Class: miscellaneous natural or artificial environment

miscellaneous natural or artificial environment

URI: mixs.vocab:MiscellaneousNaturalOrArtificialEnvironment

Children

• MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIGSEukaryote - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIGSOrg - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIGSPlant - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIGSVirus - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIMAG - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSurvey - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIMS - Combinatorial checklist Metagenome or Environmental with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMISAG - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package miscellaneous natural or artificial environment
• MiscellaneousNaturalOrArtificialEnvironmentMIUVIG - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package miscellaneous natural or artificial environment

Referenced by Class

Attributes

Own

• lat_lon _0..1
  • 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
• miscellaneous natural or artificial environment➞depth _0..1
  • 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: QuantityValue
  • Example: 10 meter None
• miscellaneous natural or artificial environment➞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 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
• miscellaneous natural or artificial environment➞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
  • Example: 100 meter None
• miscellaneous natural or artificial environment➞temp _0..1
  • Description: Temperature of the sample at the time of sampling.
  • Range: QuantityValue
  • Example: 25 degree Celsius None
• 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 (http://purl.bioontology.org/ontology/GAZ)
  • Range: String
  • Example: USA: Maryland, Bethesda None
• 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: Date
  • Example: 2018-05-11T10:00:00+01:00; 2018-05-11 None
• env_broad_scale _0..1
  • 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
  • Range: String
  • Example: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean None
• env_local_scale _0..1
  • 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.
  • Range: String
  • Example: 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]. None
• env_medium _0..1
  • 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).
  • Range: String
  • Example: 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] None
• miscellaneous natural or artificial environment➞alkalinity _0..1
  • 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
• miscellaneous natural or artificial environment➞ammonium _0..1
  • Description: Concentration of ammonium in the sample
  • Range: QuantityValue
  • Example: 1.5 milligram per liter None
• miscellaneous natural or artificial environment➞biomass _0..*
  • 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
• miscellaneous natural or artificial environment➞bromide _0..1
  • Description: Concentration of bromide
  • Range: QuantityValue
  • Example: 0.05 parts per million None
• miscellaneous natural or artificial environment➞calcium _0..1
  • Description: Concentration of calcium in the sample
  • Range: QuantityValue
  • Example: 0.2 micromole per liter None
• miscellaneous natural or artificial environment➞chem_administration _0..*
  • 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
• miscellaneous natural or artificial environment➞chloride _0..1
  • Description: Concentration of chloride in the sample
  • Range: QuantityValue
  • Example: 5000 milligram per liter None
• miscellaneous natural or artificial environment➞chlorophyll _0..1
  • Description: Concentration of chlorophyll
  • Range: QuantityValue
  • Example: 5 milligram per cubic meter None
• miscellaneous natural or artificial environment➞density _0..1
  • 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
• miscellaneous natural or artificial environment➞diether_lipids _0..*
  • Description: Concentration of diether lipids; can include multiple types of diether lipids
  • Range: String
  • Example: 0.2 nanogram per liter None
• miscellaneous natural or artificial environment➞diss_carb_dioxide _0..1
  • Description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample
  • Range: QuantityValue
  • Example: 5 milligram per liter None
• miscellaneous natural or artificial environment➞diss_hydrogen _0..1
  • Description: Concentration of dissolved hydrogen
  • Range: QuantityValue
  • Example: 0.3 micromole per liter None
• miscellaneous natural or artificial environment➞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
  • Example: 2059 micromole per kilogram None
• miscellaneous natural or artificial environment➞diss_org_nitro _0..1
  • Description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
  • Range: QuantityValue
  • Example: 0.05 micromole per liter None
• miscellaneous natural or artificial environment➞diss_oxygen _0..1
  • Description: Concentration of dissolved oxygen
  • Range: QuantityValue
  • Example: 175 micromole per kilogram None
• miscellaneous natural or artificial environment➞misc_param _0..*
  • Description: Any other measurement performed or parameter collected, that is not listed here
  • Range: String
  • Example: Bicarbonate ion concentration;2075 micromole per kilogram None
• miscellaneous natural or artificial environment➞nitrate _0..1
  • Description: Concentration of nitrate in the sample
  • Range: QuantityValue
  • Example: 65 micromole per liter None
• miscellaneous natural or artificial environment➞nitrite _0..1
  • Description: Concentration of nitrite in the sample
  • Range: QuantityValue
  • Example: 0.5 micromole per liter None
• miscellaneous natural or artificial environment➞nitro _0..1
  • Description: Concentration of nitrogen (total)
  • Range: QuantityValue
  • Example: 4.2 micromole per liter None
• miscellaneous natural or artificial environment➞org_carb _0..1
  • Description: Concentration of organic carbon
  • Range: QuantityValue
  • Example: 1.5 microgram per liter None
• miscellaneous natural or artificial environment➞org_matter _0..1
  • Description: Concentration of organic matter
  • Range: QuantityValue
  • Example: 1.75 milligram per cubic meter None
• miscellaneous natural or artificial environment➞org_nitro _0..1
  • Description: Concentration of organic nitrogen
  • Range: QuantityValue
  • Example: 4 micromole per liter None
• miscellaneous natural or artificial environment➞organism_count _0..*
  • 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: organism_count_enum
  • Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
• miscellaneous natural or artificial environment➞oxy_stat_samp _0..1
  • Description: Oxygenation status of sample
  • Range: oxy_stat_samp_enum
  • Example: aerobic None
• miscellaneous natural or artificial environment➞ph _0..1
  • Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
  • Range: Double
  • Example: 7.2 None
• miscellaneous natural or artificial environment➞perturbation _0..*
  • 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
• miscellaneous natural or artificial environment➞phosphate _0..1
  • Description: Concentration of phosphate
  • Range: QuantityValue
  • Example: 0.7 micromole per liter None
• miscellaneous natural or artificial environment➞phosplipid_fatt_acid _0..*
  • Description: Concentration of phospholipid fatty acids; can include multiple values
  • Range: String
  • Example: 2.98 milligram per liter None
• miscellaneous natural or artificial environment➞potassium _0..1
  • Description: Concentration of potassium in the sample
  • Range: QuantityValue
  • Example: 463 milligram per liter None
• miscellaneous natural or artificial environment➞pressure _0..1
  • Description: Pressure to which the sample is subject to, in atmospheres
  • Range: QuantityValue
  • Example: 50 atmosphere None
• miscellaneous natural or artificial environment➞salinity _0..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.
  • Range: QuantityValue
  • Example: 25 practical salinity unit None
• miscellaneous natural or artificial environment➞samp_store_dur _0..1
  • Description: Duration for which the sample was stored
  • Range: String
  • Example: P1Y6M None
• miscellaneous natural or artificial environment➞samp_store_loc _0..1
  • Description: Location at which sample was stored, usually name of a specific freezer/room
  • Range: String
  • Example: Freezer no:5 None
• miscellaneous natural or artificial environment➞samp_store_temp _0..1
  • Description: Temperature at which sample was stored, e.g. -80 degree Celsius
  • Range: QuantityValue
  • Example: -80 degree Celsius None
• miscellaneous natural or artificial environment➞silicate _0..1
  • Description: Concentration of silicate
  • Range: QuantityValue
  • Example: 0.05 micromole per liter None
• miscellaneous natural or artificial environment➞sodium _0..1
  • Description: Sodium concentration in the sample
  • Range: QuantityValue
  • Example: 10.5 milligram per liter None
• miscellaneous natural or artificial environment➞sulfate _0..1
  • Description: Concentration of sulfate in the sample
  • Range: QuantityValue
  • Example: 5 micromole per liter None
• miscellaneous natural or artificial environment➞sulfide _0..1
  • Description: Concentration of sulfide in the sample
  • Range: QuantityValue
  • Example: 2 micromole per liter None
• miscellaneous natural or artificial environment➞water_current _0..1
  • Description: Measurement of magnitude and direction of flow within a fluid
  • Range: QuantityValue
  • Example: 10 cubic meter per second None
• miscellaneous natural or artificial environment➞samp_name _1..1
  • 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.
  • Range: String
  • Example: ISDsoil1 None
• miscellaneous natural or artificial environment➞project_name _1..1
  • Description: Name of the project within which the sequencing was organized
  • Range: String
  • Example: Forest soil metagenome None
• miscellaneous natural or artificial environment➞samp_vol_we_dna_ext _0..1
  • Description: Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).
  • Range: QuantityValue
  • Example: 1500 milliliter None