Class: WaterMIMARKSSpecimen

Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package water

URI: mixs.vocab:WaterMIMARKSSpecimen

Parents

• is_a: Water - water

Uses Mixins

• mixin: MIMARKSSpecimen - Minimal Information about a Marker Specimen: specimen

Attributes

Inherited from water:

• alkalinity _OPT
  • Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
  • range: QuantityValue
  • Example: 50 milligram per liter None
• alkalinity_method _OPT
  • Description: Method used for alkalinity measurement
  • range: String
  • Example: titration None
• alkyl_diethers _OPT
  • Description: Concentration of alkyl diethers
  • range: QuantityValue
  • Example: 0.005 mole per liter None
• alt _OPT
  • 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
  • range: QuantityValue
  • Example: 100 meter None
• aminopept_act _OPT
  • Description: Measurement of aminopeptidase activity
  • range: QuantityValue
  • Example: 0.269 mole per liter per hour None
• ammonium _OPT
  • Description: Concentration of ammonium in the sample
  • range: QuantityValue
  • Example: 1.5 milligram per liter None
• atmospheric_data _OPT
  • Description: Measurement of atmospheric data; can include multiple data
  • range: String
  • Example: wind speed;9 knots None
• bac_prod _OPT
  • Description: Bacterial production in the water column measured by isotope uptake
  • range: QuantityValue
  • Example: 5 milligram per cubic meter per day None
• bac_resp _OPT
  • Description: Measurement of bacterial respiration in the water column
  • range: QuantityValue
  • Example: 300 micromole oxygen per liter per hour None
• bacteria_carb_prod _OPT
  • Description: Measurement of bacterial carbon production
  • range: QuantityValue
  • Example: 2.53 microgram per liter per hour None
• biomass _OPT
  • Description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
  • range: String
  • Example: total;20 gram None
• bishomohopanol _OPT
  • Description: Concentration of bishomohopanol
  • range: QuantityValue
  • Example: 14 microgram per liter None
• bromide _OPT
  • Description: Concentration of bromide
  • range: QuantityValue
  • Example: 0.05 parts per million None
• calcium _OPT
  • Description: Concentration of calcium in the sample
  • range: QuantityValue
  • Example: 0.2 micromole per liter None
• carb_nitro_ratio _OPT
  • Description: Ratio of amount or concentrations of carbon to nitrogen
  • range: QuantityValue
  • Example: 0.417361111 None
• chem_administration _OPT
  • 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: String
  • Example: agar [CHEBI:2509];2018-05-11T20:00Z None
• chloride _OPT
  • Description: Concentration of chloride in the sample
  • range: QuantityValue
  • Example: 5000 milligram per liter None
• chlorophyll _OPT
  • Description: Concentration of chlorophyll
  • range: QuantityValue
  • Example: 5 milligram per cubic meter None
• collection_date _OPT
  • 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: Date
  • Example: 2018-05-11T10:00:00+01:00 None
• conduc _OPT
  • Description: Electrical conductivity of water
  • range: QuantityValue
  • Example: 10 milliSiemens per centimeter None
• density _OPT
  • Description: Density of the sample, which is its mass per unit volume (aka volumetric mass density)
  • range: QuantityValue
  • Example: 1000 kilogram per cubic meter None
• depth _OPT
  • 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.
  • range: String
  • Example: None
• diether_lipids _OPT
  • Description: Concentration of diether lipids; can include multiple types of diether lipids
  • range: String
  • Example: 0.2 nanogram per liter None
• diss_carb_dioxide _OPT
  • Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample
  • range: QuantityValue
  • Example: 5 milligram per liter None
• diss_hydrogen _OPT
  • Description: Concentration of dissolved hydrogen
  • range: QuantityValue
  • Example: 0.3 micromole per liter None
• diss_inorg_carb _OPT
  • Description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
  • range: QuantityValue
  • Example: 2059 micromole per kilogram None
• diss_inorg_nitro _OPT
  • Description: Concentration of dissolved inorganic nitrogen
  • range: QuantityValue
  • Example: 761 micromole per liter None
• diss_inorg_phosp _OPT
  • Description: Concentration of dissolved inorganic phosphorus in the sample
  • range: QuantityValue
  • Example: 56.5 micromole per liter None
• diss_org_carb _OPT
  • Description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
  • range: QuantityValue
  • Example: 197 micromole per liter None
• diss_org_nitro _OPT
  • Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
  • range: QuantityValue
  • Example: 0.05 micromole per liter None
• diss_oxygen _OPT
  • Description: Concentration of dissolved oxygen
  • range: QuantityValue
  • Example: 175 micromole per kilogram None
• down_par _OPT
  • Description: Visible waveband radiance and irradiance measurements in the water column
  • range: QuantityValue
  • Example: 28.71 microEinstein per square meter per second None
• elev _OPT
  • 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
  • Example: 100 meter None
• env_broad_scale _OPT

  • Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]

    termLabel [termID]

    termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

  • range: String
  • Example: forest biome [ENVO:01000174] None
• env_local_scale _OPT

  • Description: In this field, report the entity or entities which are in your sample or specimen’s 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: String
  • Example: litter layer [ENVO:01000338] None
• env_medium _OPT

  • 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 ENVO’s 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: String
  • Example: soil [ENVO:00001998] None
• fluor _OPT
  • Description: Raw or converted fluorescence of water
  • range: QuantityValue
  • Example: 2.5 volts None
• geo_loc_name _OPT
  • 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: String
  • Example: Germany;North Rhine-Westphalia;Eifel National Park None
• glucosidase_act _OPT
  • Description: Measurement of glucosidase activity
  • range: QuantityValue
  • Example: 5 mol per liter per hour None
• lat_lon _OPT
  • 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
  • range: String
  • Example: 50.586825 6.408977 None
• light_intensity _OPT
  • Description: Measurement of light intensity
  • range: QuantityValue
  • Example: 0.3 lux None
• magnesium _OPT
  • Description: Concentration of magnesium in the sample
  • range: QuantityValue
  • Example: 52.8 micromole per kilogram None
• mean_frict_vel _OPT
  • Description: Measurement of mean friction velocity
  • range: QuantityValue
  • Example: 0.5 meter per second None
• mean_peak_frict_vel _OPT
  • Description: Measurement of mean peak friction velocity
  • range: QuantityValue
  • Example: 1 meter per second None
• misc_param _OPT
  • Description: Any other measurement performed or parameter collected, that is not listed here
  • range: String
  • Example: Bicarbonate ion concentration;2075 micromole per kilogram None
• n_alkanes _OPT
  • Description: Concentration of n-alkanes; can include multiple n-alkanes
  • range: String
  • Example: n-hexadecane;100 milligram per liter None
• nitrate _OPT
  • Description: Concentration of nitrate in the sample
  • range: QuantityValue
  • Example: 65 micromole per liter None
• nitrite _OPT
  • Description: Concentration of nitrite in the sample
  • range: QuantityValue
  • Example: 0.5 micromole per liter None
• nitro _OPT
  • Description: Concentration of nitrogen (total)
  • range: QuantityValue
  • Example: 4.2 micromole per liter None
• org_carb _OPT
  • Description: Concentration of organic carbon
  • range: QuantityValue
  • Example: 1.5 microgram per liter None
• org_matter _OPT
  • Description: Concentration of organic matter
  • range: QuantityValue
  • Example: 1.75 milligram per cubic meter None
• org_nitro _OPT
  • Description: Concentration of organic nitrogen
  • range: QuantityValue
  • Example: 4 micromole per liter None
• organism_count _OPT
  • 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:
  • Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
• oxy_stat_samp _OPT
  • Description: Oxygenation status of sample
  • range:
  • Example: aerobic None
• part_org_carb _OPT
  • Description: Concentration of particulate organic carbon
  • range: QuantityValue
  • Example: 1.92 micromole per liter None
• part_org_nitro _OPT
  • Description: Concentration of particulate organic nitrogen
  • range: QuantityValue
  • Example: 0.3 micromole per liter None
• perturbation _OPT
  • 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: String
  • Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None
• petroleum_hydrocarb _OPT
  • Description: Concentration of petroleum hydrocarbon
  • range: QuantityValue
  • Example: 0.05 micromole per liter None
• ph _OPT
  • Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
  • range: Double
  • Example: 7.2 None
• phaeopigments _OPT
  • Description: Concentration of phaeopigments; can include multiple phaeopigments
  • range: String
  • Example: 2.5 milligram per cubic meter None
• phosphate _OPT
  • Description: Concentration of phosphate
  • range: QuantityValue
  • Example: 0.7 micromole per liter None
• phosplipid_fatt_acid _OPT
  • Description: Concentration of phospholipid fatty acids; can include multiple values
  • range: String
  • Example: 2.98 milligram per liter None
• photon_flux _OPT
  • Description: Measurement of photon flux
  • range: QuantityValue
  • Example: 3.926 micromole photons per second per square meter None
• potassium _OPT
  • Description: Concentration of potassium in the sample
  • range: QuantityValue
  • Example: 463 milligram per liter None
• pressure _OPT
  • Description: Pressure to which the sample is subject to, in atmospheres
  • range: QuantityValue
  • Example: 50 atmosphere None
• primary_prod _OPT
  • Description: Measurement of primary production, generally measured as isotope uptake
  • range: QuantityValue
  • Example: 100 milligram per cubic meter per day None
• redox_potential _OPT
  • Description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
  • range: QuantityValue
  • Example: 300 millivolt None
• salinity _OPT
  • 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
  • Example: 25 practical salinity unit None
• samp_store_dur _OPT
  • Description: Duration for which the sample was stored
  • range: String
  • Example: P1Y6M None
• samp_store_loc _OPT
  • Description: Location at which sample was stored, usually name of a specific freezer/room
  • range: String
  • Example: Freezer no:5 None
• samp_store_temp _OPT
  • Description: Temperature at which sample was stored, e.g. -80 degree Celsius
  • range: QuantityValue
  • Example: -80 degree Celsius None
• samp_vol_we_dna_ext _OPT
  • Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction
  • range: QuantityValue
  • Example: 1500 milliliter None
• silicate _OPT
  • Description: Concentration of silicate
  • range: QuantityValue
  • Example: 0.05 micromole per liter None
• size_frac_low _OPT
  • 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
  • Example: 0.2 micrometer None
• size_frac_up _OPT
  • 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
  • Example: 20 micrometer None
• sodium _OPT
  • Description: Sodium concentration in the sample
  • range: QuantityValue
  • Example: 10.5 milligram per liter None
• soluble_react_phosp _OPT
  • Description: Concentration of soluble reactive phosphorus
  • range: QuantityValue
  • Example: 0.1 milligram per liter None
• sulfate _OPT
  • Description: Concentration of sulfate in the sample
  • range: QuantityValue
  • Example: 5 micromole per liter None
• sulfide _OPT
  • Description: Concentration of sulfide in the sample
  • range: QuantityValue
  • Example: 2 micromole per liter None
• suspend_part_matter _OPT
  • Description: Concentration of suspended particulate matter
  • range: QuantityValue
  • Example: 0.5 milligram per liter None
• temp _OPT
  • Description: Temperature of the sample at the time of sampling
  • range: QuantityValue
  • Example: 25 degree Celsius None
• tidal_stage _OPT
  • Description: Stage of tide
  • range:
  • Example: high tide None
• tot_depth_water_col _OPT
  • Description: Measurement of total depth of water column
  • range: QuantityValue
  • Example: 500 meter None
• tot_diss_nitro _OPT
  • Description: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
  • range: QuantityValue
  • Example: 40 microgram per liter None
• tot_inorg_nitro _OPT
  • Description: Total inorganic nitrogen content
  • range: QuantityValue
  • Example: 40 microgram per liter None
• tot_nitro _OPT
  • 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
  • range: QuantityValue
  • Example: 50 micromole per liter None
• tot_part_carb _OPT
  • Description: Total particulate carbon content
  • range: QuantityValue
  • Example: 35 micromole per liter None
• tot_phosp _OPT
  • Description: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
  • range: QuantityValue
  • Example: 0.03 milligram per liter None
• turbidity _OPT
  • Description: Measure of the amount of cloudiness or haziness in water caused by individual particles
  • range: QuantityValue
  • Example: 0.3 nephelometric turbidity units None
• water_current _OPT
  • Description: Measurement of magnitude and direction of flow within a fluid
  • range: QuantityValue
  • Example: 10 cubic meter per second None

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞adapters _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞assembly_software _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞chimera_check _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞env_package _OPT
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞experimental_factor _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞investigation_type _REQ
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_layout _OPT
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_reads_seqd _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_screen _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_size _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_vector _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞mid _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞nucl_acid_amp _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞nucl_acid_ext _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞pcr_cond _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞pcr_primers _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞project_name _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞rel_to_oxygen _OPT
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_mat_process _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_size _OPT
  • range: QuantityValue

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sample_collect_device _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sample_collect_method _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sample_name _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞seq_meth _REQ
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞seq_quality_check _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞size_frac _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sop _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞source_mat_id _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞submitted_to_insdc _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞target_gene _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞target_subfragment _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞url _OPT
  • range: String