MIMAG: metagenome-assembled genome, soil; version 6.0 Package

You can download package details in xml format or as an Excel spreadsheet.

Name

Environmental Package

Description

Use for metagenome-assembled genome sequences produced using computational binning tools that group sequences into individual organism genome assemblies starting from metagenomic data sets. Organism cannot contain the term 'metagenome'. Use the MIUVIG package for virus genomes. Before creating BioSamples for prokaryotic and eukaryotic MAGs, please read and follow the MAG submission instructions at https://www.ncbi.nlm.nih.gov/genbank/wgsfaq/#metagen.

Mandatory Attributes

isolate

• Harmonized nameisolate
• Descriptionidentification or description of the specific individual from which this sample was obtained

collection date

• Harmonized namecollection_date
• Descriptionthe 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 namedepth
• DescriptionDepth 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 nameelev
• DescriptionThe elevation of the sampling site as measured by the vertical distance from mean sea level.

broad-scale environmental context

• Harmonized nameenv_broad_scale
• DescriptionAdd 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 nameenv_local_scale
• DescriptionAdd 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 nameenv_medium
• DescriptionAdd 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 namegeo_loc_name
• DescriptionGeographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-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"

isolation source

• Harmonized nameisolation_source
• DescriptionDescribes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

latitude and longitude

• Harmonized namelat_lon
• DescriptionThe 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

Optional Attributes

agrochemical additions

• Harmonized nameagrochem_addition
• Descriptionaddition of fertilizers, pesticides, etc. - amount and time of applications

aluminium saturation

• Harmonized nameal_sat
• Descriptionaluminum saturation (esp. for tropical soils)

aluminium saturation method

• Harmonized nameal_sat_meth
• Descriptionreference or method used in determining Al saturation

altitude

• Harmonized namealtitude
• DescriptionThe 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 nameannual_precpt
• DescriptionThe 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 nameannual_temp
• DescriptionMean annual temperature

collection method

• Harmonized namecollection_method
• DescriptionProcess used to collect the sample, e.g., bronchoalveolar lavage (BAL)

crop rotation

• Harmonized namecrop_rotation
• Descriptionwhether or not crop is rotated, and if yes, rotation schedule

current land use

• Harmonized namecur_land_use
• Descriptionpresent state of sample site

current vegetation

• Harmonized namecur_vegetation
• Descriptionvegetation classification from one or more standard classification systems, or agricultural crop

current vegetation method

• Harmonized namecur_vegetation_meth
• Descriptionreference or method used in vegetation classification

derived from

• Harmonized namederived_from
• DescriptionIndicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s) (SAMNxxxxxxxx).

drainage classification

• Harmonized namedrainage_class
• Descriptiondrainage classification from a standard system such as the USDA system

experimental factor

• Harmonized nameexperimental_factor
• DescriptionVariable aspect of experimental design

extreme event

• Harmonized nameextreme_event
• Descriptionunusual physical events that may have affected microbial populations

FAO classification

• Harmonized namefao_class
• Descriptionsoil classification from the FAO World Reference Database for Soil Resources

fire

• Harmonized namefire
• Descriptionhistorical and/or physical evidence of fire

flooding

• Harmonized nameflooding
• Descriptionhistorical and/or physical evidence of flooding

heavy metals

• Harmonized nameheavy_metals
• Descriptionheavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations

heavy metals method

• Harmonized nameheavy_metals_meth
• Descriptionreference or method used in determining heavy metals

horizon method

• Harmonized namehorizon_meth
• Descriptionreference or method used in determining the horizon

links to additional analysis

• Harmonized namelink_addit_analys
• Description

link to classification information

• Harmonized namelink_class_info
• Descriptionlink to digitized soil maps or other soil classification information

link to climate information

• Harmonized namelink_climate_info
• Descriptionlink to climate resource

local classification

• Harmonized namelocal_class
• Descriptionsoil classification based on local soil classification system

local classification method

• Harmonized namelocal_class_meth
• Descriptionreference or method used in determining the local soil classification

metagenome source

• Harmonized namemetagenome_source
• Descriptiondescribes the original source of a metagenome assembled genome (MAG). Examples: soil metagenome, gut metagenome

microbial biomass

• Harmonized namemicrobial_biomass
• Descriptionthe 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 namemicrobial_biomass_meth
• Descriptionreference or method used in determining microbial biomass

miscellaneous parameter

• Harmonized namemisc_param
• Descriptionany other measurement performed or parameter collected, that is not listed here

negative control type

• Harmonized nameneg_cont_type
• DescriptionThe 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 nameomics_observ_id
• DescriptionA 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 nameph
• DescriptionpH measurement

pH method

• Harmonized nameph_meth
• Descriptionreference or method used in determining pH

pooling of DNA extracts

• Harmonized namepool_dna_extracts
• Descriptionwere multiple DNA extractions mixed? how many?

positive control type

• Harmonized namepos_cont_type
• DescriptionThe 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 nameprevious_land_use
• Descriptionprevious land use and dates

previous land use method

• Harmonized nameprevious_land_use_meth
• Descriptionreference or method used in determining previous land use and dates

profile position

• Harmonized nameprofile_position
• Descriptioncross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas

reference for biomaterial

• Harmonized nameref_biomaterial
• DescriptionPrimary publication or genome report

relationship to oxygen

• Harmonized namerel_to_oxygen
• DescriptionIs 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 namesalinity_meth
• Descriptionreference or method used in determining salinity

sample collection device or method

• Harmonized namesamp_collect_device
• DescriptionMethod or device employed for collecting sample

sample material processing

• Harmonized namesamp_mat_process
• DescriptionProcessing applied to the sample during or after isolation

sample size

• Harmonized namesamp_size
• DescriptionAmount or size of sample (volume, mass or area) that was collected

sample volume or weight for DNA extraction

• Harmonized namesamp_vol_we_dna_ext
• Descriptionvolume (mL) or weight (g) of sample processed for DNA extraction

mean seasonal precipitation

• Harmonized nameseason_precpt
• DescriptionThe 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 nameseason_temp
• DescriptionMean seasonal temperature

sieving

• Harmonized namesieving
• Descriptioncollection design of pooled samples and/or sieve size and amount of sample sieved

size fraction selected

• Harmonized namesize_frac
• DescriptionFiltering pore size used in sample preparation, e.g., 0-0.22 micrometer

slope aspect

• Harmonized nameslope_aspect
• Descriptionthe 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 nameslope_gradient
• Descriptioncommonly 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 namesoil_horizon
• Descriptionspecific 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 namesoil_text_measure
• Descriptionthe 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 namesoil_texture_meth
• Descriptionreference or method used in determining soil texture

soil type

• Harmonized namesoil_type
• Descriptionsoil series name or other lower-level classification

soil type method

• Harmonized namesoil_type_meth
• Descriptionreference or method used in determining soil series name or other lower-level classification

source material identifiers

• Harmonized namesource_material_id
• Descriptionunique 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 namestore_cond
• Descriptionexplain how and for how long the soil sample was stored before DNA extraction.

tillage

• Harmonized nametillage
• Descriptionnote method(s) used for tilling

total N method

• Harmonized nametot_n_meth
• Descriptionreference or method used in determining the total N

total nitrogen

• Harmonized nametot_nitro
• Descriptiontotal nitrogen content of the sample

total nitrogen content method

• Harmonized nametot_nitro_cont_meth
• DescriptionReference or method used in determining the total nitrogen

total organic carbon method

• Harmonized nametot_org_c_meth
• Descriptionreference or method used in determining total organic C

total organic carbon

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

water content

• Harmonized namewater_content
• Descriptionwater content measurement

water content of soil method

• Harmonized namewater_content_soil_meth
• Descriptionreference or method used in determining the water content of soil