Class: biosample
A material sample. It may be environmental (encompassing many organisms) or isolate or tissue. An environmental sample containing genetic material from multiple individuals is commonly referred to as a biosample.
URI: nmdc:Biosample
Identifier prefixes
GOLD
Parents
is_a: NamedThing - a databased entity or concept/class
Referenced by Class
Attributes
Own
type 0..1
Description: An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.
Range: String
Example: nmdc:Biosample None
Example: nmdc:Study None
-
Description: A list of alternative identifiers for the entity.
Range: String
biosample➞part of 1..*
Description: Links a resource to another resource that either logically or physically includes it.
Range: NamedThing
agrochem_addition 0..1
Description: Addition of fertilizers, pesticides, etc. - amount and time of applications
Range: QuantityValue
alkalinity 0..1
Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
Range: QuantityValue
alkalinity_method 0..1
Description: Method used for alkalinity measurement
Range: TextValue
alkyl_diethers 0..1
Description: Concentration of alkyl diethers
Range: QuantityValue
alt 0..1
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 earthbs 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
Range: QuantityValue
in subsets: (environment)
al_sat 0..1
Description: Aluminum saturation (esp. For tropical soils)
Range: QuantityValue
al_sat_meth 0..1
Description: Reference or method used in determining Al saturation
Range: TextValue
aminopept_act 0..1
Description: Measurement of aminopeptidase activity
Range: QuantityValue
ammonium 0..1
Description: Concentration of ammonium in the sample
Range: QuantityValue
annual_precpt 0..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.
Range: QuantityValue
annual_temp 0..1
Description: Mean annual temperature
Range: QuantityValue
bacteria_carb_prod 0..1
Description: Measurement of bacterial carbon production
Range: QuantityValue
bishomohopanol 0..1
Description: Concentration of bishomohopanol
Range: QuantityValue
bromide 0..1
Description: Concentration of bromide
Range: QuantityValue
calcium 0..1
Description: Concentration of calcium in the sample
Range: QuantityValue
carb_nitro_ratio 0..1
Description: Ratio of amount or concentrations of carbon to nitrogen
Range: QuantityValue
chem_administration 0..1
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
Range: ControlledTermValue
chloride 0..1
Description: Concentration of chloride in the sample
Range: QuantityValue
chlorophyll 0..1
Description: Concentration of chlorophyll
Range: QuantityValue
collection_date 0..1
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
Range: TimestampValue
in subsets: (environment)
cur_land_use 0..1
Description: Present state of sample site
Range: TextValue
cur_vegetation 0..1
Description: Vegetation classification from one or more standard classification systems, or agricultural crop
Range: TextValue
cur_vegetation_meth 0..1
Description: Reference or method used in vegetation classification
Range: TextValue
crop_rotation 0..1
Description: Whether or not crop is rotated, and if yes, rotation schedule
Range: TextValue
density 0..1
Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density)
Range: QuantityValue
depth 0..1
Description: Depth is defined as 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
Range: QuantityValue
in subsets: (environment)
diss_carb_dioxide 0..1
Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample
Range: QuantityValue
diss_hydrogen 0..1
Description: Concentration of dissolved hydrogen
Range: QuantityValue
diss_inorg_carb 0..1
Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
Range: QuantityValue
diss_inorg_phosp 0..1
Description: Concentration of dissolved inorganic phosphorus in the sample
Range: QuantityValue
diss_org_carb 0..1
Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
Range: QuantityValue
diss_org_nitro 0..1
Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
Range: QuantityValue
diss_oxygen 0..1
Description: Concentration of dissolved oxygen
Range: QuantityValue
drainage_class 0..1
Description: Drainage classification from a standard system such as the USDA system
Range: TextValue
elev 0..1
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
Range: QuantityValue
in subsets: (environment)
env_package 0..1
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
Range: TextValue
in subsets: (mixs extension)
biosample➞env_broad_scale 1..1
Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVOUs biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html
Range: ControlledTermValue
in subsets: (environment)
biosample➞env_local_scale 1..1
Description: In this field, report the entity or entities which are in your sample or specimenUs local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: 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]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html
Range: ControlledTermValue
in subsets: (environment)
biosample➞env_medium 1..1
Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVOUs environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: 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. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html
Range: ControlledTermValue
in subsets: (environment)
extreme_event 0..1
Description: Unusual physical events that may have affected microbial populations
Range: TimestampValue
fao_class 0..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
Range: TextValue
fire 0..1
Description: Historical and/or physical evidence of fire
Range: TimestampValue
flooding 0..1
Description: Historical and/or physical evidence of flooding
Range: TimestampValue
geo_loc_name 0..1
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 (v 1.512) (http://purl.bioontology.org/ontology/GAZ)
Range: TextValue
in subsets: (environment)
glucosidase_act 0..1
Description: Measurement of glucosidase activity
Range: QuantityValue
heavy_metals 0..1
Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations
Range: QuantityValue
heavy_metals_meth 0..1
Description: Reference or method used in determining heavy metals
Range: TextValue
horizon 0..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
Range: TextValue
horizon_meth 0..1
Description: Reference or method used in determining the horizon
Range: TextValue
biosample➞lat_lon 0..1
Description: This is currently a required field but it’s not clear if this should be required for human hosts
Range: GeolocationValue
in subsets: (environment)
link_addit_analys 0..1
Description: Link to additional analysis results performed on the sample
Range: TextValue
link_class_info 0..1
Description: Link to digitized soil maps or other soil classification information
Range: TextValue
link_climate_info 0..1
Description: Link to climate resource
Range: TextValue
local_class 0..1
Description: Soil classification based on local soil classification system
Range: TextValue
local_class_meth 0..1
Description: Reference or method used in determining the local soil classification
Range: TextValue
magnesium 0..1
Description: Concentration of magnesium in the sample
Range: QuantityValue
mean_frict_vel 0..1
Description: Measurement of mean friction velocity
Range: QuantityValue
mean_peak_frict_vel 0..1
Description: Measurement of mean peak friction velocity
Range: QuantityValue
microbial_biomass 0..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
Range: QuantityValue
-
Description: Reference or method used in determining microbial biomass
Range: TextValue
misc_param 0..1
Description: Any other measurement performed or parameter collected, that is not listed here
Range: QuantityValue
n_alkanes 0..1
Description: Concentration of n-alkanes; can include multiple n-alkanes
Range: QuantityValue
nitrate 0..1
Description: Concentration of nitrate in the sample
Range: QuantityValue
nitrite 0..1
Description: Concentration of nitrite in the sample
Range: QuantityValue
org_matter 0..1
Description: Concentration of organic matter
Range: QuantityValue
org_nitro 0..1
Description: Concentration of organic nitrogen
Range: QuantityValue
organism_count 0..1
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)
Range: QuantityValue
oxy_stat_samp 0..1
Description: Oxygenation status of sample
Range: TextValue
part_org_carb 0..1
Description: Concentration of particulate organic carbon
Range: QuantityValue
perturbation 0..1
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
Range: TextValue
petroleum_hydrocarb 0..1
Description: Concentration of petroleum hydrocarbon
Range: QuantityValue
ph 0..1
Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
Range: QuantityValue
ph_meth 0..1
Description: Reference or method used in determining ph
Range: TextValue
phaeopigments 0..1
Description: Concentration of phaeopigments; can include multiple phaeopigments
Range: QuantityValue
phosplipid_fatt_acid 0..1
Description: Concentration of phospholipid fatty acids; can include multiple values
Range: QuantityValue
pool_dna_extracts 0..1
Description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given
Range: TextValue
potassium 0..1
Description: Concentration of potassium in the sample
Range: QuantityValue
pressure 0..1
Description: Pressure to which the sample is subject to, in atmospheres
Range: QuantityValue
previous_land_use 0..1
Description: Previous land use and dates
Range: TextValue
-
Description: Reference or method used in determining previous land use and dates
Range: TextValue
profile_position 0..1
Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
Range: TextValue
redox_potential 0..1
Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
Range: QuantityValue
salinity 0..1
Description: Salinity is the total concentration of all dissolved salts in a water 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
Range: QuantityValue
salinity_meth 0..1
Description: Reference or method used in determining salinity
Range: TextValue
samp_collect_device 0..1
Description: The method or device employed for collecting the sample
Range: TextValue
in subsets: (nucleic acid sequence source)
samp_mat_process 0..1
Description: Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
Range: ControlledTermValue
in subsets: (nucleic acid sequence source)
samp_store_dur 0..1
Description: Duration for which the sample was stored
Range: TextValue
samp_store_loc 0..1
Description: Location at which sample was stored, usually name of a specific freezer/room
Range: TextValue
samp_store_temp 0..1
Description: Temperature at which sample was stored, e.g. -80 degree Celsius
Range: QuantityValue
samp_vol_we_dna_ext 0..1
Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction
Range: QuantityValue
season_temp 0..1
Description: Mean seasonal temperature
Range: QuantityValue
season_precpt 0..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.
Range: QuantityValue
sieving 0..1
Description: Collection design of pooled samples and/or sieve size and amount of sample sieved
Range: QuantityValue
size_frac_low 0..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
Range: QuantityValue
size_frac_up 0..1
Description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
Range: QuantityValue
slope_gradient 0..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
Range: QuantityValue
slope_aspect 0..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); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.
Range: QuantityValue
sodium 0..1
Description: Sodium concentration in the sample
Range: QuantityValue
soil_type 0..1
Description: Soil series name or other lower-level classification
Range: TextValue
soil_type_meth 0..1
Description: Reference or method used in determining soil series name or other lower-level classification
Range: TextValue
store_cond 0..1
Description: Explain how and for how long the soil sample was stored before DNA extraction
Range: TextValue
sulfate 0..1
Description: Concentration of sulfate in the sample
Range: QuantityValue
sulfide 0..1
Description: Concentration of sulfide in the sample
Range: QuantityValue
temp 0..1
Description: Temperature of the sample at the time of sampling
Range: QuantityValue
texture 0..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.
Range: QuantityValue
texture_meth 0..1
Description: Reference or method used in determining soil texture
Range: TextValue
tillage 0..1
Description: Note method(s) used for tilling
Range: TextValue
tidal_stage 0..1
Description: Stage of tide
Range: TextValue
tot_carb 0..1
Description: Total carbon content
Range: QuantityValue
tot_depth_water_col 0..1
Description: Measurement of total depth of water column
Range: QuantityValue
tot_diss_nitro 0..1
Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
Range: QuantityValue
tot_org_carb 0..1
Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
Range: QuantityValue
tot_org_c_meth 0..1
Description: Reference or method used in determining total organic carbon
Range: TextValue
tot_nitro_content 0..1
Description: Total nitrogen content of the sample
Range: QuantityValue
-
Description: Reference or method used in determining the total nitrogen
Range: TextValue
tot_phosp 0..1
Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
Range: QuantityValue
water_content 0..1
Description: Water content measurement
Range: QuantityValue
-
Description: Reference or method used in determining the water content of soil
Range: TextValue
ecosystem 0..1
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.
Range: String
ecosystem_category 0..1
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.
Range: String
ecosystem_type 0..1
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.
Range: String
ecosystem_subtype 0..1
Description: Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.
Range: String
specific_ecosystem 0..1
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.
Range: String
add_date 0..1
Description: The date on which the information was added to the database.
Range: String
community 0..1
Range: String
depth2 0..1
Range: QuantityValue
habitat 0..1
Range: String
host_name 0..1
Range: String
identifier 0..1
Range: String
location 0..1
Range: String
mod_date 0..1
Description: The last date on which the database information was modified.
Range: String
ncbi_taxonomy_name 0..1
Range: String
-
Range: String
salinity_category 0..1
Description: Categorcial description of the sample’s salinity. Examples: halophile, halotolerant, hypersaline, huryhaline
Range: String
-
Range: String
-
Range: String
subsurface_depth 0..1
Range: QuantityValue
subsurface_depth2 0..1
Range: QuantityValue
-
Description: identifiers for corresponding sample in GOLD
Range: ExternalIdentifier
Example: https://identifiers.org/gold:Gb0312930 None
INSDC biosample identifiers 0..*
Description: identifiers for corresponding sample in INSDC
Range: ExternalIdentifier
Example: https://identifiers.org/biosample:SAMEA5989477 None
Example: https://identifiers.org/biosample:SAMD00212331 I13_N_5-10 sample from Soil fungal diversity along elevational gradients
INSDC secondary sample identifiers 0..*
Description: secondary identifiers for corresponding sample in INSDC
Range: ExternalIdentifier
Example: https://identifiers.org/insdc.sra:DRS166340 I13_N_5-10 sample from Soil fungal diversity along elevational gradients
Inherited from named thing:
Other properties
Aliases: | sample | |
material sample | ||
specimen | ||
biospecimen | ||
Alt Descriptions: | 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. (embl.ena) | |
In Subsets: | sample subset | |
Exact Mappings: | OBI:0000747 | |
NCIT:C43412 |