:
tag: occurrence
value: '1'
description: Name of plant structure the sample was obtained from; for Plant Ontology
(PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
sex of it can be recorded here.
title: plant structure
examples:
- value: epidermis [PO:0005679]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- plant structure
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0001060
alias: plant_struc
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
pollutants:
name: pollutants
annotations:
expected_value:
tag: expected_value
value: pollutant name;measurement value
preferred_unit:
tag: preferred_unit
value: gram, mole per liter, milligram per liter, microgram per cubic meter
occurrence:
tag: occurrence
value: m
description: Pollutant types and, amount or concentrations measured at the time
of sampling; can report multiple pollutants by entering numeric values preceded
by name of pollutant
title: pollutants
examples:
- value: lead;0.15 microgram per cubic meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pollutants
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000107
alias: pollutants
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
porosity:
name: porosity
annotations:
expected_value:
tag: expected_value
value: measurement value or range
preferred_unit:
tag: preferred_unit
value: percentage
occurrence:
tag: occurrence
value: '1'
description: Porosity of deposited sediment is volume of voids divided by the
total volume of sample
title: porosity
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- porosity
rank: 1000
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000211
alias: porosity
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000430
alias: potassium
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000127
alias: pour_point
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
pre_treatment:
name: pre_treatment
annotations:
expected_value:
tag: expected_value
value: pre-treatment type
occurrence:
tag: occurrence
value: '1'
description: The process of pre-treatment removes materials that can be easily
collected from the raw wastewater
title: pre-treatment
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- pre-treatment
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000348
alias: pre_treatment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
pres_animal_insect:
name: pres_animal_insect
annotations:
expected_value:
tag: expected_value
value: enumeration;count
occurrence:
tag: occurrence
value: '1'
description: The type and number of animals or insects present in the sampling
space.
title: presence of pets, animals, or insects
examples:
- value: cat;5
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- presence of pets, animals, or insects
rank: 1000
is_a: core field
slot_uri: MIXS:0000819
alias: pres_animal_insect
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
pattern: ^(cat|dog|rodent|snake|other);\d+$
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: 1000
is_a: core field
slot_uri: MIXS:0000412
alias: pressure
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
prev_land_use_meth:
name: prev_land_use_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining previous land use and dates
title: history/previous land use method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/previous land use method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000316
alias: prev_land_use_meth
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
previous_land_use:
name: previous_land_use
annotations:
expected_value:
tag: expected_value
value: land use name;date
occurrence:
tag: occurrence
value: '1'
description: Previous land use and dates
title: history/previous land use
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/previous land use
rank: 1000
is_a: core field
string_serialization: '{text};{timestamp}'
slot_uri: MIXS:0000315
alias: previous_land_use
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
primary_prod:
name: primary_prod
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: milligram per cubic meter per day, gram per square meter per day
occurrence:
tag: occurrence
value: '1'
description: Measurement of primary production, generally measured as isotope
uptake
title: primary production
examples:
- value: 100 milligram per cubic meter per day
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- primary production
rank: 1000
is_a: core field
slot_uri: MIXS:0000728
alias: primary_prod
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
primary_treatment:
name: primary_treatment
annotations:
expected_value:
tag: expected_value
value: primary treatment type
occurrence:
tag: occurrence
value: '1'
description: The process to produce both a generally homogeneous liquid capable
of being treated biologically and a sludge that can be separately treated or
processed
title: primary treatment
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- primary treatment
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000349
alias: primary_treatment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000452
alias: prod_rate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0001008
alias: prod_start_date
owner: Biosample
domain_of:
- Biosample
range: TimestampValue
multivalued: false
profile_position:
name: profile_position
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Cross-sectional position in the hillslope where sample was collected.sample
area position in relation to surrounding areas
title: profile position
examples:
- value: summit
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- profile position
rank: 1000
is_a: core field
slot_uri: MIXS:0001084
alias: profile_position
owner: Biosample
domain_of:
- Biosample
range: profile_position_enum
multivalued: false
quad_pos:
name: quad_pos
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The quadrant position of the sampling room within the building
title: quadrant position
examples:
- value: West side
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- quadrant position
rank: 1000
is_a: core field
slot_uri: MIXS:0000820
alias: quad_pos
owner: Biosample
domain_of:
- Biosample
range: quad_pos_enum
multivalued: false
radiation_regm:
name: radiation_regm
annotations:
expected_value:
tag: expected_value
value: radiation type name;radiation amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: rad, gray
occurrence:
tag: occurrence
value: m
description: Information about treatment involving exposure of plant or a plant
part to a particular radiation regimen; should include the radiation type, amount
or intensity administered, treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment; can include multiple radiation regimens
title: radiation regimen
examples:
- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- radiation regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000575
alias: radiation_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
rainfall_regm:
name: rainfall_regm
annotations:
expected_value:
tag: expected_value
value: measurement value;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: millimeter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving an exposure to a given amount
of rainfall, treatment regimen including how many times the treatment was repeated,
how long each treatment lasted, and the start and end time of the entire treatment;
can include multiple regimens
title: rainfall regimen
examples:
- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rainfall regimen
rank: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000576
alias: rainfall_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
reactor_type:
name: reactor_type
annotations:
expected_value:
tag: expected_value
value: reactor type name
occurrence:
tag: occurrence
value: '1'
description: Anaerobic digesters can be designed and engineered to operate using
a number of different process configurations, as batch or continuous, mesophilic,
high solid or low solid, and single stage or multistage
title: reactor type
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- reactor type
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000350
alias: reactor_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
redox_potential:
name: redox_potential
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millivolt
occurrence:
tag: occurrence
value: '1'
description: Redox potential, measured relative to a hydrogen cell, indicating
oxidation or reduction potential
title: redox potential
examples:
- value: 300 millivolt
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- redox potential
rank: 1000
is_a: core field
slot_uri: MIXS:0000182
alias: redox_potential
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
rel_air_humidity:
name: rel_air_humidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percentage
occurrence:
tag: occurrence
value: '1'
description: Partial vapor and air pressure, density of the vapor and air, or
by the actual mass of the vapor and air
title: relative air humidity
examples:
- value: 80%
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- relative air humidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000121
alias: rel_air_humidity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
rel_humidity_out:
name: rel_humidity_out
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram of air, kilogram of air
occurrence:
tag: occurrence
value: '1'
description: The recorded outside relative humidity value at the time of sampling
title: outside relative humidity
examples:
- value: 12 per kilogram of air
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- outside relative humidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000188
alias: rel_humidity_out
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
rel_samp_loc:
name: rel_samp_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The sampling location within the train car
title: relative sampling location
examples:
- value: center of car
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- relative sampling location
rank: 1000
is_a: core field
slot_uri: MIXS:0000821
alias: rel_samp_loc
owner: Biosample
domain_of:
- Biosample
range: rel_samp_loc_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000303
alias: reservoir
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000134
alias: resins_pc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_air_exch_rate:
name: room_air_exch_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: liter per hour
occurrence:
tag: occurrence
value: '1'
description: The rate at which outside air replaces indoor air in a given space
title: room air exchange rate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room air exchange rate
rank: 1000
is_a: core field
slot_uri: MIXS:0000169
alias: room_air_exch_rate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
room_architec_elem:
name: room_architec_elem
annotations:
expected_value:
tag: expected_value
value: free text
occurrence:
tag: occurrence
value: '1'
description: The unique details and component parts that, together, form the architecture
of a distinguisahable space within a built structure
title: room architectural elements
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room architectural elements
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000233
alias: room_architec_elem
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
room_condt:
name: room_condt
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The condition of the room at the time of sampling
title: room condition
examples:
- value: new
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000822
alias: room_condt
owner: Biosample
domain_of:
- Biosample
range: room_condt_enum
multivalued: false
room_connected:
name: room_connected
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: List of rooms connected to the sampling room by a doorway
title: rooms connected by a doorway
examples:
- value: office
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooms connected by a doorway
rank: 1000
is_a: core field
slot_uri: MIXS:0000826
alias: room_connected
owner: Biosample
domain_of:
- Biosample
range: room_connected_enum
multivalued: false
room_count:
name: room_count
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The total count of rooms in the built structure including all room
types
title: room count
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room count
rank: 1000
is_a: core field
slot_uri: MIXS:0000234
alias: room_count
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_dim:
name: room_dim
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: The length, width and height of sampling room
title: room dimensions
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room dimensions
rank: 1000
is_a: core field
string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'
slot_uri: MIXS:0000192
alias: room_dim
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_door_dist:
name: room_door_dist
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: Distance between doors (meters) in the hallway between the sampling
room and adjacent rooms
title: room door distance
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room door distance
rank: 1000
is_a: core field
string_serialization: '{integer} {unit}'
slot_uri: MIXS:0000193
alias: room_door_dist
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_door_share:
name: room_door_share
annotations:
expected_value:
tag: expected_value
value: room name;room number
occurrence:
tag: occurrence
value: '1'
description: List of room(s) (room number, room name) sharing a door with the
sampling room
title: rooms that share a door with sampling room
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooms that share a door with sampling room
rank: 1000
is_a: core field
string_serialization: '{text};{integer}'
slot_uri: MIXS:0000242
alias: room_door_share
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_hallway:
name: room_hallway
annotations:
expected_value:
tag: expected_value
value: room name;room number
occurrence:
tag: occurrence
value: '1'
description: List of room(s) (room number, room name) located in the same hallway
as sampling room
title: rooms that are on the same hallway
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooms that are on the same hallway
rank: 1000
is_a: core field
string_serialization: '{text};{integer}'
slot_uri: MIXS:0000238
alias: room_hallway
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_loc:
name: room_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The position of the room within the building
title: room location in building
examples:
- value: interior room
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room location in building
rank: 1000
is_a: core field
slot_uri: MIXS:0000823
alias: room_loc
owner: Biosample
domain_of:
- Biosample
range: room_loc_enum
multivalued: false
room_moist_dam_hist:
name: room_moist_dam_hist
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The history of moisture damage or mold in the past 12 months. Number
of events of moisture damage or mold observed
title: room moisture damage or mold history
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room moisture damage or mold history
rank: 1000
is_a: core field
slot_uri: MIXS:0000235
alias: room_moist_dam_hist
owner: Biosample
domain_of:
- Biosample
range: integer
multivalued: false
room_net_area:
name: room_net_area
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square feet, square meter
occurrence:
tag: occurrence
value: '1'
description: The net floor area of sampling room. Net area excludes wall thicknesses
title: room net area
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room net area
rank: 1000
is_a: core field
string_serialization: '{integer} {unit}'
slot_uri: MIXS:0000194
alias: room_net_area
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_occup:
name: room_occup
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Count of room occupancy at time of sampling
title: room occupancy
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room occupancy
rank: 1000
is_a: core field
slot_uri: MIXS:0000236
alias: room_occup
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
room_samp_pos:
name: room_samp_pos
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The horizontal sampling position in the room relative to architectural
elements
title: room sampling position
examples:
- value: south corner
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room sampling position
rank: 1000
is_a: core field
slot_uri: MIXS:0000824
alias: room_samp_pos
owner: Biosample
domain_of:
- Biosample
range: room_samp_pos_enum
multivalued: false
room_type:
name: room_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The main purpose or activity of the sampling room. A room is any
distinguishable space within a structure
title: room type
examples:
- value: bathroom
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room type
rank: 1000
is_a: core field
slot_uri: MIXS:0000825
alias: room_type
owner: Biosample
domain_of:
- Biosample
range: room_type_enum
multivalued: false
room_vol:
name: room_vol
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic feet, cubic meter
occurrence:
tag: occurrence
value: '1'
description: Volume of sampling room
title: room volume
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room volume
rank: 1000
is_a: core field
string_serialization: '{integer} {unit}'
slot_uri: MIXS:0000195
alias: room_vol
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_wall_share:
name: room_wall_share
annotations:
expected_value:
tag: expected_value
value: room name;room number
occurrence:
tag: occurrence
value: '1'
description: List of room(s) (room number, room name) sharing a wall with the
sampling room
title: rooms that share a wall with sampling room
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooms that share a wall with sampling room
rank: 1000
is_a: core field
string_serialization: '{text};{integer}'
slot_uri: MIXS:0000243
alias: room_wall_share
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
room_window_count:
name: room_window_count
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: Number of windows in the room
title: room window count
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- room window count
rank: 1000
is_a: core field
slot_uri: MIXS:0000237
alias: room_window_count
owner: Biosample
domain_of:
- Biosample
range: integer
multivalued: false
root_cond:
name: root_cond
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url or free text
occurrence:
tag: occurrence
value: '1'
description: Relevant rooting conditions such as field plot size, sowing density,
container dimensions, number of plants per container.
title: rooting conditions
examples:
- value: http://himedialabs.com/TD/PT158.pdf
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting conditions
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001061
alias: root_cond
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
root_med_carbon:
name: root_med_carbon
annotations:
expected_value:
tag: expected_value
value: carbon source name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Source of organic carbon in the culture rooting medium; e.g. sucrose.
title: rooting medium carbon
examples:
- value: sucrose
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium carbon
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000577
alias: root_med_carbon
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
root_med_macronutr:
name: root_med_macronutr
annotations:
expected_value:
tag: expected_value
value: macronutrient name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Measurement of the culture rooting medium macronutrients (N,P, K,
Ca, Mg, S); e.g. KH2PO4 (170 mg/L).
title: rooting medium macronutrients
examples:
- value: KH2PO4;170 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium macronutrients
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000578
alias: root_med_macronutr
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
root_med_micronutr:
name: root_med_micronutr
annotations:
expected_value:
tag: expected_value
value: micronutrient name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L).
title: rooting medium micronutrients
examples:
- value: H3BO3;6.2 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium micronutrients
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000579
alias: root_med_micronutr
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
root_med_ph:
name: root_med_ph
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: pH measurement of the culture rooting medium; e.g. 5.5.
title: rooting medium pH
examples:
- value: '7.5'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium pH
rank: 1000
is_a: core field
slot_uri: MIXS:0001062
alias: root_med_ph
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
root_med_regl:
name: root_med_regl
annotations:
expected_value:
tag: expected_value
value: regulator name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Growth regulators in the culture rooting medium such as cytokinins,
auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA.
title: rooting medium regulators
examples:
- value: abscisic acid;0.75 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium regulators
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000581
alias: root_med_regl
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
root_med_solid:
name: root_med_solid
annotations:
expected_value:
tag: expected_value
value: name
occurrence:
tag: occurrence
value: '1'
description: Specification of the solidifying agent in the culture rooting medium;
e.g. agar.
title: rooting medium solidifier
examples:
- value: agar
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium solidifier
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001063
alias: root_med_solid
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
root_med_suppl:
name: root_med_suppl
annotations:
expected_value:
tag: expected_value
value: supplement name;measurement value
preferred_unit:
tag: preferred_unit
value: milligram per liter
occurrence:
tag: occurrence
value: '1'
description: Organic supplements of the culture rooting medium, such as vitamins,
amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid
(0.5 mg/L).
title: rooting medium organic supplements
examples:
- value: nicotinic acid;0.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- rooting medium organic supplements
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000580
alias: root_med_suppl
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000183
alias: salinity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
salinity_meth:
name: salinity_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining salinity
title: salinity method
examples:
- value: https://doi.org/10.1007/978-1-61779-986-0_28
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- salinity method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000341
alias: salinity_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
salt_regm:
name: salt_regm
annotations:
expected_value:
tag: expected_value
value: salt name;salt amount;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: gram, microgram, mole per liter, gram per liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving use of salts as supplement
to liquid and soil growth media; should include the name of salt, amount administered,
treatment regimen including how many times the treatment was repeated, how long
each treatment lasted, and the start and end time of the entire treatment; can
include multiple salt regimens
title: salt regimen
examples:
- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- salt regimen
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000582
alias: salt_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
samp_capt_status:
name: samp_capt_status
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Reason for the sample
title: sample capture status
examples:
- value: farm sample
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample capture status
rank: 1000
is_a: core field
slot_uri: MIXS:0000860
alias: samp_capt_status
owner: Biosample
domain_of:
- Biosample
range: samp_capt_status_enum
multivalued: false
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
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection device
rank: 1000
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000002
alias: samp_collec_device
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
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
examples:
- value: swabbing
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample collection method
rank: 1000
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001225
alias: samp_collec_method
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0001015
alias: samp_collect_point
owner: Biosample
domain_of:
- Biosample
range: samp_collect_point_enum
multivalued: false
samp_dis_stage:
name: samp_dis_stage
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Stage of the disease at the time of sample collection, e.g. inoculation,
penetration, infection, growth and reproduction, dissemination of pathogen.
title: sample disease stage
examples:
- value: infection
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample disease stage
rank: 1000
is_a: core field
slot_uri: MIXS:0000249
alias: samp_dis_stage
owner: Biosample
domain_of:
- Biosample
range: samp_dis_stage_enum
multivalued: false
samp_floor:
name: samp_floor
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The floor of the building, where the sampling room is located
title: sampling floor
examples:
- value: 4th floor
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sampling floor
rank: 1000
is_a: core field
slot_uri: MIXS:0000828
alias: samp_floor
owner: Biosample
domain_of:
- Biosample
range: samp_floor_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} - {float} {unit}'
slot_uri: MIXS:0000136
alias: samp_loc_corr_rate
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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, storing samples in ethanol
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample material processing
rank: 1000
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000016
alias: samp_mat_process
owner: Biosample
domain_of:
- Biosample
range: ControlledTermValue
multivalued: false
samp_md:
name: samp_md
annotations:
expected_value:
tag: expected_value
value: measurement value;enumeration
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: In non deviated well, measured depth is equal to the true vertical
depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated
wells, the MD is the length of trajectory of the borehole measured from the
same reference or datum. Common datums used are ground level (GL), drilling
rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).
If "other" is specified, please propose entry in "additional info" field
title: sample measured depth
examples:
- value: 1534 meter;MSL
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample measured depth
rank: 1000
is_a: core field
slot_uri: MIXS:0000413
alias: samp_md
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000463
alias: samp_preserv
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
samp_room_id:
name: samp_room_id
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: Sampling room number. This ID should be consistent with the designations
on the building floor plans
title: sampling room ID or name
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sampling room ID or name
rank: 1000
is_a: core field
slot_uri: MIXS:0000244
alias: samp_room_id
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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
examples:
- value: 5 liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- amount or size of sample collected
rank: 1000
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000001
alias: samp_size
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
samp_sort_meth:
name: samp_sort_meth
annotations:
expected_value:
tag: expected_value
value: description of method
occurrence:
tag: occurrence
value: m
description: Method by which samples are sorted; open face filter collecting total
suspended particles, prefilter to remove particles larger than X micrometers
in diameter, where common values of X would be 10 and 2.5 full size sorting
in a cascade impactor.
title: sample size sorting method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample size sorting method
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000216
alias: samp_sort_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
string_serialization: '{duration}'
slot_uri: MIXS:0000116
alias: samp_store_dur
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000755
alias: samp_store_loc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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 sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample storage temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000110
alias: samp_store_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000999
alias: samp_subtype
owner: Biosample
domain_of:
- Biosample
range: samp_subtype_enum
multivalued: false
samp_taxon_id:
name: samp_taxon_id
annotations:
expected_value:
tag: expected_value
value: Taxonomy ID
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome’ for mock community/positive controls, or
'blank sample' for negative controls.
title: Taxonomy ID of DNA sample
comments:
- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Taxonomy ID of DNA sample
rank: 1000
is_a: investigation field
slot_uri: MIXS:0001320
alias: samp_taxon_id
owner: Biosample
domain_of:
- Biosample
range: ControlledIdentifiedTermValue
multivalued: false
samp_time_out:
name: samp_time_out
annotations:
expected_value:
tag: expected_value
value: time
preferred_unit:
tag: preferred_unit
value: hour
occurrence:
tag: occurrence
value: '1'
description: The recent and long term history of outside sampling
title: sampling time outside
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sampling time outside
rank: 1000
is_a: core field
slot_uri: MIXS:0000196
alias: samp_time_out
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000410
alias: samp_transport_cond
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
samp_tvdss:
name: samp_tvdss
annotations:
expected_value:
tag: expected_value
value: measurement value or measurement value range
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: Depth of the sample i.e. The vertical distance between the sea level
and the sampled position in the subsurface. Depth can be reported as an interval
for subsurface samples e.g. 1325.75-1362.25 m
title: sample true vertical depth subsea
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample true vertical depth subsea
rank: 1000
is_a: core field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000409
alias: samp_tvdss
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000998
alias: samp_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
samp_weather:
name: samp_weather
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The weather on the sampling day
title: sampling day weather
examples:
- value: foggy
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sampling day weather
rank: 1000
is_a: core field
slot_uri: MIXS:0000827
alias: samp_weather
owner: Biosample
domain_of:
- Biosample
range: samp_weather_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000296
alias: samp_well_name
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000131
alias: saturates_pc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
season:
name: season
annotations:
expected_value:
tag: expected_value
value: NCIT:C94729
occurrence:
tag: occurrence
value: '1'
description: The season when sampling occurred. Any of the four periods into which
the year is divided by the equinoxes and solstices. This field accepts terms
listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
title: season
examples:
- value: autumn [NCIT:C94733]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- season
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000829
alias: season
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
season_environment:
name: season_environment
annotations:
expected_value:
tag: expected_value
value: seasonal environment name;treatment interval and duration
occurrence:
tag: occurrence
value: m
description: Treatment involving an exposure to a particular season (e.g. Winter,
summer, rabi, rainy etc.), treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment
title: seasonal environment
examples:
- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- seasonal environment
rank: 1000
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001068
alias: season_environment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
season_precpt:
name: season_precpt
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: millimeter
occurrence:
tag: occurrence
value: '1'
description: The average of all seasonal precipitation values known, or an estimated
equivalent value derived by such methods as regional indexes or Isohyetal maps.
title: average seasonal precipitation
todos:
- check validation & examples. always mm? so value only? Or value + unit
notes:
- mean and average are the same thing, but it seems like bad practice to not be
consistent. Changed mean to average
comments:
- Seasons are defined as spring (March, April, May), summer (June, July, August),
autumn (September, October, November) and winter (December, January, February).
examples:
- value: 0.4 inch
- value: 10.16 mm
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean seasonal precipitation
rank: 1000
is_a: core field
slot_uri: MIXS:0000645
alias: season_precpt
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
season_temp:
name: season_temp
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: Mean seasonal temperature
title: mean seasonal temperature
examples:
- value: 18 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- mean seasonal temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000643
alias: season_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
season_use:
name: season_use
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The seasons the space is occupied
title: seasonal use
examples:
- value: Winter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- seasonal use
rank: 1000
is_a: core field
slot_uri: MIXS:0000830
alias: season_use
owner: Biosample
domain_of:
- Biosample
range: season_use_enum
multivalued: false
secondary_treatment:
name: secondary_treatment
annotations:
expected_value:
tag: expected_value
value: secondary treatment type
occurrence:
tag: occurrence
value: '1'
description: The process for substantially degrading the biological content of
the sewage
title: secondary treatment
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- secondary treatment
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000351
alias: secondary_treatment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
sediment_type:
name: sediment_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Information about the sediment type based on major constituents
title: sediment type
examples:
- value: biogenous
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sediment type
rank: 1000
is_a: core field
slot_uri: MIXS:0001078
alias: sediment_type
owner: Biosample
domain_of:
- Biosample
range: sediment_type_enum
multivalued: false
sequencing field:
name: sequencing field
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
abstract: true
alias: sequencing_field
owner: Biosample
domain_of:
- Biosample
range: string
sewage_type:
name: sewage_type
annotations:
expected_value:
tag: expected_value
value: sewage type name
occurrence:
tag: occurrence
value: '1'
description: Type of wastewater treatment plant as municipial or industrial
title: sewage type
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sewage type
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000215
alias: sewage_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
shad_dev_water_mold:
name: shad_dev_water_mold
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Signs of the presence of mold or mildew on the shading device
title: shading device signs of water/mold
examples:
- value: no presence of mold visible
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- shading device signs of water/mold
rank: 1000
is_a: core field
string_serialization: '[presence of mold visible|no presence of mold visible]'
slot_uri: MIXS:0000834
alias: shad_dev_water_mold
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
shading_device_cond:
name: shading_device_cond
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The physical condition of the shading device at the time of sampling
title: shading device condition
examples:
- value: new
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- shading device condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000831
alias: shading_device_cond
owner: Biosample
domain_of:
- Biosample
range: shading_device_cond_enum
multivalued: false
shading_device_loc:
name: shading_device_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The location of the shading device in relation to the built structure
title: shading device location
examples:
- value: exterior
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- shading device location
rank: 1000
is_a: core field
string_serialization: '[exterior|interior]'
slot_uri: MIXS:0000832
alias: shading_device_loc
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
shading_device_mat:
name: shading_device_mat
annotations:
expected_value:
tag: expected_value
value: material name
occurrence:
tag: occurrence
value: '1'
description: The material the shading device is composed of
title: shading device material
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- shading device material
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000245
alias: shading_device_mat
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
shading_device_type:
name: shading_device_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of shading device
title: shading device type
examples:
- value: slatted aluminum awning
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- shading device type
rank: 1000
is_a: core field
slot_uri: MIXS:0000835
alias: shading_device_type
owner: Biosample
domain_of:
- Biosample
range: shading_device_type_enum
multivalued: false
sieving:
name: sieving
annotations:
expected_value:
tag: expected_value
value: design name and/or size;amount
occurrence:
tag: occurrence
value: '1'
description: Collection design of pooled samples and/or sieve size and amount
of sample sieved
title: composite design/sieving
todos:
- check validation and examples
comments:
- Describe how samples were composited or sieved.
- Use 'sample link' to indicate which samples were combined.
examples:
- value: combined 2 cores | 4mm sieved
- value: 4 mm sieved and homogenized
- value: 50 g | 5 cores | 2 mm sieved
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- composite design/sieving
rank: 1000
is_a: core field
string_serialization: '{{text}|{float} {unit}};{float} {unit}'
slot_uri: MIXS:0000322
alias: sieving
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
silicate:
name: silicate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Concentration of silicate
title: silicate
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- silicate
rank: 1000
is_a: core field
slot_uri: MIXS:0000184
alias: silicate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: nucleic acid sequence source field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
alias: size_frac
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
size_frac_low:
name: size_frac_low
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: micrometer
occurrence:
tag: occurrence
value: '1'
description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.
Materials larger than the size threshold are excluded from the sample
title: size-fraction lower threshold
examples:
- value: 0.2 micrometer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- size-fraction lower threshold
rank: 1000
is_a: core field
slot_uri: MIXS:0000735
alias: size_frac_low
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
size_frac_up:
name: size_frac_up
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: micrometer
occurrence:
tag: occurrence
value: '1'
description: Refers to the mesh/pore size used to retain the sample. Materials
smaller than the size threshold are excluded from the sample
title: size-fraction upper threshold
examples:
- value: 20 micrometer
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- size-fraction upper threshold
rank: 1000
is_a: core field
slot_uri: MIXS:0000736
alias: size_frac_up
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
slope_aspect:
name: slope_aspect
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree
occurrence:
tag: occurrence
value: '1'
description: The direction a slope faces. While looking down a slope use a compass
to record the direction you are facing (direction or degrees). This measure
provides an indication of sun and wind exposure that will influence soil temperature
and evapotranspiration.
title: slope aspect
comments:
- Aspect is the orientation of slope, measured clockwise in degrees from 0 to
360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270
is west-facing.
examples:
- value: '35'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- slope aspect
rank: 1000
is_a: core field
slot_uri: MIXS:0000647
alias: slope_aspect
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
slope_gradient:
name: slope_gradient
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percentage
occurrence:
tag: occurrence
value: '1'
description: Commonly called 'slope'. The angle between ground surface and a horizontal
line (in percent). This is the direction that overland water would flow. This
measure is usually taken with a hand level meter or clinometer
title: slope gradient
todos:
- Slope is a percent. How does the validation work? Check to correct examples
examples:
- value: 10%
- value: 10 %
- value: '0.10'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- slope gradient
rank: 1000
is_a: core field
slot_uri: MIXS:0000646
alias: slope_gradient
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
sludge_retent_time:
name: sludge_retent_time
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: hours
occurrence:
tag: occurrence
value: '1'
description: The time activated sludge remains in reactor
title: sludge retention time
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sludge retention time
rank: 1000
is_a: core field
slot_uri: MIXS:0000669
alias: sludge_retent_time
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000428
alias: sodium
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
soil_horizon:
name: soil_horizon
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Specific layer in the land area which measures parallel to the soil
surface and possesses physical characteristics which differ from the layers
above and beneath
title: soil horizon
examples:
- value: A horizon
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil horizon
rank: 1000
is_a: core field
slot_uri: MIXS:0001082
alias: soil_horizon
owner: Biosample
domain_of:
- Biosample
range: soil_horizon_enum
multivalued: false
soil_text_measure:
name: soil_text_measure
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: The relative proportion of different grain sizes of mineral particles
in a soil, as described using a standard system; express as % sand (50 um to
2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty
clay loam) optional.
title: soil texture measurement
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil texture measurement
rank: 1000
is_a: core field
slot_uri: MIXS:0000335
alias: soil_text_measure
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
soil_texture_meth:
name: soil_texture_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining soil texture
title: soil texture method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil texture method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000336
alias: soil_texture_meth
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
soil_type:
name: soil_type
annotations:
expected_value:
tag: expected_value
value: ENVO_00001998
occurrence:
tag: occurrence
value: '1'
description: Description of the soil type or classification. This field accepts
terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms
can be separated by pipes.
title: soil type
examples:
- value: plinthosol [ENVO:00002250]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil type
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000332
alias: soil_type
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
soil_type_meth:
name: soil_type_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining soil series name or other
lower-level classification
title: soil type method
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil type method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000334
alias: soil_type_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
solar_irradiance:
name: solar_irradiance
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: kilowatts per square meter per day, ergs per square centimeter per
second
occurrence:
tag: occurrence
value: '1'
description: The amount of solar energy that arrives at a specific area of a surface
during a specific time interval
title: solar irradiance
examples:
- value: 1.36 kilowatts per square meter per day
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- solar irradiance
rank: 1000
is_a: core field
slot_uri: MIXS:0000112
alias: solar_irradiance
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
soluble_inorg_mat:
name: soluble_inorg_mat
annotations:
expected_value:
tag: expected_value
value: soluble inorganic material name;measurement value
preferred_unit:
tag: preferred_unit
value: gram, microgram, mole per liter, gram per liter, parts per million
occurrence:
tag: occurrence
value: m
description: Concentration of substances such as ammonia, road-salt, sea-salt,
cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
title: soluble inorganic material
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soluble inorganic material
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000672
alias: soluble_inorg_mat
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
soluble_org_mat:
name: soluble_org_mat
annotations:
expected_value:
tag: expected_value
value: soluble organic material name;measurement value
preferred_unit:
tag: preferred_unit
value: gram, microgram, mole per liter, gram per liter, parts per million
occurrence:
tag: occurrence
value: m
description: Concentration of substances such as urea, fruit sugars, soluble proteins,
drugs, pharmaceuticals, etc.
title: soluble organic material
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soluble organic material
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000673
alias: soluble_org_mat
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
soluble_react_phosp:
name: soluble_react_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: Concentration of soluble reactive phosphorus
title: soluble reactive phosphorus
examples:
- value: 0.1 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soluble reactive phosphorus
rank: 1000
is_a: core field
slot_uri: MIXS:0000738
alias: soluble_react_phosp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
source_mat_id:
name: source_mat_id
annotations:
expected_value:
tag: expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
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.
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/).
examples:
- value: IGSN:AU1243
- value: UUID:24f1467a-40f4-11ed-b878-0242ac120002
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- source material identifiers
rank: 1000
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000026
alias: source_mat_id
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
space_typ_state:
name: space_typ_state
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Customary or normal state of the space
title: space typical state
examples:
- value: typically occupied
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- space typical state
rank: 1000
is_a: core field
string_serialization: '[typically occupied|typically unoccupied]'
slot_uri: MIXS:0000770
alias: space_typ_state
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
specific:
name: specific
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'The building specifications. If design is chosen, indicate phase:
conceptual, schematic, design development, construction documents'
title: specifications
examples:
- value: construction
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- specifications
rank: 1000
is_a: core field
slot_uri: MIXS:0000836
alias: specific
owner: Biosample
domain_of:
- Biosample
range: specific_enum
multivalued: false
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: 1000
is_a: gold_path_field
alias: specific_ecosystem
owner: Biosample
domain_of:
- Biosample
- Study
range: string
specific_humidity:
name: specific_humidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram of air, kilogram of air
occurrence:
tag: occurrence
value: '1'
description: The mass of water vapour in a unit mass of moist air, usually expressed
as grams of vapour per kilogram of air, or, in air conditioning, as grains per
pound.
title: specific humidity
examples:
- value: 15 per kilogram of air
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- specific humidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000214
alias: specific_humidity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
sr_dep_env:
name: sr_dep_env
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).
If "other" is specified, please propose entry in "additional info" field
title: source rock depositional environment
examples:
- value: Marine
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- source rock depositional environment
rank: 1000
is_a: core field
slot_uri: MIXS:0000996
alias: sr_dep_env
owner: Biosample
domain_of:
- Biosample
range: sr_dep_env_enum
multivalued: false
sr_geol_age:
name: sr_geol_age
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).
If "other" is specified, please propose entry in "additional info" field'
title: source rock geological age
examples:
- value: Silurian
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- source rock geological age
rank: 1000
is_a: core field
slot_uri: MIXS:0000997
alias: sr_geol_age
owner: Biosample
domain_of:
- Biosample
range: sr_geol_age_enum
multivalued: false
sr_kerog_type:
name: sr_kerog_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic
and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/
fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris
(terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).
If "other" is specified, please propose entry in "additional info" field'
title: source rock kerogen type
examples:
- value: Type IV
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- source rock kerogen type
rank: 1000
is_a: core field
slot_uri: MIXS:0000994
alias: sr_kerog_type
owner: Biosample
domain_of:
- Biosample
range: sr_kerog_type_enum
multivalued: false
sr_lithology:
name: sr_lithology
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).
If "other" is specified, please propose entry in "additional info" field
title: source rock lithology
examples:
- value: Coal
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- source rock lithology
rank: 1000
is_a: core field
slot_uri: MIXS:0000995
alias: sr_lithology
owner: Biosample
domain_of:
- Biosample
range: sr_lithology_enum
multivalued: false
standing_water_regm:
name: standing_water_regm
annotations:
expected_value:
tag: expected_value
value: standing water type;treatment interval and duration
occurrence:
tag: occurrence
value: m
description: Treatment involving an exposure to standing water during a plant's
life span, types can be flood water or standing water, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple regimens
title: standing water regimen
examples:
- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- standing water regimen
rank: 1000
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001069
alias: standing_water_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
store_cond:
name: store_cond
annotations:
expected_value:
tag: expected_value
value: storage condition type;duration
occurrence:
tag: occurrence
value: '1'
description: Explain how and for how long the soil sample was stored before DNA
extraction (fresh/frozen/other).
title: storage conditions
examples:
- value: -20 degree Celsius freezer;P2Y10D
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- storage conditions
rank: 1000
is_a: core field
string_serialization: '{text};{duration}'
slot_uri: MIXS:0000327
alias: store_cond
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
substructure_type:
name: substructure_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: The substructure or under building is that largely hidden section
of the building which is built off the foundations to the ground floor level
title: substructure type
examples:
- value: basement
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- substructure type
rank: 1000
is_a: core field
slot_uri: MIXS:0000767
alias: substructure_type
owner: Biosample
domain_of:
- Biosample
range: substructure_type_enum
multivalued: 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: 1000
is_a: core field
slot_uri: MIXS:0000423
alias: sulfate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000407
alias: sulfate_fw
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000424
alias: sulfide
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
surf_air_cont:
name: surf_air_cont
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: Contaminant identified on surface
title: surface-air contaminant
examples:
- value: radon
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- surface-air contaminant
rank: 1000
is_a: core field
slot_uri: MIXS:0000759
alias: surf_air_cont
owner: Biosample
domain_of:
- Biosample
range: surf_air_cont_enum
multivalued: true
surf_humidity:
name: surf_humidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: percentage
occurrence:
tag: occurrence
value: '1'
description: 'Surfaces: water activity as a function of air and material moisture'
title: surface humidity
examples:
- value: 10%
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- surface humidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000123
alias: surf_humidity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
surf_material:
name: surf_material
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Surface materials at the point of sampling
title: surface material
examples:
- value: wood
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- surface material
rank: 1000
is_a: core field
slot_uri: MIXS:0000758
alias: surf_material
owner: Biosample
domain_of:
- Biosample
range: surf_material_enum
multivalued: false
surf_moisture:
name: surf_moisture
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: parts per million, gram per cubic meter, gram per square meter
occurrence:
tag: occurrence
value: '1'
description: Water held on a surface
title: surface moisture
examples:
- value: 0.01 gram per square meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- surface moisture
rank: 1000
is_a: core field
slot_uri: MIXS:0000128
alias: surf_moisture
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
surf_moisture_ph:
name: surf_moisture_ph
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: ph measurement of surface
title: surface moisture pH
examples:
- value: '7'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- surface moisture pH
rank: 1000
is_a: core field
slot_uri: MIXS:0000760
alias: surf_moisture_ph
owner: Biosample
domain_of:
- Biosample
range: double
multivalued: false
surf_temp:
name: surf_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 of the surface at the time of sampling
title: surface temperature
examples:
- value: 15 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- surface temperature
rank: 1000
is_a: core field
slot_uri: MIXS:0000125
alias: surf_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
suspend_part_matter:
name: suspend_part_matter
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 suspended particulate matter
title: suspended particulate matter
examples:
- value: 0.5 milligram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- suspended particulate matter
rank: 1000
is_a: core field
slot_uri: MIXS:0000741
alias: suspend_part_matter
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000150
alias: suspend_solids
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
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: 1000
is_a: core field
slot_uri: MIXS:0000120
alias: tan
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: environment field
slot_uri: MIXS:0000113
alias: temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
temp_out:
name: temp_out
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The recorded temperature value at sampling time outside
title: temperature outside house
examples:
- value: 5 degree Celsius
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- temperature outside house
rank: 1000
is_a: core field
slot_uri: MIXS:0000197
alias: temp_out
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tertiary_treatment:
name: tertiary_treatment
annotations:
expected_value:
tag: expected_value
value: tertiary treatment type
occurrence:
tag: occurrence
value: '1'
description: The process providing a final treatment stage to raise the effluent
quality before it is discharged to the receiving environment
title: tertiary treatment
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- tertiary treatment
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000352
alias: tertiary_treatment
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
tidal_stage:
name: tidal_stage
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Stage of tide
title: tidal stage
examples:
- value: high tide
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- tidal stage
rank: 1000
is_a: core field
slot_uri: MIXS:0000750
alias: tidal_stage
owner: Biosample
domain_of:
- Biosample
range: tidal_stage_enum
multivalued: false
tillage:
name: tillage
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: m
description: Note method(s) used for tilling
title: history/tillage
examples:
- value: chisel
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- history/tillage
rank: 1000
is_a: core field
slot_uri: MIXS:0001081
alias: tillage
owner: Biosample
domain_of:
- Biosample
range: tillage_enum
multivalued: true
tiss_cult_growth_med:
name: tiss_cult_growth_med
annotations:
expected_value:
tag: expected_value
value: PMID,DOI,url or free text
occurrence:
tag: occurrence
value: '1'
description: Description of plant tissue culture growth media used
title: tissue culture growth media
examples:
- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- tissue culture growth media
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001070
alias: tiss_cult_growth_med
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000154
alias: toluene
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_carb:
name: tot_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Total carbon content
title: total carbon
todos:
- is this inorganic and organic? both? could use some clarification.
- ug/L doesn't seem like the right units. Should check this slots usage in databases
and re-evaluate. I couldn't find any references that provided this data in this
format
examples:
- value: 1 ug/L
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total carbon
rank: 1000
is_a: core field
slot_uri: MIXS:0000525
alias: tot_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_depth_water_col:
name: tot_depth_water_col
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter
occurrence:
tag: occurrence
value: '1'
description: Measurement of total depth of water column
title: total depth of water column
examples:
- value: 500 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total depth of water column
rank: 1000
is_a: core field
slot_uri: MIXS:0000634
alias: tot_depth_water_col
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_diss_nitro:
name: tot_diss_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured
by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'
title: total dissolved nitrogen
examples:
- value: 40 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total dissolved nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000744
alias: tot_diss_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_inorg_nitro:
name: tot_inorg_nitro
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter
occurrence:
tag: occurrence
value: '1'
description: Total inorganic nitrogen content
title: total inorganic nitrogen
examples:
- value: 40 microgram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total inorganic nitrogen
rank: 1000
is_a: core field
slot_uri: MIXS:0000745
alias: tot_inorg_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000105
alias: tot_iron
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000102
alias: tot_nitro
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_nitro_cont_meth:
name: tot_nitro_cont_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining the total nitrogen
title: total nitrogen content method
examples:
- value: https://doi.org/10.2134/agronmonogr9.2.c32
- value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total nitrogen content method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000338
alias: tot_nitro_cont_meth
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
tot_nitro_content:
name: tot_nitro_content
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 content of the sample
title: total nitrogen content
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total nitrogen content
rank: 1000
is_a: core field
slot_uri: MIXS:0000530
alias: tot_nitro_content
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_org_c_meth:
name: tot_org_c_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining total organic carbon
title: total organic carbon method
examples:
- value: https://doi.org/10.1080/07352680902776556
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total organic carbon method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000337
alias: tot_org_c_meth
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
tot_org_carb:
name: tot_org_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: gram Carbon per kilogram sample material
occurrence:
tag: occurrence
value: '1'
description: 'Definition for soil: total organic carbon content of the soil, definition
otherwise: total organic carbon content'
title: total organic carbon
todos:
- check description. How are they different?
examples:
- value: 5 mg N/ L
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total organic carbon
rank: 1000
is_a: core field
slot_uri: MIXS:0000533
alias: tot_org_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_part_carb:
name: tot_part_carb
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Total particulate carbon content
title: total particulate carbon
examples:
- value: 35 micromole per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total particulate carbon
rank: 1000
is_a: core field
slot_uri: MIXS:0000747
alias: tot_part_carb
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000117
alias: tot_phosp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
tot_phosphate:
name: tot_phosphate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: microgram per liter, micromole per liter
occurrence:
tag: occurrence
value: '1'
description: Total amount or concentration of phosphate
title: total phosphate
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- total phosphate
rank: 1000
is_a: core field
slot_uri: MIXS:0000689
alias: tot_phosphate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000419
alias: tot_sulfur
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
train_line:
name: train_line
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The subway line name
title: train line
examples:
- value: red
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- train line
rank: 1000
is_a: core field
slot_uri: MIXS:0000837
alias: train_line
owner: Biosample
domain_of:
- Biosample
range: train_line_enum
multivalued: false
train_stat_loc:
name: train_stat_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The train station collection location
title: train station collection location
examples:
- value: forest hills
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- train station collection location
rank: 1000
is_a: core field
slot_uri: MIXS:0000838
alias: train_stat_loc
owner: Biosample
domain_of:
- Biosample
range: train_stat_loc_enum
multivalued: false
train_stop_loc:
name: train_stop_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The train stop collection location
title: train stop collection location
examples:
- value: end
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- train stop collection location
rank: 1000
is_a: core field
slot_uri: MIXS:0000839
alias: train_stop_loc
owner: Biosample
domain_of:
- Biosample
range: train_stop_loc_enum
multivalued: false
turbidity:
name: turbidity
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: formazin turbidity unit, formazin nephelometric units
occurrence:
tag: occurrence
value: '1'
description: Measure of the amount of cloudiness or haziness in water caused by
individual particles
title: turbidity
examples:
- value: 0.3 nephelometric turbidity units
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- turbidity
rank: 1000
is_a: core field
slot_uri: MIXS:0000191
alias: turbidity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000397
alias: tvdss_of_hcr_press
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000394
alias: tvdss_of_hcr_temp
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
typ_occup_density:
name: typ_occup_density
annotations:
expected_value:
tag: expected_value
value: measurement value
occurrence:
tag: occurrence
value: '1'
description: Customary or normal density of occupants
title: typical occupant density
examples:
- value: '25'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- typical occupant density
rank: 1000
is_a: core field
slot_uri: MIXS:0000771
alias: typ_occup_density
owner: Biosample
domain_of:
- Biosample
range: double
multivalued: false
ventilation_rate:
name: ventilation_rate
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per minute, liters per second
occurrence:
tag: occurrence
value: '1'
description: Ventilation rate of the system in the sampled premises
title: ventilation rate
examples:
- value: 750 cubic meter per minute
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ventilation rate
rank: 1000
is_a: core field
slot_uri: MIXS:0000114
alias: ventilation_rate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
ventilation_type:
name: ventilation_type
annotations:
expected_value:
tag: expected_value
value: ventilation type name
occurrence:
tag: occurrence
value: '1'
description: Ventilation system used in the sampled premises
title: ventilation type
examples:
- value: Operable windows
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- ventilation type
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000756
alias: ventilation_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000152
alias: vfa
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000408
alias: vfa_fw
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
vis_media:
name: vis_media
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The building visual media
title: visual media
examples:
- value: 3D scans
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- visual media
rank: 1000
is_a: core field
slot_uri: MIXS:0000840
alias: vis_media
owner: Biosample
domain_of:
- Biosample
range: vis_media_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{float} {unit};{float} {unit}'
slot_uri: MIXS:0000126
alias: viscosity
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
volatile_org_comp:
name: volatile_org_comp
annotations:
expected_value:
tag: expected_value
value: volatile organic compound name;measurement value
preferred_unit:
tag: preferred_unit
value: microgram per cubic meter, parts per million, nanogram per liter
occurrence:
tag: occurrence
value: m
description: Concentration of carbon-based chemicals that easily evaporate at
room temperature; can report multiple volatile organic compounds by entering
numeric values preceded by name of compound
title: volatile organic compounds
examples:
- value: formaldehyde;500 nanogram per liter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- volatile organic compounds
rank: 1000
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000115
alias: volatile_org_comp
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
wall_area:
name: wall_area
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square meter
occurrence:
tag: occurrence
value: '1'
description: The total area of the sampled room's walls
title: wall area
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall area
rank: 1000
is_a: core field
slot_uri: MIXS:0000198
alias: wall_area
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
wall_const_type:
name: wall_const_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The building class of the wall defined by the composition of the
building elements and fire-resistance rating.
title: wall construction type
examples:
- value: fire resistive
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall construction type
rank: 1000
is_a: core field
slot_uri: MIXS:0000841
alias: wall_const_type
owner: Biosample
domain_of:
- Biosample
range: wall_const_type_enum
multivalued: false
wall_finish_mat:
name: wall_finish_mat
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The material utilized to finish the outer most layer of the wall
title: wall finish material
examples:
- value: wood
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall finish material
rank: 1000
is_a: core field
slot_uri: MIXS:0000842
alias: wall_finish_mat
owner: Biosample
domain_of:
- Biosample
range: wall_finish_mat_enum
multivalued: false
wall_height:
name: wall_height
annotations:
expected_value:
tag: expected_value
value: value
preferred_unit:
tag: preferred_unit
value: centimeter
occurrence:
tag: occurrence
value: '1'
description: The average height of the walls in the sampled room
title: wall height
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall height
rank: 1000
is_a: core field
slot_uri: MIXS:0000221
alias: wall_height
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
wall_loc:
name: wall_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The relative location of the wall within the room
title: wall location
examples:
- value: north
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall location
rank: 1000
is_a: core field
slot_uri: MIXS:0000843
alias: wall_loc
owner: Biosample
domain_of:
- Biosample
range: wall_loc_enum
multivalued: false
wall_surf_treatment:
name: wall_surf_treatment
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The surface treatment of interior wall
title: wall surface treatment
examples:
- value: paneling
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall surface treatment
rank: 1000
is_a: core field
slot_uri: MIXS:0000845
alias: wall_surf_treatment
owner: Biosample
domain_of:
- Biosample
range: wall_surf_treatment_enum
multivalued: false
wall_texture:
name: wall_texture
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The feel, appearance, or consistency of a wall surface
title: wall texture
examples:
- value: popcorn
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall texture
rank: 1000
is_a: core field
slot_uri: MIXS:0000846
alias: wall_texture
owner: Biosample
domain_of:
- Biosample
range: wall_texture_enum
multivalued: false
wall_thermal_mass:
name: wall_thermal_mass
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: joule per degree Celsius
occurrence:
tag: occurrence
value: '1'
description: The ability of the wall to provide inertia against temperature fluctuations.
Generally this means concrete or concrete block that is either exposed or covered
only with paint
title: wall thermal mass
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall thermal mass
rank: 1000
is_a: core field
slot_uri: MIXS:0000222
alias: wall_thermal_mass
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
wall_water_mold:
name: wall_water_mold
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Signs of the presence of mold or mildew on a wall
title: wall signs of water/mold
examples:
- value: no presence of mold visible
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wall signs of water/mold
rank: 1000
is_a: core field
string_serialization: '[presence of mold visible|no presence of mold visible]'
slot_uri: MIXS:0000844
alias: wall_water_mold
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
wastewater_type:
name: wastewater_type
annotations:
expected_value:
tag: expected_value
value: wastewater type name
occurrence:
tag: occurrence
value: '1'
description: The origin of wastewater such as human waste, rainfall, storm drains,
etc.
title: wastewater type
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wastewater type
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000353
alias: wastewater_type
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
water_cont_soil_meth:
name: water_cont_soil_meth
annotations:
expected_value:
tag: expected_value
value: PMID,DOI or url
occurrence:
tag: occurrence
value: '1'
description: Reference or method used in determining the water content of soil
title: water content method
todos:
- Why is it soil water content method in the name but not the title? Is this slot
used in other samples?
- Soil water content can be measure MANY ways and often, multiple ways are used
in one experiment (gravimetric water content and water holding capacity and
water filled pore space, to name a few).
- Should this be multi valued? How to we manage and validate this?
comments:
- Required if providing water content
examples:
- value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503
- value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water content method
rank: 1000
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000323
alias: water_cont_soil_meth
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: false
water_content:
name: water_content
annotations:
expected_value:
tag: expected_value
value: string
preferred_unit:
tag: preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
description: Water content measurement
title: water content
todos:
- value in preferred unit is too limiting. need to change this
- check and correct validation so examples are accepted
- how to manage multiple water content methods?
examples:
- value: 0.75 g water/g dry soil
- value: 75% water holding capacity
- value: 1.1 g fresh weight/ dry weight
- value: 10% water filled pore space
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water content
rank: 1000
is_a: core field
slot_uri: MIXS:0000185
alias: water_content
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: true
water_current:
name: water_current
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: cubic meter per second, knots
occurrence:
tag: occurrence
value: '1'
description: Measurement of magnitude and direction of flow within a fluid
title: water current
examples:
- value: 10 cubic meter per second
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water current
rank: 1000
is_a: core field
slot_uri: MIXS:0000203
alias: water_current
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000454
alias: water_cut
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
water_feat_size:
name: water_feat_size
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: square meter
occurrence:
tag: occurrence
value: '1'
description: The size of the water feature
title: water feature size
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water feature size
rank: 1000
is_a: core field
slot_uri: MIXS:0000223
alias: water_feat_size
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
water_feat_type:
name: water_feat_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of water feature present within the building being sampled
title: water feature type
examples:
- value: stream
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water feature type
rank: 1000
is_a: core field
slot_uri: MIXS:0000847
alias: water_feat_type
owner: Biosample
domain_of:
- Biosample
range: water_feat_type_enum
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000453
alias: water_prod_rate
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
water_temp_regm:
name: water_temp_regm
annotations:
expected_value:
tag: expected_value
value: measurement value;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: degree Celsius
occurrence:
tag: occurrence
value: m
description: Information about treatment involving an exposure to water with varying
degree of temperature, treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment; can include multiple regimens
title: water temperature regimen
examples:
- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- water temperature regimen
rank: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000590
alias: water_temp_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
watering_regm:
name: watering_regm
annotations:
expected_value:
tag: expected_value
value: measurement value;treatment interval and duration
preferred_unit:
tag: preferred_unit
value: milliliter, liter
occurrence:
tag: occurrence
value: m
description: Information about treatment involving an exposure to watering frequencies,
treatment regimen including how many times the treatment was repeated, how long
each treatment lasted, and the start and end time of the entire treatment; can
include multiple regimens
title: watering regimen
examples:
- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
- value: 75% water holding capacity; constant
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- watering regimen
rank: 1000
is_a: core field
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000591
alias: watering_regm
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: true
inlined: true
inlined_as_list: true
weekday:
name: weekday
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The day of the week when sampling occurred
title: weekday
examples:
- value: Sunday
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- weekday
rank: 1000
is_a: core field
slot_uri: MIXS:0000848
alias: weekday
owner: Biosample
domain_of:
- Biosample
range: weekday_enum
multivalued: false
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: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000297
alias: win
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
wind_direction:
name: wind_direction
annotations:
expected_value:
tag: expected_value
value: wind direction name
occurrence:
tag: occurrence
value: '1'
description: Wind direction is the direction from which a wind originates
title: wind direction
examples:
- value: Northwest
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wind direction
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000757
alias: wind_direction
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
wind_speed:
name: wind_speed
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: meter per second, kilometer per hour
occurrence:
tag: occurrence
value: '1'
description: Speed of wind measured at the time of sampling
title: wind speed
examples:
- value: 21 kilometer per hour
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- wind speed
rank: 1000
is_a: core field
slot_uri: MIXS:0000118
alias: wind_speed
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
window_cond:
name: window_cond
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The physical condition of the window at the time of sampling
title: window condition
examples:
- value: rupture
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window condition
rank: 1000
is_a: core field
slot_uri: MIXS:0000849
alias: window_cond
owner: Biosample
domain_of:
- Biosample
range: window_cond_enum
multivalued: false
window_cover:
name: window_cover
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of window covering
title: window covering
examples:
- value: curtains
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window covering
rank: 1000
is_a: core field
slot_uri: MIXS:0000850
alias: window_cover
owner: Biosample
domain_of:
- Biosample
range: window_cover_enum
multivalued: false
window_horiz_pos:
name: window_horiz_pos
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The horizontal position of the window on the wall
title: window horizontal position
examples:
- value: middle
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window horizontal position
rank: 1000
is_a: core field
slot_uri: MIXS:0000851
alias: window_horiz_pos
owner: Biosample
domain_of:
- Biosample
range: window_horiz_pos_enum
multivalued: false
window_loc:
name: window_loc
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The relative location of the window within the room
title: window location
examples:
- value: west
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window location
rank: 1000
is_a: core field
slot_uri: MIXS:0000852
alias: window_loc
owner: Biosample
domain_of:
- Biosample
range: window_loc_enum
multivalued: false
window_mat:
name: window_mat
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of material used to finish a window
title: window material
examples:
- value: wood
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window material
rank: 1000
is_a: core field
slot_uri: MIXS:0000853
alias: window_mat
owner: Biosample
domain_of:
- Biosample
range: window_mat_enum
multivalued: false
window_open_freq:
name: window_open_freq
annotations:
expected_value:
tag: expected_value
value: value
occurrence:
tag: occurrence
value: '1'
description: The number of times windows are opened per week
title: window open frequency
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window open frequency
rank: 1000
is_a: core field
slot_uri: MIXS:0000246
alias: window_open_freq
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
window_size:
name: window_size
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: inch, meter
occurrence:
tag: occurrence
value: '1'
description: The window's length and width
title: window area/size
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window area/size
rank: 1000
is_a: core field
string_serialization: '{float} {unit} x {float} {unit}'
slot_uri: MIXS:0000224
alias: window_size
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
window_status:
name: window_status
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Defines whether the windows were open or closed during environmental
testing
title: window status
examples:
- value: open
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window status
rank: 1000
is_a: core field
string_serialization: '[closed|open]'
slot_uri: MIXS:0000855
alias: window_status
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
window_type:
name: window_type
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The type of windows
title: window type
examples:
- value: fixed window
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window type
rank: 1000
is_a: core field
slot_uri: MIXS:0000856
alias: window_type
owner: Biosample
domain_of:
- Biosample
range: window_type_enum
multivalued: false
window_vert_pos:
name: window_vert_pos
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: The vertical position of the window on the wall
title: window vertical position
examples:
- value: middle
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window vertical position
rank: 1000
is_a: core field
slot_uri: MIXS:0000857
alias: window_vert_pos
owner: Biosample
domain_of:
- Biosample
range: window_vert_pos_enum
multivalued: false
window_water_mold:
name: window_water_mold
annotations:
expected_value:
tag: expected_value
value: enumeration
occurrence:
tag: occurrence
value: '1'
description: Signs of the presence of mold or mildew on the window.
title: window signs of water/mold
examples:
- value: no presence of mold visible
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- window signs of water/mold
rank: 1000
is_a: core field
string_serialization: '[presence of mold visible|no presence of mold visible]'
slot_uri: MIXS:0000854
alias: window_water_mold
owner: Biosample
domain_of:
- Biosample
range: TextValue
multivalued: false
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: 1000
is_a: core field
slot_uri: MIXS:0000156
alias: xylene
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
multivalued: false
zinc:
name: zinc
annotations:
expected_value:
tag: expected_value
value: measurement value
preferred_unit:
tag: preferred_unit
value: mg/kg (ppm)
occurrence:
tag: occurrence
value: '1'
description: Concentration of zinc in the sample
title: zinc
examples:
- value: 2.5 mg/kg
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.ornl.gov/content/bio-scales-0
aliases:
- zinc
rank: 1000
alias: zinc
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
add_date:
name: add_date
description: The date on which the information was added to the database.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: add_date
owner: Biosample
domain_of:
- Biosample
- DataGeneration
range: string
community:
name: community
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: community
owner: Biosample
domain_of:
- Biosample
range: string
habitat:
name: habitat
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: habitat
owner: Biosample
domain_of:
- FieldResearchSite
- Biosample
range: string
host_name:
name: host_name
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: host_name
owner: Biosample
domain_of:
- Biosample
range: string
location:
name: location
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: location
owner: Biosample
domain_of:
- Biosample
range: string
mod_date:
name: mod_date
description: The last date on which the database information was modified.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: mod_date
owner: Biosample
domain_of:
- Biosample
- DataGeneration
range: string
ncbi_taxonomy_name:
name: ncbi_taxonomy_name
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: ncbi_taxonomy_name
owner: Biosample
domain_of:
- Biosample
range: string
proport_woa_temperature:
name: proport_woa_temperature
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: proport_woa_temperature
owner: Biosample
domain_of:
- Biosample
range: string
salinity_category:
name: salinity_category
description: 'Categorical description of the sample''s salinity. Examples: halophile,
halotolerant, hypersaline, huryhaline'
notes:
- maps to gold:salinity
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-metadata/pull/297
rank: 1000
alias: salinity_category
owner: Biosample
domain_of:
- Biosample
range: string
sample_collection_site:
name: sample_collection_site
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: sample_collection_site
owner: Biosample
domain_of:
- Biosample
range: string
soluble_iron_micromol:
name: soluble_iron_micromol
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: soluble_iron_micromol
owner: Biosample
domain_of:
- Biosample
range: string
subsurface_depth:
name: subsurface_depth
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: subsurface_depth
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
dna_absorb1:
name: dna_absorb1
description: 260/280 measurement of DNA sample purity
title: DNA absorbance 260/280
comments:
- Recommended value is between 1 and 3.
examples:
- value: '2.02'
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: biomaterial_purity
alias: dna_absorb1
owner: Biosample
domain_of:
- Biosample
- ProcessedSample
slot_group: JGI-Metagenomics
range: float
recommended: true
dna_absorb2:
name: dna_absorb2
description: 260/230 measurement of DNA sample purity
title: DNA absorbance 260/230
comments:
- Recommended value is between 1 and 3.
examples:
- value: '2.02'
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: biomaterial_purity
alias: dna_absorb2
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: float
recommended: true
dna_collect_site:
name: dna_collect_site
description: Provide information on the site your DNA sample was collected from
title: DNA collection site
examples:
- value: untreated pond water
from_schema: https://w3id.org/nmdc/nmdc
rank: 15
string_serialization: '{text}'
alias: dna_collect_site
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_concentration:
name: dna_concentration
title: DNA concentration in ng/ul
comments:
- Units must be in ng/uL. Enter the numerical part only. Must be calculated using
a fluorometric method. Acceptable values are 0-2000.
examples:
- value: '100'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- nmdc:nucleic_acid_concentration
rank: 5
alias: dna_concentration
owner: Biosample
domain_of:
- Biosample
- ProcessedSample
slot_group: JGI-Metagenomics
range: float
recommended: true
minimum_value: 0
maximum_value: 2000
dna_cont_type:
name: dna_cont_type
description: Tube or plate (96-well)
title: DNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
alias: dna_cont_type
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: JgiContTypeEnum
recommended: true
dna_container_id:
name: dna_container_id
title: DNA container label
comments:
- Must be unique across all tubes and plates, and <20 characters. All samples
in a plate should have the same plate label.
examples:
- value: Pond_MT_041618
from_schema: https://w3id.org/nmdc/nmdc
rank: 9
string_serialization: '{text < 20 characters}'
alias: dna_container_id
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_dnase:
name: dna_dnase
title: DNase treatment DNA
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
rank: 13
alias: dna_dnase
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: YesNoEnum
recommended: true
dna_isolate_meth:
name: dna_isolate_meth
description: Describe the method/protocol/kit used to extract DNA/RNA.
title: DNA isolation method
examples:
- value: phenol/chloroform extraction
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Sample Isolation Method
rank: 16
string_serialization: '{text}'
alias: dna_isolate_meth
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_organisms:
name: dna_organisms
description: List any organisms known or suspected to grow in co-culture, as well
as estimated % of the organism in that culture.
title: DNA expected organisms
examples:
- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
(1%)
from_schema: https://w3id.org/nmdc/nmdc
rank: 14
string_serialization: '{text}'
alias: dna_organisms
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_project_contact:
name: dna_project_contact
title: DNA seq project contact
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: John Jones
from_schema: https://w3id.org/nmdc/nmdc
rank: 18
string_serialization: '{text}'
alias: dna_project_contact
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_samp_id:
name: dna_samp_id
title: DNA sample ID
todos:
- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't
have two identifiers. How to force uniqueness? Moot because that column will
be prefilled?
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: '187654'
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{text}'
alias: dna_samp_id
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_sample_format:
name: dna_sample_format
description: Solution in which the DNA sample has been suspended
title: DNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
alias: dna_sample_format
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: DNASampleFormatEnum
recommended: true
dna_sample_name:
name: dna_sample_name
description: Give the DNA sample a name that is meaningful to you. Sample names
must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
title: DNA sample name
examples:
- value: JGI_pond_041618
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{text}'
alias: dna_sample_name
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_seq_project:
name: dna_seq_project
title: DNA seq project ID
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: '1191234'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Seq Project ID
rank: 1
string_serialization: '{text}'
alias: dna_seq_project
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_seq_project_pi:
name: dna_seq_project_pi
title: DNA seq project PI
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: Jane Johnson
from_schema: https://w3id.org/nmdc/nmdc
rank: 17
string_serialization: '{text}'
alias: dna_seq_project_pi
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_seq_project_name:
name: dna_seq_project_name
title: DNA seq project name
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: JGI Pond metagenomics
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
alias: dna_seq_project_name
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dna_volume:
name: dna_volume
title: DNA volume in ul
comments:
- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This
form accepts values < 25, but JGI may refuse to process them unless permission
has been granted by a project manager
examples:
- value: '25'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{float}'
alias: dna_volume
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: float
recommended: true
minimum_value: 0
maximum_value: 1000
proposal_dna:
name: proposal_dna
title: DNA proposal ID
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: '504000'
from_schema: https://w3id.org/nmdc/nmdc
rank: 19
string_serialization: '{text}'
alias: proposal_dna
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metagenomics
range: string
recommended: true
dnase_rna:
name: dnase_rna
title: DNase treated
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Was Sample DNAse treated?
rank: 13
alias: dnase_rna
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: YesNoEnum
recommended: true
proposal_rna:
name: proposal_rna
title: RNA proposal ID
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: '504000'
from_schema: https://w3id.org/nmdc/nmdc
rank: 19
string_serialization: '{text}'
alias: proposal_rna
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_absorb1:
name: rna_absorb1
description: 260/280 measurement of RNA sample purity
title: RNA absorbance 260/280
comments:
- Recommended value is between 1 and 3.
examples:
- value: '2.02'
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
string_serialization: '{float}'
alias: rna_absorb1
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: float
recommended: true
rna_absorb2:
name: rna_absorb2
description: 260/230 measurement of RNA sample purity
title: RNA absorbance 260/230
comments:
- Recommended value is between 1 and 3.
examples:
- value: '2.02'
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
string_serialization: '{float}'
alias: rna_absorb2
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: float
recommended: true
rna_collect_site:
name: rna_collect_site
description: Provide information on the site your RNA sample was collected from
title: RNA collection site
examples:
- value: untreated pond water
from_schema: https://w3id.org/nmdc/nmdc
rank: 15
string_serialization: '{text}'
alias: rna_collect_site
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_concentration:
name: rna_concentration
title: RNA concentration in ng/ul
comments:
- Units must be in ng/uL. Enter the numerical part only. Must be calculated using
a fluorometric method. Acceptable values are 0-2000.
examples:
- value: '100'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- nmdc:nucleic_acid_concentration
rank: 5
string_serialization: '{float}'
alias: rna_concentration
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: float
recommended: true
minimum_value: 0
maximum_value: 1000
rna_cont_type:
name: rna_cont_type
description: Tube or plate (96-well)
title: RNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
alias: rna_cont_type
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: JgiContTypeEnum
recommended: true
rna_cont_well:
name: rna_cont_well
title: RNA plate position
comments:
- Required when 'plate' is selected for container type.
- Leave blank if the sample will be shipped in a tube.
- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not
pass validation.
- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).
examples:
- value: B2
from_schema: https://w3id.org/nmdc/nmdc
rank: 11
string_serialization: '{96 well plate pos}'
alias: rna_cont_well
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
rna_container_id:
name: rna_container_id
title: RNA container label
comments:
- Must be unique across all tubes and plates, and <20 characters. All samples
in a plate should have the same plate label.
examples:
- value: Pond_MT_041618
from_schema: https://w3id.org/nmdc/nmdc
rank: 9
string_serialization: '{text < 20 characters}'
alias: rna_container_id
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_isolate_meth:
name: rna_isolate_meth
description: Describe the method/protocol/kit used to extract DNA/RNA.
title: RNA isolation method
examples:
- value: phenol/chloroform extraction
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Sample Isolation Method
rank: 16
string_serialization: '{text}'
alias: rna_isolate_meth
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_organisms:
name: rna_organisms
description: List any organisms known or suspected to grow in co-culture, as well
as estimated % of the organism in that culture.
title: RNA expected organisms
examples:
- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
(1%)
from_schema: https://w3id.org/nmdc/nmdc
rank: 14
string_serialization: '{text}'
alias: rna_organisms
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_project_contact:
name: rna_project_contact
title: RNA seq project contact
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: John Jones
from_schema: https://w3id.org/nmdc/nmdc
rank: 18
string_serialization: '{text}'
alias: rna_project_contact
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_samp_id:
name: rna_samp_id
title: RNA sample ID
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: '187654'
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{text}'
alias: rna_samp_id
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_sample_format:
name: rna_sample_format
description: Solution in which the RNA sample has been suspended
title: RNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
alias: rna_sample_format
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: RNASampleFormatEnum
recommended: true
rna_sample_name:
name: rna_sample_name
description: Give the RNA sample a name that is meaningful to you. Sample names
must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
title: RNA sample name
examples:
- value: JGI_pond_041618
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{text}'
alias: rna_sample_name
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
minimum_value: 0
maximum_value: 2000
rna_seq_project:
name: rna_seq_project
title: RNA seq project ID
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: '1191234'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Seq Project ID
rank: 1
string_serialization: '{text}'
alias: rna_seq_project
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_seq_project_pi:
name: rna_seq_project_pi
title: RNA seq project PI
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: Jane Johnson
from_schema: https://w3id.org/nmdc/nmdc
rank: 17
string_serialization: '{text}'
alias: rna_seq_project_pi
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_seq_project_name:
name: rna_seq_project_name
title: RNA seq project name
comments:
- Do not edit these values. A template will be provided by NMDC in which these
values have been pre-filled.
examples:
- value: JGI Pond metatranscriptomics
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
alias: rna_seq_project_name
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: string
recommended: true
rna_volume:
name: rna_volume
title: RNA volume in ul
comments:
- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This
form accepts values < 25, but JGI may refuse to process them unless permission
has been granted by a project manager
examples:
- value: '25'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{float}'
alias: rna_volume
owner: Biosample
domain_of:
- Biosample
slot_group: JGI-Metatranscriptomics
range: float
recommended: true
minimum_value: 0
maximum_value: 1000
collection_date_inc:
name: collection_date_inc
description: Date the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 2
string_serialization: '{date, arbitrary precision}'
alias: collection_date_inc
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
collection_time:
name: collection_time
description: The time of sampling, either as an instance (single point) or interval.
title: collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 1
string_serialization: '{time, seconds optional}'
alias: collection_time
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
collection_time_inc:
name: collection_time_inc
description: Time the incubation was harvested/collected/ended. Only relevant
for incubation samples.
title: incubation collection time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 3
string_serialization: '{time, seconds optional}'
alias: collection_time_inc
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
experimental_factor_other:
name: experimental_factor_other
description: Other details about your sample that you feel can't be accurately
represented in the available columns.
title: experimental factor- other
comments:
- This slot accepts open-ended text about your sample.
- We recommend using key:value pairs.
- Provided pairs will be considered for inclusion as future slots/terms in this
data collection template.
examples:
- value: 'experimental treatment: value'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000008
- MIXS:0000300
rank: 7
string_serialization: '{text}'
alias: experimental_factor_other
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
filter_method:
name: filter_method
description: Type of filter used or how the sample was filtered
title: filter method
comments:
- describe the filter or provide a catalog number and manufacturer
examples:
- value: C18
- value: Basix PES, 13-100-106 FisherSci
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000765
rank: 6
string_serialization: '{text}'
alias: filter_method
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
isotope_exposure:
name: isotope_exposure
description: List isotope exposure or addition applied to your sample.
title: isotope exposure/addition
todos:
- Can we make the H218O correctly super and subscripted?
comments:
- This is required when your experimental design includes the use of isotopically
labeled compounds
examples:
- value: 13C glucose
- value: H218O
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000751
rank: 16
string_serialization: '{termLabel} {[termID]}; {timestamp}'
alias: isotope_exposure
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
micro_biomass_c_meth:
name: micro_biomass_c_meth
description: Reference or method used in determining microbial biomass carbon
title: microbial biomass carbon method
todos:
- How should we separate values? | or ;? lets be consistent
comments:
- required if "microbial_biomass_c" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 11
string_serialization: '{PMID}|{DOI}|{URL}'
alias: micro_biomass_c_meth
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
micro_biomass_n_meth:
name: micro_biomass_n_meth
description: Reference or method used in determining microbial biomass nitrogen
title: microbial biomass nitrogen method
comments:
- required if "microbial_biomass_n" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(87)90052-6
- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000339
rank: 13
string_serialization: '{PMID}|{DOI}|{URL}'
alias: micro_biomass_n_meth
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
microbial_biomass_c:
name: microbial_biomass_c
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass carbon
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug C/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 10
string_serialization: '{float} {unit}'
alias: microbial_biomass_c
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
microbial_biomass_n:
name: microbial_biomass_n
description: The part of the organic matter in the soil that constitutes living
microorganisms smaller than 5-10 micrometer.
title: microbial biomass nitrogen
comments:
- If you provide this, correction factors used for conversion to the final units
and method are required
examples:
- value: 0.05 ug N/g dry soil
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 12
string_serialization: '{float} {unit}'
alias: microbial_biomass_n
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
non_microb_biomass:
name: non_microb_biomass
description: Amount of biomass; should include the name for the part of biomass
measured, e.g.insect, plant, total. Can include multiple measurements separated
by ;
title: non-microbial biomass
examples:
- value: insect 0.23 ug; plant 1g
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000174
- MIXS:0000650
rank: 8
string_serialization: '{text};{float} {unit}'
alias: non_microb_biomass
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
non_microb_biomass_method:
name: non_microb_biomass_method
description: Reference or method used in determining biomass
title: non-microbial biomass method
comments:
- required if "non-microbial biomass" is provided
examples:
- value: https://doi.org/10.1038/s41467-021-26181-3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000650
rank: 9
string_serialization: '{PMID}|{DOI}|{URL}'
alias: non_microb_biomass_method
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
org_nitro_method:
name: org_nitro_method
description: Method used for obtaining organic nitrogen
title: organic nitrogen method
comments:
- required if "org_nitro" is provided
examples:
- value: https://doi.org/10.1016/0038-0717(85)90144-0
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000338
- MIXS:0000205
rank: 14
string_serialization: '{PMID}|{DOI}|{URL}'
alias: org_nitro_method
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
other_treatment:
name: other_treatment
description: Other treatments applied to your samples that are not applicable
to the provided fields
title: other treatments
notes:
- Values entered here will be used to determine potential new slots.
comments:
- This is an open text field to provide any treatments that cannot be captured
in the provided slots.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000300
rank: 15
string_serialization: '{text}'
alias: other_treatment
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
start_date_inc:
name: start_date_inc
description: Date the incubation was started. Only relevant for incubation samples.
title: incubation start date
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision
date only
comments:
- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021
are all acceptable.
examples:
- value: 2021-04-15, 2021-04 and 2021 are all acceptable.
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 4
string_serialization: '{date, arbitrary precision}'
alias: start_date_inc
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
start_time_inc:
name: start_time_inc
description: Time the incubation was started. Only relevant for incubation samples.
title: incubation start time, GMT
notes:
- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional
time only
comments:
- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'
examples:
- value: 13:33 or 13:33:55
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIXS:0000011
rank: 5
string_serialization: '{time, seconds optional}'
alias: start_time_inc
owner: Biosample
domain_of:
- Biosample
slot_group: MIxS Inspired
range: string
recommended: true
project_id:
name: project_id
description: Proposal IDs or names associated with dataset
title: project ID
from_schema: https://w3id.org/nmdc/nmdc
rank: 1
string_serialization: '{text}'
alias: project_id
owner: Biosample
domain_of:
- Biosample
slot_group: EMSL
range: string
recommended: true
replicate_number:
name: replicate_number
description: If sending biological replicates, indicate the rep number here.
title: replicate number
comments:
- This will guide staff in ensuring your samples are blocked & randomized correctly
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{integer}'
alias: replicate_number
owner: Biosample
domain_of:
- Biosample
slot_group: EMSL
range: string
recommended: true
sample_shipped:
name: sample_shipped
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample sent to EMSL.
title: sample shipped amount
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: 15 g
- value: 100 uL
- value: 5 mL
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{float} {unit}'
alias: sample_shipped
owner: Biosample
domain_of:
- Biosample
slot_group: EMSL
range: string
recommended: true
sample_type:
name: sample_type
description: Type of sample being submitted
title: sample type
comments:
- This can vary from 'environmental package' if the sample is an extraction.
examples:
- value: water extracted soil
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
alias: sample_type
owner: Biosample
domain_of:
- Biosample
slot_group: EMSL
range: SampleTypeEnum
recommended: true
technical_reps:
name: technical_reps
description: If sending technical replicates of the same sample, indicate the
replicate count.
title: number technical replicate
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{integer}'
alias: technical_reps
owner: Biosample
domain_of:
- Biosample
slot_group: EMSL
range: string
recommended: true
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
alias: analysis_type
owner: Biosample
domain_of:
- Biosample
slot_group: Sample ID
range: AnalysisTypeEnum
recommended: true
multivalued: true
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
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}'
alias: sample_link
owner: Biosample
domain_of:
- Biosample
slot_group: Sample ID
range: string
recommended: true
multivalued: true
bulk_elect_conductivity:
name: bulk_elect_conductivity
description: Electrical conductivity is a measure of the ability to carry electric
current, which is mostly dictated by the chemistry of and amount of water.
title: bulk electrical conductivity
comments:
- Provide the value output of the field instrument.
examples:
- value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')
description: The conductivity measurement was 0.017 millisiemens per centimeter.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: bulk_elect_conductivity
owner: Biosample
domain_of:
- Biosample
range: QuantityValue
infiltrations:
name: infiltrations
description: The amount of time it takes to complete each infiltration activity
examples:
- value: '[''00:01:32'', ''00:00:53'']'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1
aliases:
- infiltration_1
- infiltration_2
rank: 1000
list_elements_ordered: true
alias: infiltrations
owner: Biosample
domain_of:
- Biosample
range: string
multivalued: true
pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$
id:
name: id
description: An NMDC assigned unique identifier for a biosample submitted to NMDC.
notes:
- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
will be accepted
- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
via per-class id slot usage assertions
- minting authority shoulders should probably be enumerated and checked in the
pattern
examples:
- value: nmdc:mgmag-00-x012.1_7_c1
description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
identifier: true
alias: id
owner: Biosample
domain_of:
- NamedThing
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
structured_pattern:
syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: Biosample
domain_of:
- PersonValue
- NamedThing
- Protocol
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: Biosample
domain_of:
- ImageValue
- NamedThing
range: string
alternative_identifiers:
name: alternative_identifiers
description: Unique identifier for a biosample submitted to additional resources.
Matches the entity that has been submitted to NMDC
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: Biosample
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
type:
name: type
description: the class_uri of the class that has been instantiated
notes:
- replaces legacy nmdc:type slot
- makes it easier to read example data files
- required for polymorphic MongoDB collections
examples:
- value: nmdc:Biosample
- value: nmdc:Study
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/1048
- https://github.com/microbiomedata/nmdc-schema/issues/1233
- https://github.com/microbiomedata/nmdc-schema/issues/248
rank: 1000
slot_uri: rdf:type
designates_type: true
alias: type
owner: Biosample
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
class_uri: nmdc:Biosample
unique_keys:
samp_name_unique_key:
unique_key_name: samp_name_unique_key
unique_key_slots:
- samp_name
rules:
- preconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: .+
postconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
description: DNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: dna_well_requires_plate
- preconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
postconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: DNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case. Waiting for value_present
validation to be added to runtime
title: dna_plate_requires_well
- preconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: .+
postconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
description: RNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: rna_well_requires_plate
- preconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
postconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: RNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case. Waiting for value_present
validation to be added to runtime
title: rna_plate_requires_well