Class: soil

soil

URI: mixs.vocab:Soil

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Children

  • SoilMIGSBacteria - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil
  • SoilMIGSEukaryote - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package soil
  • SoilMIGSOrg - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package soil
  • SoilMIGSPlant - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package soil
  • SoilMIGSVirus - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package soil
  • SoilMIMAG - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil
  • SoilMIMARKSSpecimen - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package soil
  • SoilMIMARKSSurvey - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil
  • SoilMIMS - Combinatorial checklist Metagenome or Environmental with environmental package soil
  • SoilMISAG - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package soil
  • SoilMIUVIG - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package soil

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
  • soil➞depth 1..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
  • 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
  • soil➞elev 1..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
  • 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
  • soil➞cur_land_use 0..1
    • Description: Present state of sample site
    • Range: cur_land_use_enum
    • Example: conifers None
  • soil➞cur_vegetation 0..1
    • Description: Vegetation classification from one or more standard classification systems, or agricultural crop
    • Range: String
    • Example: None
  • soil➞cur_vegetation_meth 0..1
    • Description: Reference or method used in vegetation classification
    • Range: String
    • Example: None
  • soil➞previous_land_use 0..1
    • Description: Previous land use and dates
    • Range: String
    • Example: None
  • soil➞prev_land_use_meth 0..1
    • Description: Reference or method used in determining previous land use and dates
    • Range: String
    • Example: None
  • soil➞crop_rotation 0..1
    • Description: Whether or not crop is rotated, and if yes, rotation schedule
    • Range: String
    • Example: yes;R2/2017-01-01/2018-12-31/P6M None
  • soil➞agrochem_addition 0..*
    • Description: Addition of fertilizers, pesticides, etc. - amount and time of applications
    • Range: String
    • Example: roundup;5 milligram per liter;2018-06-21 None
  • soil➞tillage 0..*
    • Description: Note method(s) used for tilling
    • Range: tillage_enum
    • Example: chisel None
  • soil➞fire 0..1
    • Description: Historical and/or physical evidence of fire
    • Range: Date
    • Example: None
  • soil➞flooding 0..1
    • Description: Historical and/or physical evidence of flooding
    • Range: Date
    • Example: None
  • soil➞extreme_event 0..1
    • Description: Unusual physical events that may have affected microbial populations
    • Range: Date
    • Example: None
  • soil➞soil_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: soil_horizon_enum
    • Example: A horizon None
  • soil➞horizon_meth 0..1
    • Description: Reference or method used in determining the horizon
    • Range: String
    • Example: None
  • soil➞sieving 0..1
    • Description: Collection design of pooled samples and/or sieve size and amount of sample sieved
    • Range: String
    • Example: None
  • soil➞water_content 0..1
    • Description: Water content measurement
    • Range: QuantityValue
    • Example: None
  • soil➞water_cont_soil_meth 0..1
    • Description: Reference or method used in determining the water content of soil
    • Range: String
    • Example: None
  • soil➞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: String
    • Example: yes;5 None
  • soil➞store_cond 0..1
    • Description: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).
    • Range: String
    • Example: -20 degree Celsius freezer;P2Y10D None
  • soil➞link_climate_info 0..1
    • Description: Link to climate resource
    • Range: String
    • Example: None
  • soil➞annual_temp 0..1
    • Description: Mean annual temperature
    • Range: QuantityValue
    • Example: 12.5 degree Celsius None
  • soil➞season_temp 0..1
    • Description: Mean seasonal temperature
    • Range: QuantityValue
    • Example: 18 degree Celsius None
  • soil➞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
    • Example: None
  • soil➞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
    • Example: None
  • soil➞link_class_info 0..1
    • Description: Link to digitized soil maps or other soil classification information
    • Range: String
    • Example: None
  • soil➞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: fao_class_enum
    • Example: Luvisols None
  • soil➞local_class 0..1
    • Description: Soil classification based on local soil classification system
    • Range: String
    • Example: None
  • soil➞local_class_meth 0..1
    • Description: Reference or method used in determining the local soil classification
    • Range: String
    • Example: None
  • soil➞soil_type 0..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.
    • Range: String
    • Example: plinthosol [ENVO:00002250] None
  • soil➞soil_type_meth 0..1
    • Description: Reference or method used in determining soil series name or other lower-level classification
    • Range: String
    • Example: None
  • soil➞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
    • Example: None
  • soil➞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
    • Example: None
  • soil➞profile_position 0..1
    • Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
    • Range: profile_position_enum
    • Example: summit None
  • soil➞drainage_class 0..1
    • Description: Drainage classification from a standard system such as the USDA system
    • Range: drainage_class_enum
    • Example: well None
  • soil➞soil_text_measure 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
    • Example: None
  • soil➞soil_texture_meth 0..1
    • Description: Reference or method used in determining soil texture
    • Range: String
    • Example: None
  • soil➞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
  • soil➞ph_meth 0..1
    • Description: Reference or method used in determining ph
    • Range: String
    • Example: None
  • soil➞tot_org_carb 0..1
    • Description: Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
    • Range: QuantityValue
    • Example: None
  • soil➞tot_org_c_meth 0..1
    • Description: Reference or method used in determining total organic carbon
    • Range: String
    • Example: None
  • soil➞tot_nitro_content 0..1
    • Description: Total nitrogen content of the sample
    • Range: QuantityValue
    • Example: None
  • soil➞tot_nitro_cont_meth 0..1
    • Description: Reference or method used in determining the total nitrogen
    • Range: String
    • Example: None
  • soil➞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
    • Example: None
  • soil➞micro_biomass_meth 0..1
    • Description: Reference or method used in determining microbial biomass
    • Range: String
    • Example: None
  • soil➞link_addit_analys 0..1
    • Description: Link to additional analysis results performed on the sample
    • Range: String
    • Example: None
  • soil➞extreme_salinity 0..1
    • Description: Measured salinity
    • Range: QuantityValue
    • Example: None
  • soil➞salinity_meth 0..1
    • Description: Reference or method used in determining salinity
    • Range: String
    • Example: None
  • soil➞heavy_metals 0..*
    • Description: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.
    • Range: String
    • Example: mercury;0.09 micrograms per gram None
  • soil➞heavy_metals_meth 0..1
    • Description: Reference or method used in determining heavy metals
    • Range: String
    • Example: None
  • soil➞al_sat 0..1
    • Description: Aluminum saturation (esp. For tropical soils)
    • Range: QuantityValue
    • Example: None
  • soil➞al_sat_meth 0..1
    • Description: Reference or method used in determining Al saturation
    • Range: String
    • Example: None
  • soil➞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
  • soil➞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
  • soil➞project_name 1..1
    • Description: Name of the project within which the sequencing was organized
    • Range: String
    • Example: Forest soil metagenome None
  • soil➞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