MIGS: cultured bacteria/archaea, plant-associated; version 6.0 Package

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

See SAMN02866194 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

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"

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".

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 temperature regimen

• Harmonized nameair_temp_regm
• Descriptioninformation about treatment involving an exposure to varying temperatures; should include the temperature, treatment duration, interval and total experimental duration; can include different temperature regimens

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.

ancestral data

• Harmonized nameances_data
• DescriptionInformation about either pedigree or other ancestral information description, e.g., parental variety in case of mutant or selection, A/3*B (meaning [(A x B) x B] x B)

antibiotic regimen

• Harmonized nameantibiotic_regm
• Descriptioninformation about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment duration, interval and total experimental duration; can include multiple antibiotic regimens

biological status

• Harmonized namebiol_stat
• DescriptionThe level of genome modification, e.g., wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant

biotic regimen

• Harmonized namebiotic_regm
• DescriptionInformation about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi

observed biotic relationship

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

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

chemical mutagen

• Harmonized namechem_mutagen
• Descriptiontreatment involving use of mutagens; should include the name of mutagen, amount administered, treatment duration, interval and total experimental duration; can include multiple mutagen regimens

climate environment

• Harmonized nameclimate_environment
• Descriptiontreatment involving an exposure to a particular climate; can include multiple climates

collection method

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

culture rooting medium

• Harmonized namecult_root_med
• DescriptionName or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g., Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors

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.

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

fertilizer regimen

• Harmonized namefertilizer_regm
• Descriptioninformation about treatment involving the use of fertilizers; should include the name fertilizer, amount administered, treatment duration, interval and total experimental duration; can include multiple fertilizer regimens

fungicide regimen

• Harmonized namefungicide_regm
• Descriptioninformation about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment duration, interval and total experimental duration; can include multiple fungicide regimens

gaseous environment

• Harmonized namegaseous_environment
• Descriptionuse of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens

genetic modification

• Harmonized namegenetic_mod
• DescriptionGenetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection

gravity

• Harmonized namegravity
• Descriptioninformation about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; can include multiple treatments

growth facility

• Harmonized namegrowth_facil
• DescriptionType of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research

growth habit

• Harmonized namegrowth_habit
• DescriptionCharacteristic shape, appearance or growth form of a plant species, e.g., erect, semi-erect, spreading, prostrate

growth hormone regimen

• Harmonized namegrowth_hormone_regm
• Descriptioninformation about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment duration, interval and total experimental duration; can include multiple growth hormone regimens

herbicide regimen

• Harmonized nameherbicide_regm
• Descriptioninformation about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment duration, interval and total experimental duration; can include multiple regimens

host age

• Harmonized namehost_age
• DescriptionAge of host at the time of sampling

host common name

• Harmonized namehost_common_name
• DescriptionThe natural language (non-taxonomic) name of the host organism, e.g., mouse

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 dry mass

• Harmonized namehost_dry_mass
• Descriptionmeasurement of dry mass

host genotype

• Harmonized namehost_genotype
• Description

host height

• Harmonized namehost_height
• Descriptionthe height of subject

host length

• Harmonized namehost_length
• Descriptionthe length of subject

host life stage

• Harmonized namehost_life_stage
• Descriptiondescription of host life stage

host phenotype

• Harmonized namehost_phenotype
• Description

host subspecific genetic lineage

• Harmonized namehost_subspecf_genlin
• DescriptionInformation about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123

observed host symbionts

• Harmonized namehost_symbiont
• DescriptionThe taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host

host taxonomy ID

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

host total mass

• Harmonized namehost_tot_mass
• Descriptiontotal mass of the host at collection, the unit depends on host

host wet mass

• Harmonized namehost_wet_mass
• Descriptionmeasurement of wet mass

humidity regimen

• Harmonized namehumidity_regm
• Descriptioninformation about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment duration, interval and total experimental duration; can include multiple regimens

isolation source

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

light regimen

• Harmonized namelight_regm
• DescriptionInformation about treatment(s) involving exposure to light, including both light intensity and quality

mechanical damage

• Harmonized namemechanical_damage
• Descriptioninformation about any mechanical damage exerted on the plant; can include multiple damages and sites

mineral nutrient regimen

• Harmonized namemineral_nutr_regm
• Descriptioninformation about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple mineral nutrient regimens

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

non mineral nutrient regimen

• Harmonized namenon_mineral_nutr_regm
• Descriptioninformation about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment duration, interval and total experimental duration; can include multiple non-mineral nutrient regimens

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

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

pesticide regimen

• Harmonized namepesticide_regm
• Descriptioninformation about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment duration, interval and total experimental duration; can include multiple pesticide regimens

pH regimen

• Harmonized nameph_regm
• Descriptioninformation about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen

plant growth medium

• Harmonized nameplant_growth_med
• DescriptionType of the media used for growing sampled plants, e.g., soil [ENVO:00001998]

plant product

• Harmonized nameplant_product
• Descriptionsubstance produced by the plant, where the sample was obtained from

plant sex

• Harmonized nameplant_sex
• DescriptionSex of the reproductive parts on the whole plant, e.g., androdioecious, androecious, androgynous, androgynomonoecious, andromonoecious, bisexual, dichogamous, diclinous, dioecious, gynodioecious, gynoecious, gynomonoecious, hermaphroditic, imperfect, monoclinous, monoecious, perfect, polygamodioecious, polygamomonoecious, polygamous, protandrous, protogynous, subandroecious, subdioecious, subgynoecious, synoecious, trimonoecious, trioecious, unisexual

plant structure

• Harmonized nameplant_struc
• DescriptionName of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g., petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here

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

radiation regimen

• Harmonized nameradiation_regm
• Descriptioninformation about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment duration, interval and total experimental duration; can include multiple radiation regimens

rainfall regimen

• Harmonized namerainfall_regm
• Descriptioninformation about treatment involving an exposure to a given amount of rainfall; can include multiple regimens

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

rooting conditions

• Harmonized nameroot_cond
• DescriptionRelevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container

rooting medium carbon

• Harmonized nameroot_med_carbon
• DescriptionSource of organic carbon in the culture rooting medium, e.g., sucrose

rooting medium macronutrients

• Harmonized nameroot_med_macronutr
• DescriptionMeasurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S), e.g., KH2PO4 (170mg/L)

rooting medium micronutrients

• Harmonized nameroot_med_micronutr
• DescriptionMeasurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo), e.g., H3BO3 (6.2mg/L)

rooting medium pH

• Harmonized nameroot_med_ph
• DescriptionpH measurement of the culture rooting medium, e.g., 5.5

rooting medium regulators

• Harmonized nameroot_med_regl
• DescriptionGrowth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid, e.g., 0.5 mg/L NAA

rooting medium solidifier

• Harmonized nameroot_med_solid
• DescriptionSpecification of the solidifying agent in the culture rooting medium, e.g., agar

rooting medium organic supplements

• Harmonized nameroot_med_suppl
• DescriptionOrganic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal, e.g., nicotinic acid (0.5 mg/L)

salt regimen

• Harmonized namesalt_regm
• Descriptioninformation about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment duration, interval and total experimental duration; can include multiple salt regimens

sample capture status

• Harmonized namesamp_capt_status
• DescriptionReason for the sample, e.g., active surveillance in response to an outbreak, active surveillance not initiated by an outbreak, farm sample, market sample

sample collection device or method

• Harmonized namesamp_collect_device
• DescriptionMethod or device employed for collecting sample

sample disease stage

• Harmonized namesamp_dis_stage
• DescriptionStage of the disease at the time of sample collection, e.g., dissemination, growth and reproduction, infection, inoculation, penetration

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

seasonal environment

• Harmonized nameseason_environment
• Descriptiontreatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)

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.

standing water regimen

• Harmonized namestanding_water_regm
• Descriptiontreatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water; can include multiple regimens

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

tissue culture growth media

• Harmonized nametiss_cult_growth_med
• Descriptiondescription of plant tissue culture growth media used

trophic level

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

water temperature regimen

• Harmonized namewater_temp_regm
• Descriptioninformation about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens

watering regimen

• Harmonized namewatering_regm
• Descriptioninformation about treatment involving an exposure to watering frequencies; can include multiple regimens