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Microbial

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Here is a link to NCBI definition page for the microbial 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}

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}

Optional

alkalinity

The alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate.

format: {float} {unit}

alkyl_diethers

The concentration of alkyl dithers.

format: {float} {unit}

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

aminopept_act

The measurement of amino peptidase activity.

format: {float} {unit}

ammonium

The concentration of ammonium.

format: {float} {unit}

bacteria_carb_prod

The measurement of bacterial carbon production.

format: {float} {unit}

biomass

The amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements.

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

bishomohopanol

The concentration of bishomohopanol.

format: {float} {unit}

bromide

The concentration of bromide.

format: {float} {unit}

calcium

The concentration of calcium.

format: {float} {unit}

carb_nitro_ratio

The ratio of amount or concentrations of carbon to nitrogen.

format: {float} {unit}

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.

format: {term}; {timestamp}

chloride

The concentration of chloride.

format: {float} {unit}

chlorophyll

The concentration of chlorophyll.

format: {float} {unit}

diether_lipids

The concentration of diether lipids; can include multiple types of diether lipids.

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

diss_carb_dioxide

The concentration of dissolved carbon dioxide.

format: {float} {unit}

diss_hydrogen

The concentration of dissolved hydrogen.

format: {float} {unit}

diss_inorg_carb

The dissolved inorganic carbon concentration.

format: {float} {unit}

diss_org_carb

The concentration of dissolved organic carbon.

format: {float} {unit}

diss_org_nitro

The dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2.

format: {float} {unit}

diss_oxygen

The concentration of dissolved oxygen.

format: {float} {unit}

glucosidase_act

The measurement of glucosidase activity.

format: {float} {unit}

magnesium

The concentration of magnesium.

format: {float} {unit}

mean_frict_vel

The measurement of mean friction velocity.

format: {float} {unit}

mean_peak_frict_vel

The measurement of mean peak friction velocity.

format: {float} {unit}

methane

The methane (gas) amount or concentration at the time of sampling.

format: {float} {unit}

n_alkanes

The concentration of n-alkanes; can include multiple n-alkanes.

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

nitrate

The concentration of nitrate.

format: {float} {unit}

nitrite

The concentration of nitrite.

format: {float} {unit}

nitro

The concentration of nitrogen (total).

format: {float} {unit}

org_carb

The concentration of organic carbon.

format: {float} {unit}

org_matter

The concentration of organic matter.

format: {float} {unit}

org_nitro

The concentration of organic nitrogen.

format: {float} {unit}

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']

part_org_carb

The concentration of particulate organic carbon.

format: {float} {unit}

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}

petroleum_hydrocarb

The concentration of petroleum hydrocarbon.

format: {float} {unit}

ph

The pH measurement.

format: {float} {unit}

phaeopigments

The concentration of phaeopigments; can include multiple phaeopigments.

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

phosphate

The concentration of phosphate.

format: {float} {unit}

phosplipid_fatt_acid

The concentration of phospholipid fatty acids; can include multiple values.

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

potassium

The concentration of potassium.

format: {float} {unit}

pressure

The pressure to which the sample is subject, in atmospheres.

format: {float} {unit}

redox_potential

The redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential.

format: {float} {unit}

rel_to_oxygen

Aerobic or anaerobic

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

salinity

The salinity measurement.

format: {float} {unit}

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_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}

silicate

The concentration of silicate.

format: {float} {unit}

sodium

The concentration of sodium.

format: {float} {unit}

sulfate

The concentration of sulfate.

format: {float} {unit}

sulfide

The concentration of sulfide.

format: {float} {unit}

temp

The temperature of the sample at time of sampling.

format: {float} {unit}

tot_carb

The total carbon contents.

format: {float} {unit}

tot_nitro

The total nitrogen concentration, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen.

format: {float} {unit}

tot_org_carb

Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content.

format: {float} {unit}

turbidity

The turbidity measurement.

format: {float} {unit}

water_content

The water content measurement.

format: {float} {unit}

user_defined

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