Class: SoilMIMARKSSurvey

Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package soil

URI: mixs.vocab:SoilMIMARKSSurvey

Parents

• is_a: Soil - soil

Uses Mixins

• mixin: MIMARKSSurvey - Minimal Information about a Marker Specimen: survey

Attributes

Inherited from soil:

• agrochem_addition _OPT
  • Description: Addition of fertilizers, pesticides, etc. - amount and time of applications
  • range: String
  • Example: roundup;5 milligram per liter;2018-06-21 None
• al_sat _OPT
  • Description: Aluminum saturation (esp. For tropical soils)
  • range: QuantityValue
  • Example: None
• al_sat_meth _OPT
  • Description: Reference or method used in determining Al saturation
  • range: String
  • Example: 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
• annual_precpt _OPT
  • 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
• annual_temp _OPT
  • Description: Mean annual temperature
  • range: QuantityValue
  • Example: 12.5 degree Celsius 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
• crop_rotation _OPT
  • 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
• cur_land_use _OPT
  • Description: Present state of sample site
  • range:
  • Example: conifers None
• cur_vegetation _OPT
  • Description: Vegetation classification from one or more standard classification systems, or agricultural crop
  • range: String
  • Example: None
• cur_vegetation_meth _OPT
  • Description: Reference or method used in vegetation classification
  • range: String
  • Example: 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
• drainage_class _OPT
  • Description: Drainage classification from a standard system such as the USDA system
  • range:
  • Example: well 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
• extreme_event _OPT
  • Description: Unusual physical events that may have affected microbial populations
  • range: Date
  • Example: None
• extreme_salinity _OPT
  • Description: Measured salinity
  • range: QuantityValue
  • Example: None
• fao_class _OPT
  • 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:
  • Example: Luvisols None
• fire _OPT
  • Description: Historical and/or physical evidence of fire
  • range: Date
  • Example: None
• flooding _OPT
  • Description: Historical and/or physical evidence of flooding
  • range: Date
  • Example: 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
• heavy_metals _OPT
  • Description: Heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations
  • range: String
  • Example: None
• heavy_metals_meth _OPT
  • Description: Reference or method used in determining heavy metals
  • range: String
  • Example: None
• horizon _OPT
  • 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:
  • Example: A horizon None
• horizon_meth _OPT
  • Description: Reference or method used in determining the horizon
  • range: String
  • Example: 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
• link_addit_analys _OPT
  • Description: Link to additional analysis results performed on the sample
  • range: String
  • Example: None
• link_class_info _OPT
  • Description: Link to digitized soil maps or other soil classification information
  • range: String
  • Example: None
• link_climate_info _OPT
  • Description: Link to climate resource
  • range: String
  • Example: None
• local_class _OPT
  • Description: Soil classification based on local soil classification system
  • range: String
  • Example: None
• local_class_meth _OPT
  • Description: Reference or method used in determining the local soil classification
  • range: String
  • Example: None
• microbial_biomass _OPT
  • 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
• microbial_biomass_meth _OPT
  • Description: Reference or method used in determining microbial biomass
  • range: String
  • Example: 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
• 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
• ph_meth _OPT
  • Description: Reference or method used in determining ph
  • range: String
  • Example: None
• pool_dna_extracts _OPT
  • 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
• previous_land_use _OPT
  • Description: Previous land use and dates
  • range: String
  • Example: None
• previous_land_use_meth _OPT
  • Description: Reference or method used in determining previous land use and dates
  • range: String
  • Example: None
• profile_position _OPT
  • Description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
  • range:
  • Example: summit None
• salinity_meth _OPT
  • Description: Reference or method used in determining salinity
  • range: String
  • Example: 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
• season_precpt _OPT
  • 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
• season_temp _OPT
  • Description: Mean seasonal temperature
  • range: QuantityValue
  • Example: 18 degree Celsius None
• sieving _OPT
  • Description: Collection design of pooled samples and/or sieve size and amount of sample sieved
  • range: String
  • Example: None
• slope_aspect _OPT
  • 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
• slope_gradient _OPT
  • 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_type _OPT
  • Description: Soil series name or other lower-level classification
  • range: String
  • Example: None
• soil_type_meth _OPT
  • Description: Reference or method used in determining soil series name or other lower-level classification
  • range: String
  • Example: None
• store_cond _OPT
  • Description: Explain how and for how long the soil sample was stored before DNA extraction
  • range: String
  • Example: -20 degree Celsius freezer;P2Y10D None
• texture _OPT
  • 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
• texture_meth _OPT
  • Description: Reference or method used in determining soil texture
  • range: String
  • Example: None
• tillage _OPT
  • Description: Note method(s) used for tilling
  • range:
  • Example: chisel None
• tot_nitro_content _OPT
  • Description: Total nitrogen content of the sample
  • range: QuantityValue
  • Example: None
• tot_nitro_content_meth _OPT
  • Description: Reference or method used in determining the total nitrogen
  • range: String
  • Example: None
• tot_org_c_meth _OPT
  • Description: Reference or method used in determining total organic carbon
  • range: String
  • 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
• water_content _OPT
  • Description: Water content measurement
  • range: QuantityValue
  • Example: None
• water_content_soil_meth _OPT
  • Description: Reference or method used in determining the water content of soil
  • range: String
  • Example: None

Mixed in from MIMARKS survey:

• MIMARKS survey➞biotic_relationship _OPT
  • range:

Mixed in from MIMARKS survey:

• MIMARKS survey➞chimera_check _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞env_package _OPT
  • range:

Mixed in from MIMARKS survey:

• MIMARKS survey➞experimental_factor _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞extrachrom_elements _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞investigation_type _REQ
  • range:

Mixed in from MIMARKS survey:

• MIMARKS survey➞isol_growth_condt _REQ
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞nucl_acid_amp _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞nucl_acid_ext _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞pcr_cond _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞pcr_primers _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞project_name _REQ
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞rel_to_oxygen _OPT
  • range:

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_mat_process _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_size _OPT
  • range: QuantityValue

Mixed in from MIMARKS survey:

• MIMARKS survey➞sample_collect_device _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞sample_collect_method _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞sample_name _REQ
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞seq_meth _REQ
  • range:

Mixed in from MIMARKS survey:

• MIMARKS survey➞seq_quality_check _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞sop _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞source_mat_id _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞submitted_to_insdc _REQ
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞subspecf_gen_lin _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞target_gene _REQ
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞target_subfragment _OPT
  • range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞trophic_level _OPT
  • range:

Mixed in from MIMARKS survey:

• MIMARKS survey➞url _OPT
  • range: String