Plant-associated

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

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"

Host

• Harmonized name: host

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

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 temperature regimen

• Harmonized name: air_temp_regm

• Description: information 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 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.

Ancestral data

• Harmonized name: ances_data

• Description: Information 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 name: antibiotic_regm

• Description: information 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 name: biol_stat

• Description: The level of genome modification, e.g., wild, natural, semi-natural, inbred line, breeder's line, hybrid, clonal selection, mutant

Biotic regimen

• Harmonized name: biotic_regm

• Description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi

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

Chemical mutagen

• Harmonized name: chem_mutagen

• Description: treatment 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 name: climate_environment

• Description: treatment involving an exposure to a particular climate; can include multiple climates

Collection method

• Harmonized name: collection_method

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

Culture rooting medium

• Harmonized name: cult_root_med

• Description: Name 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 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.

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.

Fertilizer regimen

• Harmonized name: fertilizer_regm

• Description: information 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 name: fungicide_regm

• Description: information 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 name: gaseous_environment

• Description: use 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 name: genetic_mod

• Description: Genetic 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 name: gravity

• Description: information 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 name: growth_facil

• Description: Type 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 name: growth_habit

• Description: Characteristic shape, appearance or growth form of a plant species, e.g., erect, semi-erect, spreading, prostrate

Growth hormone regimen

• Harmonized name: growth_hormone_regm

• Description: information 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 name: herbicide_regm

• Description: information 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 name: host_age

• Description: Age of host at the time of sampling

Host common name

• Harmonized name: host_common_name

• Description: The natural language (non-taxonomic) name of the host organism, e.g., mouse

Host disease

• Harmonized name: host_disease

• Description: Name 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 name: host_dry_mass

• Description: measurement of dry mass

Host genotype

• Harmonized name: host_genotype

• Description:

Host height

• Harmonized name: host_height

• Description: the height of subject

Host length

• Harmonized name: host_length

• Description: the length of subject

Host life stage

• Harmonized name: host_life_stage

• Description: Description: of host life stage

Host phenotype

• Harmonized name: host_phenotype

Host subspecific genetic lineage

• Harmonized name: host_subspecf_genlin

• Description: Information 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 name: host_symbiont

• Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host

Host taxonomy ID

• Harmonized name: host_taxid

• Description: NCBI taxonomy ID of the host, e.g. 9606

Host total mass

• Harmonized name: host_tot_mass

• Description: total mass of the host at collection, the unit depends on host

Host wet mass

• Harmonized name: host_wet_mass

• Description: measurement of wet mass

Humidity regimen

• Harmonized name: humidity_regm

• Description: information 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 name: isolation_source

• Description: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Light regimen

• Harmonized name: light_regm

• Description: Information about treatment(s) involving exposure to light, including both light intensity and quality

Mechanical damage

• Harmonized name: mechanical_damage

• Description: information about any mechanical damage exerted on the plant; can include multiple damages and sites

Mineral nutrient regimen

• Harmonized name: mineral_nutr_regm

• Description: information 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 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

Non mineral nutrient regimen

• Harmonized name: non_mineral_nutr_regm

• Description: information 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 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

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

Pesticide regimen

• Harmonized name: pesticide_regm

• Description: information 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 name: ph_regm

• Description: information about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen

Plant growth medium

• Harmonized name: plant_growth_med

• Description: Type of the media used for growing sampled plants, e.g., soil [ENVO:00001998]

Plant product

• Harmonized name: plant_product

• Description: substance produced by the plant, where the sample was obtained from

Plant sex

• Harmonized name: plant_sex

• Description: Sex 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 name: plant_struc

• Description: Name 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 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

Radiation regimen

• Harmonized name: radiation_regm

• Description: information 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 name: rainfall_regm

• Description: information about treatment involving an exposure to a given amount of rainfall; can include multiple regimens

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

Rooting conditions

• Harmonized name: root_cond

• Description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container

Rooting medium carbon

• Harmonized name: root_med_carbon

• Description: Source of organic carbon in the culture rooting medium, e.g., sucrose

Rooting medium macronutrients

• Harmonized name: root_med_macronutr

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

Rooting medium micronutrients

• Harmonized name: root_med_micronutr

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

Rooting medium pH

• Harmonized name: root_med_ph

• Description: pH measurement of the culture rooting medium, e.g., 5.5

Rooting medium regulators

• Harmonized name: root_med_regl

• Description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid, e.g., 0.5 mg/L NAA

Rooting medium solidifier

• Harmonized name: root_med_solid

• Description: Specification of the solidifying agent in the culture rooting medium, e.g., agar

Rooting medium organic supplements

• Harmonized name: root_med_suppl

• Description: Organic 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 name: salt_regm

• Description: information 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 name: samp_capt_status

• Description: Reason 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 name: samp_collect_device

• Description: Method or device employed for collecting sample

Sample disease stage

• Harmonized name: samp_dis_stage

• Description: Stage of the disease at the time of sample collection, e.g., dissemination, growth and reproduction, infection, inoculation, penetration

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

Seasonal environment

• Harmonized name: season_environment

• Description: treatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)

Size fraction selected

• Harmonized name: size_frac

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

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.

Standing water regimen

• Harmonized name: standing_water_regm

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

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Tissue culture growth media

• Harmonized name: tiss_cult_growth_med

• Description: Description: of plant tissue culture growth media used

Water temperature regimen

• Harmonized name: water_temp_regm

• Description: information about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens

Watering regimen

• Harmonized name: watering_regm

• Description: information about treatment involving an exposure to watering frequencies; can include multiple regimens