Air

Mandatory Attributes Optional Attributes

Mandatory Attributes

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.

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

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

Air particulate matter concentration

• Harmonized name: air_pm_concen

• Description: Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM

Barometric pressure

• Harmonized name: barometric_press

• Description: Force per unit area exerted against a surface by the weight of air above that surface

Carbon dioxide

• Harmonized name: carb_dioxide

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

Carbon monoxide

• Harmonized name: carb_monoxide

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

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

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

Elevation

• Harmonized name: elev

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

Humidity

• Harmonized name: humidity

• Description: Amount of water vapour in the air, at the time of sampling

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.

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

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.

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

Oxygen

• Harmonized name: oxygen

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

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

Pollutants

• Harmonized name: pollutants

• Description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant

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

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

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 salinity

• Harmonized name: samp_salinity

• Description: The amount of salt dissolved within the collected sample

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

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

Size fraction selected

• Harmonized name: size_frac

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

Solar irradiance

• Harmonized name: solar_irradiance

• Description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval

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.

Temperature

• Harmonized name: temp

• Description: Temperature of the sample at time of sampling

Ventilation rate

• Harmonized name: ventilation_rate

• Description: Ventilation rate of the system in the sampled premises

Ventilation type

• Harmonized name: ventilation_type

• Description: Ventilation system used in the sampled premises

Volatile organic compounds

• Harmonized name: volatile_org_comp

• Description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound

Wind direction

• Harmonized name: wind_direction

• Description: Wind direction is the direction from which a wind originates

Wind speed

• Harmonized name: wind_speed

• Description: Speed of wind measured at the time of sampling