MIMARKS: survey, sediment; version 6.0 Package

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

See SAMN02866459 for example record of this type of BioSample.

Name

Environmental Package

Description

Use for any type of marker gene sequences, eg, 16S, 18S, 23S, 28S rRNA or COI obtained directly from the environment, without culturing or identification of the organisms. Organism must be a metagenome, where lineage starts with unclassified sequences and scientific name ends with 'metagenome'.

Mandatory Attributes

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"

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

alkalinity

• Harmonized namealkalinity
• Descriptionalkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate

alkyl diethers

• Harmonized namealkyl_diethers
• Descriptionconcentration of alkyl diethers

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.

aminopeptidase activity

• Harmonized nameaminopept_act
• Descriptionmeasurement of aminopeptidase activity

ammonium

• Harmonized nameammonium
• Descriptionconcentration of ammonium

bacterial carbon production

• Harmonized namebacteria_carb_prod
• Descriptionmeasurement of bacterial carbon production

biomass

• Harmonized namebiomass
• Descriptionamount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements

bishomohopanol

• Harmonized namebishomohopanol
• Descriptionconcentration of bishomohopanol

bromide

• Harmonized namebromide
• Descriptionconcentration of bromide

calcium

• Harmonized namecalcium
• Descriptionconcentration of calcium

carbon/nitrogen ratio

• Harmonized namecarb_nitro_ratio
• Descriptionratio of amount or concentrations of carbon to nitrogen

chemical administration

• Harmonized namechem_administration
• Descriptionlist 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) (v1.72), please see http://bioportal.bioontology.org/visualize/44603

chloride

• Harmonized namechloride
• Descriptionconcentration of chloride

chlorophyll

• Harmonized namechlorophyll
• Descriptionconcentration of chlorophyll

collection method

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

density

• Harmonized namedensity
• Descriptiondensity of sample

diether lipids

• Harmonized namediether_lipids
• Descriptionconcentration of diether lipids; can include multiple types of diether lipids

dissolved carbon dioxide

• Harmonized namediss_carb_dioxide
• Descriptionconcentration of dissolved carbon dioxide

dissolved hydrogen

• Harmonized namediss_hydrogen
• Descriptionconcentration of dissolved hydrogen

dissolved inorganic carbon

• Harmonized namediss_inorg_carb
• Descriptiondissolved inorganic carbon concentration

dissolved organic carbon

• Harmonized namediss_org_carb
• Descriptionconcentration of dissolved organic carbon

dissolved organic nitrogen

• Harmonized namediss_org_nitro
• Descriptiondissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2

dissolved oxygen

• Harmonized namediss_oxygen
• Descriptionconcentration of dissolved oxygen

glucosidase activity

• Harmonized nameglucosidase_act
• Descriptionmeasurement of glucosidase activity

isolation source

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

magnesium

• Harmonized namemagnesium
• Descriptionconcentration of magnesium

mean friction velocity

• Harmonized namemean_frict_vel
• Descriptionmeasurement of mean friction velocity

mean peak friction velocity

• Harmonized namemean_peak_frict_vel
• Descriptionmeasurement of mean peak friction velocity

methane

• Harmonized namemethane
• Descriptionmethane (gas) amount or concentration at the time of sampling

miscellaneous parameter

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

n alkanes

• Harmonized namen_alkanes
• Descriptionconcentration of n-alkanes; can include multiple n-alkanes

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

nitrate

• Harmonized namenitrate
• Descriptionconcentration of nitrate

nitrite

• Harmonized namenitrite
• Descriptionconcentration of nitrite

nitrogen

• Harmonized namenitro
• Descriptionconcentration of nitrogen (total)

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.

organic carbon

• Harmonized nameorg_carb
• Descriptionconcentration of organic carbon

organic matter

• Harmonized nameorg_matter
• Descriptionconcentration of organic matter

organic nitrogen

• Harmonized nameorg_nitro
• Descriptionconcentration of organic nitrogen

organism count

• Harmonized nameorganism_count
• Descriptiontotal count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts

oxygenation status of sample

• Harmonized nameoxy_stat_samp
• Descriptionoxygenation status of sample

particulate organic carbon

• Harmonized namepart_org_carb
• Descriptionconcentration of particulate organic carbon

particle classification

• Harmonized nameparticle_class
• Descriptionparticles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values

perturbation

• Harmonized nameperturbation
• Descriptiontype of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

petroleum hydrocarbon

• Harmonized namepetroleum_hydrocarb
• Descriptionconcentration of petroleum hydrocarbon

pH

• Harmonized nameph
• DescriptionpH measurement

phaeopigments

• Harmonized namephaeopigments
• Descriptionconcentration of phaeopigments; can include multiple phaeopigments

phosphate

• Harmonized namephosphate
• Descriptionconcentration of phosphate

phospholipid fatty acid

• Harmonized namephosplipid_fatt_acid
• Descriptionconcentration of phospholipid fatty acids; can include multiple values

porosity

• Harmonized nameporosity
• Descriptionporosity of deposited sediment is volume of voids divided by the total volume of sample

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

potassium

• Harmonized namepotassium
• Descriptionconcentration of potassium

pressure

• Harmonized namepressure
• Descriptionpressure to which the sample is subject, in atmospheres

redox potential

• Harmonized nameredox_potential
• Descriptionredox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential

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

• Harmonized namesalinity
• Descriptionsalinity measurement

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 storage duration

• Harmonized namesamp_store_dur
• Description

sample storage location

• Harmonized namesamp_store_loc
• Description

sample storage temperature

• Harmonized namesamp_store_temp
• Description

sample volume or weight for DNA extraction

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

sediment type

• Harmonized namesediment_type
• Descriptioninformation about the sediment type based on major constituents

silicate

• Harmonized namesilicate
• Descriptionconcentration of silicate

size fraction selected

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

sodium

• Harmonized namesodium
• Descriptionsodium concentration

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.

sulfate

• Harmonized namesulfate
• Descriptionconcentration of sulfate

sulfide

• Harmonized namesulfide
• Descriptionconcentration of sulfide

temperature

• Harmonized nametemp
• Descriptiontemperature of the sample at time of sampling

tidal stage

• Harmonized nametidal_stage
• Descriptionstage of tide

total carbon

• Harmonized nametot_carb
• Descriptiontotal carbon content

total depth of water column

• Harmonized nametot_depth_water_col
• Descriptionmeasurement of total depth of water column

total nitrogen

• Harmonized nametot_nitro
• Descriptiontotal nitrogen content of the sample

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

turbidity

• Harmonized nameturbidity
• Descriptionturbidity measurement

water content

• Harmonized namewater_content
• Descriptionwater content measurement