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Plant associated

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Here is a link to NCBI definition page for the plant_associated package.

Required

sample_name

This is your group name. Mothur will fill this in for you, thanks mom!

description

Description of sample

sample_title

The title for your sample.

format: {text} 

seq_methods

The free form descriptions of methods used to create the sequencing library.

format: {text}

organism

You must choose this from the NCBI's list found here. This is controlled vocabulary. Your choices are: activated carbon metagenome, activated sludge metagenome, air metagenome, anaerobic digester metagenome, ant fungus garden metagenome, aquatic metagenome, activated carbon metagenome, activated sludge metagenome, beach sand metagenome, biofilm metagenome, biofilter metagenome, biogas fermenter metagenome, bioreactor metagenome, bioreactor sludge metagenome, clinical metagenome, coal metagenome, compost metagenome, dust metagenome, fermentation metagenome, food fermentation metagenome, food metagenome, freshwater metagenome, freshwater sediment metagenome, groundwater metagenome, halite metagenome, hot springs metagenome, hydrocarbon metagenome, hydrothermal vent metagenome, hypersaline lake metagenome, ice metagenome, indoor metagenome, industrial waste metagenome, mangrove metagenome, marine metagenome, marine sediment metagenome, microbial mat metagenome, mine drainage metagenome, mixed culture metagenome, oil production facility metagenome, paper pulp metagenome, permafrost metagenome, plastisphere metagenome, power plant metagenome, retting rhizosphere metagenome, rock metagenome, salt lake metagenome, saltern metagenome, sediment metagenome, snow metagenome, soil metagenome, stromatolite metagenome, terrestrial metagenome, tomb wall metagenome, wastewater metagenome, wetland metagenome, whale fall metagenome, algae metagenome, ant metagenome, bat metagenome, beetle metagenome, bovine gut metagenome, bovine metagenome, chicken gut metagenome, coral metagenome, echinoderm metagenome, endophyte metagenome, epibiont metagenome, fish metagenome, fossil metagenome, gill metagenome, gut metagenome, honeybee metagenome, human gut metagenome, human lung metagenome, human metagenome, human nasal/pharyngeal metagenome, human oral metagenome, human skin metagenome, insect gut metagenome, insect metagenome, mollusc metagenome, mosquito metagenome, mouse gut metagenome, mouse metagenome, mouse skin metagenome, nematode metagenome, oral metagenome, phyllosphere metagenome, pig metagenome, plant metagenome, primate metagenome, rat metagenome, root metagenome, sea squirt metagenome, seed metagenome, shoot metagenome, skin metagenome, snake metagenome, sponge metagenome, stomach metagenome, symbiont metagenome, termite gut metagenome, termite metagenome, upper respiratory tract metagenome, urine metagenome, viral metagenome, wallaby gut metagenome, wasp metagenome, synthetic metagenome, metagenome. You can modify your choice after submission.

collection_date

Date of sampling, in \"DD-Mmm-YYYY\", \"Mmm-YYYY\" or \"YYYY\" format (single instance, eg., 05-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard \"YYYY-mm-dd\" or \"YYYY-mm-ddThh:mm:ss\" (eg. 1990-11-05 or 1990-11-05T14:41:36)

format: {timestamp}

env_biome

Major class of ecologically similar communities of plants, animals, and other organisms (eg., desert, coral reef).

format: {term}

env_feature

Geographical environmental feature (eg., harbor, lake).

format: {term}

geo_loc_name

Geographical 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\".

format: {term}:{term}:{text}

lat_lon

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.

format: {float} {float}

env_material

The matter displaced by the sample (eg., air, soil, water).

format: {term}

host

The natural (as opposed to laboratory) host to the organism from which sample was obtained.

Optional

air_temp_regm

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.

antibiotic_regm

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.

altitude

The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

format: {float} m

chem_administration

The 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.

chem_mutagen

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

Treatment involving an exposure to a particular climate; can include multiple climates


format: {term}; {timestamp}

depth

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.

format: {float} m

elev

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

format: {float} {unit}

fertilizer_regm

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

fungicide_regm

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

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

gravity

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 hormone regimen

growth_hormone_regm

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

growth_med

Information about growth media for growing the plants or tissue cultured samples

herbicide_regm

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

Age of host at the time of sampling host disease

host_disease

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

Measurement of dry mass

host_genotype

host_height

Height of subject

host_infra_specific_name

Taxonomic information subspecies level

host_infra_specific_rank

Taxonomic rank information below subspecies level, such as variety, form, rank etc.

host_length

The length of subject

host_life_stage

Description of host life stage

host_phenotype

host_taxid

NCBI taxonomy ID of the host, e.g. 9606

host_tot_mass

Total mass of the host at collection, the unit depends on host

host_wet_mass

Measurement of wet mass

humidity_regm

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

mechanical_damage

Information about any mechanical damage exerted on the plant; can include multiple damages and sites

mineral_nutr_regm

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

non_mineral_nutr_regm

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

organism_count

The total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts.

format: {text};{float} {unit}

oxy_stat_samp

The oxygenation status of sample.

format: [, 'aerobic', 'anaerobic']

perturbation

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

format: {text};{interval}

pesticide_regm

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_regm

Information about treatment involving exposure of plants to varying levels of pH of the growth media; can include multiple regimen

plant_body_site

Name of body site that the sample was obtained from. For Plant Ontology (PO) (v 20) terms, see http://purl.bioontology.org/ontology/PO

plant_product

Substance produced by the plant, where the sample was obtained from

radiation_regm

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_regm

Information about treatment involving an exposure to a given amount of rainfall; can include multiple regimens

rel_to_oxygen

Aerobic or anaerobic

format: [, 'aerobe', 'anaerobe', 'facultative', 'microaerophilic', 'microanaerobe', 'obligate aerobe', 'obligate anaerobe']

salt_regm

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

samp_collect_device

Method or device employed for collecting sample

format: {text}

samp_mat_process

Processing applied to the sample during or after isolation.

format: {text|term}

samp_salinity

The sample salinity.

format: {float} {unit}

samp_size

The sample size.

format: {float} {unit}

samp_store_dur

The sample storage duration.

format: {interval}

samp_store_loc

The sample storage location. Usually name of a specific freezer/room

format: {text}

samp_store_temp

The sample storage temperature.

format: {float} {unit}

samp_vol_we_dna_ext

Volume (mL) or weight (g) of sample processed for DNA extraction

season_environment

Treatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)

source_material_id

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_regm

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

temp

The temperature of the sample at time of sampling.

format: {float} {unit}

tiss_cult_growth_med

Description of plant tissue culture growth media used

water_temp_regm

Information about treatment involving an exposure to water with varying degree of temperature; can include multiple regimens

watering_regm

Information about treatment involving an exposure to watering frequencies; can include multiple regimens

user_defined

You may create your own optional fields to describe your sample.