Microbial

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

Alkalinity

• Harmonized name: alkalinity

• Description: alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate

Alkyl diethers

• Harmonized name: alkyl_diethers

• Description: concentration of alkyl diethers

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.

Aminopeptidase activity

• Harmonized name: aminopept_act

• Description: measurement of aminopeptidase activity

Ammonium

• Harmonized name: ammonium

• Description: concentration of ammonium

Bacterial carbon production

• Harmonized name: bacteria_carb_prod

• Description: measurement of bacterial carbon production

Biomass

• Harmonized name: biomass

• Description: amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements

Bishomohopanol

• Harmonized name: bishomohopanol

• Description: concentration of bishomohopanol

Bromide

• Harmonized name: bromide

• Description: concentration of bromide

Calcium

• Harmonized name: calcium

• Description: concentration of calcium

Carbon/nitrogen ratio

• Harmonized name: carb_nitro_ratio

• Description: ratio of amount or concentrations of carbon to nitrogen

Chemical administration

• Harmonized name: chem_administration

• Description: list 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 name: chloride

• Description: concentration of chloride

Chlorophyll

• Harmonized name: chlorophyll

• Description: concentration of chlorophyll

Collection method

• Harmonized name: collection_method

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

Derived from

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

• Example: SAMN00000001, KAS24095074

Diether lipids

• Harmonized name: diether_lipids

• Description: concentration of diether lipids; can include multiple types of diether lipids

Dissolved carbon dioxide

• Harmonized name: diss_carb_dioxide

• Description: concentration of dissolved carbon dioxide

Dissolved hydrogen

• Harmonized name: diss_hydrogen

• Description: concentration of dissolved hydrogen

Dissolved inorganic carbon

• Harmonized name: diss_inorg_carb

• Description: dissolved inorganic carbon concentration

Dissolved organic carbon

• Harmonized name: diss_org_carb

• Description: concentration of dissolved organic carbon

Dissolved organic nitrogen

• Harmonized name: diss_org_nitro

• Description: dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2

Dissolved oxygen

• Harmonized name: diss_oxygen

• Description: concentration of dissolved oxygen

Glucosidase activity

• Harmonized name: glucosidase_act

• Description: measurement of glucosidase activity

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.

Magnesium

• Harmonized name: magnesium

• Description: concentration of magnesium

Mean friction velocity

• Harmonized name: mean_frict_vel

• Description: measurement of mean friction velocity

Mean peak friction velocity

• Harmonized name: mean_peak_frict_vel

• Description: measurement of mean peak friction velocity

Methane

• Harmonized name: methane

• Description: methane (gas) amount or concentration at the time of sampling

Miscellaneous parameter

• Harmonized name: misc_param

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

N-alkanes

• Harmonized name: n_alkanes

• Description: concentration of n-alkanes; can include multiple n-alkanes

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

Nitrate

• Harmonized name: nitrate

• Description: concentration of nitrate

Nitrite

• Harmonized name: nitrite

• Description: concentration of nitrite

Nitrogen

• Harmonized name: nitro

• Description: concentration of nitrogen (total)

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.

Organic carbon

• Harmonized name: org_carb

• Description: concentration of organic carbon

Organic matter

• Harmonized name: org_matter

• Description: concentration of organic matter

Organic nitrogen

• Harmonized name: org_nitro

• Description: concentration of organic nitrogen

Organism count

• Harmonized name: organism_count

• Description: total 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 name: oxy_stat_samp

• Description: oxygenation status of sample

Particulate organic carbon

• Harmonized name: part_org_carb

• Description: concentration of particulate organic carbon

Perturbation

• Harmonized name: perturbation

• Description: type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

Petroleum hydrocarbon

• Harmonized name: petroleum_hydrocarb

• Description: concentration of petroleum hydrocarbon

pH

• Harmonized name: ph

• Description: pH measurement

Phaeopigments

• Harmonized name: phaeopigments

• Description: concentration of phaeopigments; can include multiple phaeopigments

Phosphate

• Harmonized name: phosphate

• Description: concentration of phosphate

Phospholipid fatty acid

• Harmonized name: phosplipid_fatt_acid

• Description: concentration of phospholipid fatty acids; can include multiple values

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

Potassium

• Harmonized name: potassium

• Description: concentration of potassium

Pressure

• Harmonized name: pressure

• Description: pressure to which the sample is subject, in atmospheres

Redox potential

• Harmonized name: redox_potential

• Description: redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential

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

• Harmonized name: salinity

• Description: salinity measurement

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 storage duration

• Harmonized name: samp_store_dur

• Description:

Sample storage location

• Harmonized name: samp_store_loc

Sample storage temperature

• Harmonized name: samp_store_temp

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

Silicate

• Harmonized name: silicate

• Description: concentration of silicate

Size fraction selected

• Harmonized name: size_frac

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

Sodium

• Harmonized name: sodium

• Description: sodium concentration

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.

Sulfate

• Harmonized name: sulfate

• Description: concentration of sulfate

Sulfide

• Harmonized name: sulfide

• Description: concentration of sulfide

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Total carbon

• Harmonized name: tot_carb

• Description: total carbon content

Total nitrogen

• Harmonized name: tot_nitro

• Description: total nitrogen content of the sample

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

Turbidity

• Harmonized name: turbidity

• Description: turbidity measurement

Water content

• Harmonized name: water_content

• Description: water content measurement