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Wastewater

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


Optional

alkalinity

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

biochem_oxygen_dem

A measure of the relative oxygen-depletion effect of a waste contaminant

chem_administration

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_oxygen_dem

A measure of the relative oxygen-depletion effect of a waste contaminant

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

efficiency_percent

Percentage of volatile solids removed from the anaerobic digestor

emulsions

Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types

gaseous_substances

Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances

indust_eff_percent

Percentage of industrial effluents received by wastewater treatment plant

inorg_particles

Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles

misc_param

Any other measurement performed or parameter collected, that is not listed here

nitrate

Concentration of nitrate

org_particles

Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.

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}

ph

The pH measurement.

format: {float} {unit}

phosphate

Concentration of phosphate

pre_treatment

The process of pre-treatment removes materials that can be easily collected from the raw wastewater

primary_treatment

The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed

reactor_type

Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage relationship to oxygen

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

secondary_treatment

The process for substantially degrading the biological content of the sewage

sewage_type

Type of wastewater treatment plant as municipial or industrial

sludge_retent_time

The time activated sludge remains in reactor

sodium

Sodium concentration

soluble_inorg_mat

Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.

soluble_org_mat

Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, 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.

suspend_solids

Descriptionconcentration of substances including a wide variety of material, such as silt, decaying plant and animal matter, etc,; can include multiple substances temperature

temp

The temperature of the sample at time of sampling.

format: {float} {unit}

tertiary_treatment

The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment

tot_nitro

Total nitrogen content of the sample

tot_phosphate

Total amount or concentration of phosphate

wastewater_type

The origin of wastewater such as human waste, rainfall, storm drains, etc.

user_defined

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