Sediment
Here is a link to NCBI definition page for the sediment 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}
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 https://bioportal.bioontology.org/visualize/44603.
format: {term}; {timestamp}
chloride
The concentration of chloride.
format: {float} {unit}
chlorophyll
The concentration of chlorophyll.
format: {float} {unit}
density
The density of sample.
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}
particle_class
The particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values.
format: {text};{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}
porosity
The porosity of deposited sediment is volume of voids divided by the total volume of sample.
format: {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}
sediment_type
The information about the sediment type based on major constituents.
format: [, 'biogenous', 'cosmogenous', 'hydrogenous', 'lithogenous']
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}
tidal_stage
The stage of tide.
format: [, 'low', 'high']
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.