MIGS: cultured bacteria/archaea, air; version 6.0 Package

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

See SAMN02676578 for example record of this type of BioSample.

Name

Environmental Package

Description

Use for cultured bacterial or archaeal genomic sequences. Organism must have lineage Bacteria or Archaea.

Mandatory Attributes

strain

• Harmonized namestrain
• Descriptionmicrobial or eukaryotic strain name

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.

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

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 and growth condition

• Harmonized nameisol_growth_condt
• DescriptionPMID or url for isolation and growth condition specifications

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

number of replicons

• Harmonized namenum_replicons
• DescriptionNumber of replicons in nuclear genome

reference for biomaterial

• Harmonized nameref_biomaterial
• DescriptionPrimary publication or genome report

Optional Attributes

air particulate matter concentration

• Harmonized nameair_pm_concen
• Descriptionconcentration 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 namebarometric_press
• Descriptionforce per unit area exerted against a surface by the weight of air above that surface

observed biotic relationship

• Harmonized namebiotic_relationship
• DescriptionFree-living or from host (define relationship)

carbon dioxide

• Harmonized namecarb_dioxide
• Descriptioncarbon dioxide (gas) amount or concentration at the time of sampling

carbon monoxide

• Harmonized namecarb_monoxide
• Descriptioncarbon monoxide (gas) amount or concentration at the time of sampling

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

collection method

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

elevation

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

encoded traits

• Harmonized nameencoded_traits
• DescriptionTraits like antibiotic resistance/xenobiotic degration phenotypes/converting phage genes

estimated size

• Harmonized nameestimated_size
• DescriptionEstimated size of genome

extrachromosomal elements

• Harmonized nameextrachrom_elements
• DescriptionPlasmids that have significance phenotypic consequence

host

• Harmonized namehost
• DescriptionThe natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".

host disease

• Harmonized namehost_disease
• DescriptionName of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, http://bioportal.bioontology.org/ontologies/1009 or http://www.ncbi.nlm.nih.gov/mesh

host taxonomy ID

• Harmonized namehost_taxid
• DescriptionNCBI taxonomy ID of the host, e.g. 9606

humidity

• Harmonized namehumidity
• Descriptionamount of water vapour in the air, at the time of sampling

isolation source

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

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

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.

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

oxygen

• Harmonized nameoxygen
• Descriptionoxygen (gas) amount or concentration at the time of sampling

pathogenicity

• Harmonized namepathogenicity
• DescriptionTo what is the entity pathogenic

perturbation

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

pollutants

• Harmonized namepollutants
• Descriptionpollutant 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 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

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

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 salinity

• Harmonized namesamp_salinity
• Description

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

solar irradiance

• Harmonized namesolar_irradiance
• Descriptionthe amount of solar energy that arrives at a specific area of a surface during a specific time interval

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.

subspecific genetic lineage

• Harmonized namesubspecf_gen_lin
• DescriptionInformation about the genetic distinctness of the lineage (eg., biovar, serovar)

temperature

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

trophic level

• Harmonized nametrophic_level
• DescriptionFeeding position in food chain (eg., chemolithotroph)

ventilation rate

• Harmonized nameventilation_rate
• Descriptionventilation rate of the system in the sampled premises

ventilation type

• Harmonized nameventilation_type
• Descriptionventilation system used in the sampled premises

volatile organic compounds

• Harmonized namevolatile_org_comp
• Descriptionconcentration 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 namewind_direction
• Descriptionwind direction is the direction from which a wind originates

wind speed

• Harmonized namewind_speed
• Descriptionspeed of wind measured at the time of sampling