Soil

Mandatory Attributes Optional Attributes

Mandatory Attributes

Collection date

• Harmonized name: collection_date

• Description: the date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format

Depth

• Harmonized name: depth

• Description: Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.

Elevation

• Harmonized name: elev

• Description: The elevation of the sampling site as measured by the vertical distance from mean sea level.

Broad-scale environmental context

• Harmonized name: env_broad_scale

• Description: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020]

Local-scale environmental context

• Harmonized name: env_local_scale

• Description: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]

Environmental medium

• Harmonized name: env_medium

• Description: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160]

Geographic location

• Harmonized name: geo_loc_name

• Description: Geographical origin of the sample; use the appropriate name from this list https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"

Latitude and longitude

• Harmonized name: lat_lon

• Description: The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W

NCBI Taxonomy ID

• Description: NCBI’s taxonomy identifier of the organism for this sample. The NCBI taxonomy ID can be found at https://www.ncbi.nlm.nih.gov/taxonomy/. Enter 32644 (which is a taxonomy ID for unidentified organisms) for the following or similar cases: (1) when NCBI taxonomy ID is not available because NCBI taxonomy does not yet cover the organism, (2) when metagenome or environmental sample was used, whose organismal composition is unknown in advance

• Example: 9606 (for Homo sapiens), 452680 (for Pseudomonas sp. UK4)

Organism

• Description: The most descriptive organism name for this sample (to the species, if possible). In the case of a new species, provide the desired organism name. In the case of unidentified species, choose the appropriate Genus and include ‘sp.’, e.g. “Escherichia sp.”. When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g. “Pseudomonas sp. UK4”

• Example: Homo sapiens, Pseudomonas sp. UK4

Sample name

• Description: A name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every sample name from a single submitter must be unique within a single BioProject

Optional Attributes

Agrochemical additions

• Harmonized name: agrochem_addition

• Description: addition of fertilizers, pesticides, etc. - amount and time of applications

Aluminium saturation

• Harmonized name: al_sat

• Description: aluminum saturation (esp. for tropical soils)

Aluminium saturation method

• Harmonized name: al_sat_meth

• Description: reference or method used in determining Al saturation

Altitude

• Harmonized name: altitude

• Description: The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

Mean annual precipitation

• Harmonized name: annual_precpt

• Description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps

Mean annual temperature

• Harmonized name: annual_temp

• Description: Mean annual temperature

Collection method

• Harmonized name: collection_method

• Description: Process used to collect the sample, e.g., bronchoalveolar lavage (BAL)

Crop rotation

• Harmonized name: crop_rotation

• Description: whether or not crop is rotated, and if yes, rotation schedule

Current land use

• Harmonized name: cur_land_use

• Description: present state of sample site

Current vegetation

• Harmonized name: cur_vegetation

• Description: vegetation classification from one or more standard classification systems, or agricultural crop

Current vegetation method

• Harmonized name: cur_vegetation_meth

• Description: reference or method used in vegetation classification

Derived from

• Description: Indicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s)

• Example: SAMN00000001, KAS24095074

Drainage classification

• Harmonized name: drainage_class

• Description: drainage classification from a standard system such as the USDA system

Extreme event

• Harmonized name: extreme_event

• Description: unusual physical events that may have affected microbial populations

FAO classification

• Harmonized name: fao_class

• Description: soil classification from the FAO World Reference Database for Soil Resources

Fire

• Harmonized name: fire

• Description: historical and/or physical evidence of fire

Flooding

• Harmonized name: flooding

• Description: historical and/or physical evidence of flooding

Heavy metals

• Harmonized name: heavy_metals

• Description: heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations

Heavy metals method

• Harmonized name: heavy_metals_meth

• Description: reference or method used in determining heavy metals

Horizon method

• Harmonized name: horizon_meth

• Description: reference or method used in determining the horizon

Isolation source

• Harmonized name: isolation_source

• Description: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Links to additional analysis

• Harmonized name: link_addit_analys

• Description:

Link to classification information

• Harmonized name: link_class_info

• Description: link to digitized soil maps or other soil classification information

Link to climate information

• Harmonized name: link_climate_info

• Description: link to climate resource

Local classification

• Harmonized name: local_class

• Description: soil classification based on local soil classification system

Local classification method

• Harmonized name: local_class_meth

• Description: reference or method used in determining the local soil classification

Microbial biomass

• Harmonized name: microbial_biomass

• Description: the part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 µm. IF you keep this, you would need to have correction factors used for conversion to the final units, which should be mg C (or N)/kg soil).

Microbial biomass method

• Harmonized name: microbial_biomass_meth

• Description: reference or method used in determining microbial biomass

Miscellaneous parameter

• Harmonized name: misc_param

• Description: any other measurement performed or parameter collected, that is not listed here

Negative control type

• Harmonized name: neg_cont_type

• Description: The substance or equipment used as a negative control in an investigation, e.g., distilled water, phosphate buffer, empty collection device, empty collection tube, DNA-free PCR mix, sterile swab, sterile syringe

Omics Observatory ID

• Harmonized name: omics_observ_id

• Description: A unique identifier of the omics-enabled observatory (or comparable time series) your data derives from. This identifier should be provided by the OMICON ontology; if you require a new identifier for your time series, contact the ontology's developers. Information is available here: https://github.com/GLOMICON/omicon. This field is only applicable to records which derive from an omics time-series or observatory.

pH

• Harmonized name: ph

• Description: pH measurement

PH method

• Harmonized name: ph_meth

• Description: reference or method used in determining pH

Pooling of DNA extracts

• Harmonized name: pool_dna_extracts

• Description: were multiple DNA extractions mixed? how many?

Positive control type

• Harmonized name: pos_cont_type

• Description: The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive

Previous land use

• Harmonized name: previous_land_use

• Description: previous land use and dates

Previous land use method

• Harmonized name: previous_land_use_meth

• Description: reference or method used in determining previous land use and dates

Profile position

• Harmonized name: profile_position

• Description: cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas

Reference for biomaterial

• Harmonized name: ref_biomaterial

• Description: Primary publication or genome report

Relationship to oxygen

• Harmonized name: rel_to_oxygen

• Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments, eg, aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe, missing, not applicable, not collected, not provided, restricted access

Salinity method

• Harmonized name: salinity_meth

• Description: reference or method used in determining salinity

Sample collection device or method

• Harmonized name: samp_collect_device

• Description: Method or device employed for collecting sample

Sample material processing

• Harmonized name: samp_mat_process

• Description: Processing applied to the sample during or after isolation

Sample size

• Harmonized name: samp_size

• Description: Amount or size of sample (volume, mass or area) that was collected

Sample volume or weight for DNA extraction

• Harmonized name: samp_vol_we_dna_ext

• Description: volume (mL) or weight (g) of sample processed for DNA extraction

Mean seasonal precipitation

• Harmonized name: season_precpt

• Description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps

Mean seasonal temperature

• Harmonized name: season_temp

• Description: Mean seasonal temperature

Sieving

• Harmonized name: sieving

• Description: collection design of pooled samples and/or sieve size and amount of sample sieved

Size fraction selected

• Harmonized name: size_frac

• Description: Filtering pore size used in sample preparation, e.g., 0-0.22 micrometer

Slope aspect

• Harmonized name: slope_aspect

• 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°. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.

Slope gradient

• Harmonized name: slope_gradient

• 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.

Soil horizon

• Harmonized name: soil_horizon

• 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

Soil texture measurement

• Harmonized name: soil_text_measure

• 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.

Soil texture method

• Harmonized name: soil_texture_meth

• Description: reference or method used in determining soil texture

Soil type

• Harmonized name: soil_type

• Description: soil series name or other lower-level classification

Soil type method

• Harmonized name: soil_type_meth

• Description: reference or method used in determining soil series name or other lower-level classification

Source material identifiers

• Harmonized name: source_material_id

• Description: unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples.

Storage conditions

• Harmonized name: store_cond

• Description: explain how and for how long the soil sample was stored before DNA extraction.

Tillage

• Harmonized name: tillage

• Description: note method(s) used for tilling

Total N method

• Harmonized name: tot_n_meth

• Description: reference or method used in determining the total N

Total nitrogen

• Harmonized name: tot_nitro

• Description: total nitrogen content of the sample

Total nitrogen content method

• Harmonized name: tot_nitro_cont_meth

• Description: Reference or method used in determining the total nitrogen

Total organic carbon method

• Harmonized name: tot_org_c_meth

• Description: reference or method used in determining total organic C

Total organic carbon

• Harmonized name: tot_org_carb

• Description: Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content

Water content

• Harmonized name: water_content

• Description: water content measurement

Water content of soil method

• Harmonized name: water_content_soil_meth

• Description: reference or method used in determining the water content of soil