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Water

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

Contents

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


Optional

alkalinity

Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate


alkyl_diethers

Concentration of alkyl diethers

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

Asurement of aminopeptidase activity

ammonium

Concentration of ammonium

format: {float} {unit}

atmospheric_data

Measurement of atmospheric data; can include multiple data

bac_prod

Bacterial production in the water column measured by isotope uptake

bac_resp

Measurement of bacterial respiration in the water column

bacteria_carb_prod

Measurement of bacterial carbon production

biomass

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

bishomohopanol

Concentration of bishomohopanol

format: {float} {unit}

bromide

Concentration of bromide

format: {float} {unit}

calcium

Concentration of calcium

format: {float} {unit}

carb_nitro_ratio

Ratio of amount or concentrations of carbon to nitrogen

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

Concentration of chloride

format: {float} {unit}

chlorophyll

Concentration of chlorophyll

format: {float} {unit}

conduc

Electrical conductivity of water

density

Density of sample

diether_lipids

Concentration of diether lipids; can include multiple types of dither lipids

format: {float} {unit}

diss_carb_dioxide

Concentration of dissolved carbon dioxide

format: {float} {unit}

diss_hydrogen

Concentration of dissolved hydrogen

format: {float} {unit}

diss_inorg_carb

Dissolved inorganic carbon concentration

diss_inorg_nitro

Concentration of dissolved inorganic nitrogen

format: {float} {unit}

diss_inorg_phosp

Concentration of dissolved inorganic phosphorus

format: {float} {unit}

diss_org_carb

Concentration of dissolved organic carbon

format: {float} {unit}

diss_org_nitro

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

format: {float} {unit}

diss_oxygen

Concentration of dissolved oxygen

format: {float} {unit}

down_par

Visible waveband radiance and irradiance measurements in the water column

elev

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

format: {float} {unit}

fluor

Raw or converted fluorescence of water

glucosidase_act

Measurement of glucosidase activity

light_intensity

Measurement of light intensity

magnesium

Concentration of magnesium

format: {float} {unit}

mean_frict_vel

Measurement of mean friction velocity

mean_peak_frict_vel

Measurement of mean peak friction velocity

n_alkanes

Concentration of n-alkanes; can include multiple n-alkanes

format: {float} {unit}

nitrate

Concentration of nitrate

format: {float} {unit}

nitrite

Concentration of nitrite

format: {float} {unit}

nitro

Concentration of nitrogen (total)

format: {float} {unit}

org_carb

Concentration of organic carbon

format: {float} {unit}

org_matter

Concentration of organic matter

format: {float} {unit}

org_nitro

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

Concentration of particulate organic carbon

format: {float} {unit}

part_org_nitro

Concentration of particulate organic nitrogen

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

Concentration of petroleum hydrocarbon

format: {float} {unit}

ph

pH measurement

phaeopigments

Concentration of phaeopigments; can include multiple phaeopigments

format: {float} {unit}

phosphate

Concentration of phosphate

format: {float} {unit}

phosplipid_fatt_acid

Concentration of phospholipid fatty acids; can include multiple values

format: {float} {unit}

photon_flux

Measurement of photon flux

potassium

Concentration of potassium

format: {float} {unit}

pressure

Pressure to which the sample is subject, in atmospheres

format: {float} {unit}

primary_prod

Measurement of primary production

format: {float} {unit}

redox_potential

Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential

rel_to_oxygen

Aerobic or anaerobic

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


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

silicate

Concentration of silicate

format: {float} {unit}

sodium

Sodium concentration

format: {float} {unit}

soluble_react_phosp

Concentration of soluble reactive phosphorus

format: {float} {unit}

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.

sulfate

Concentration of sulfate

format: {float} {unit}

sulfide

Concentration of sulfide

format: {float} {unit}

suspend_part_matter

Concentration of suspended particulate matter

format: {float} {unit}

temp

The temperature of the sample at time of sampling.

format: {float} {unit}

tidal_stage

Stage of tide

tot_depth_water_col

Measurement of total depth of water column

tot_diss_nitro

Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen

tot_inorg_nitro

Total inorganic nitrogen content

tot_nitro

Total nitrogen content of the sample

tot_part_carb

Total particulate carbon content

tot_phosp

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

water_current

Measurement of magnitude and direction of flow within a fluid

user_defined

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