Class: SedimentMIGSBacteria

Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment

URI: mixs.vocab:SedimentMIGSBacteria

Parents

• is_a: Sediment - sediment

Uses Mixins

• mixin: MIGSBacteria - Minimal Information about a Genome Sequence: cultured bacteria/archaea

Attributes

Inherited from sediment:

• 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
• 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
• 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
• 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_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
• 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
• 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
• 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
• methane _OPT
  • Description: Methane (gas) amount or concentration at the time of sampling
  • range: QuantityValue
  • Example: 1800 parts per billion 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
• particle_class _OPT
  • 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
  • range: String
  • Example: 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
• porosity _OPT
  • Description: Porosity of deposited sediment is volume of voids divided by the total volume of sample
  • range: String
  • Example: 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
• 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
• sediment_type _OPT
  • Description: Information about the sediment type based on major constituents
  • range:
  • Example: biogenous None
• silicate _OPT
  • Description: Concentration of silicate
  • range: QuantityValue
  • Example: 0.05 micromole per liter None
• sodium _OPT
  • Description: Sodium concentration in the sample
  • range: QuantityValue
  • Example: 10.5 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
• 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_carb _OPT
  • Description: Total carbon content
  • range: QuantityValue
  • Example: None
• tot_depth_water_col _OPT
  • Description: Measurement of total depth of water column
  • range: QuantityValue
  • Example: 500 meter None
• tot_nitro_content _OPT
  • Description: Total nitrogen content of the sample
  • range: QuantityValue
  • Example: None
• tot_org_carb _OPT
  • Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
  • range: QuantityValue
  • Example: 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_content _OPT
  • Description: Water content measurement
  • range: QuantityValue
  • Example: None

Mixed in from MIGS bacteria:

• MIGS bacteria➞adapters _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞annot _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_name _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_qual _REQ
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_software _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞biotic_relationship _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞compl_score _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞compl_software _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞encoded_traits _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞env_package _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞estimated_size _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞experimental_factor _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞extrachrom_elements _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞feat_pred _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞health_disease_stat _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞host_spec_range _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞investigation_type _REQ
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞isol_growth_condt _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_layout _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_reads_seqd _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_screen _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_size _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_vector _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞nucl_acid_amp _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞nucl_acid_ext _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞num_replicons _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞number_contig _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞pathogenicity _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞project_name _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞ref_biomaterial _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞ref_db _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞rel_to_oxygen _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_mat_process _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_size _OPT
  • range: QuantityValue

Mixed in from MIGS bacteria:

• MIGS bacteria➞sample_collect_device _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sample_collect_method _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sample_name _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞seq_meth _REQ
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞sim_search_meth _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sop _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞source_mat_id _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞specific_host _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞submitted_to_insdc _REQ
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞subspecf_gen_lin _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞tax_class _OPT
  • range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞tax_ident _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞trophic_level _OPT
  • range:

Mixed in from MIGS bacteria:

• MIGS bacteria➞url _OPT
  • range: String