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Human Associated

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Here is a link to NCBI definition page for the human_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

age

The age at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees.

format: {float} {unit}

amniotic_fluid_color

The specification of the color of the amniotic fluid sample.

format: {text}

blood_blood_disord

The history of blood disorders; can include multiple disorders

format: {text}

body_mass_index

The body mass index, calculated as weight/(height)squared

format: {float} {unit}

body_product

The substance produced by the plant where the sample was obtained from.

format: {text}

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}

diet

The type of diet depending on the sample for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types.

format: {text}

diet_last_six_month

The specification of major diet changes in the last six months, if yes the change should be specified.

format: {boolean};{text}

disease

The list of diseases diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology), free text for non-human. For DO terms, please see http://gemina.svn.sourceforge.net/viewvc/gemina/trunk/Gemina/ontologies/gemina_symptom.obo?view=log

format: {term}

drug_usage

Any drug used by subject and the frequency of usage; can include multiple drugs used

format: {text};{integer}/[year|month|week|day|hour]

ethnicity

The ethnicity of the subject.

format: {integer|text}

family_relationship

The relationships to other samples in the same study; can include multiple relationships.

format: {text}; {text}

fetal_health_stat

The specification of fetal health status, should also include abortion.

format: {text}

genotype

The observed genotype.

format: {text}

gestation_state

The specification of the gestation state.

format: {text}

height

The height of subject.

format: {float} {unit}

hiv_stat

HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]

format: {boolean};{boolean}

host_body_temp

The core body temperature of the host when sample was collected.

format: {float} {unit}

host_subject_id

A unique identifier by which each subject can be referred to, de-identified, e.g. #131

format: {text}

ihmc_medication_code

can include multiple medication codes

format: {integer}

kidney_disord

The history of kidney disorders; can include multiple disorders

format: {text}

last_meal

The content of last meal and time since feeding; can include multiple values.

format: {text};{period}

maternal_health_stat

The specification of the maternal health status.

format: {text}

medic_hist_perform

Whether full medical history was collected.

format: {boolean}

nose_throat_disord

The history of nose-throat disorders; can include multiple disorders.

format: {text}

occupation

The most frequent job performed by subject.

format: {integer}

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}

pet_farm_animal

The specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present.

format: {boolean};{text}

phenotype

Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601.

format: {term}

pulmonary_disord

The history of pulmonary disorders; can include multiple disorders.

format: {text}

pulse

The resting pulse, measured as beats per minute.

format: {float} {unit}

rel_to_oxygen

Aerobic or anaerobic

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

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}

sex

The physical sex of sampled organism.

format: [, 'male', 'female', 'neuter', 'hermaphrodite', 'not determined']

smoker

The specification of smoking status.

format: {boolean}

study_complt_stat

The specification of study completion status, if no the reason should be specified

format: {boolean};[adverse event|non-compliance|lost to follow up|other-specify]

temp

The temperature of the sample at time of sampling.

format: {float} {unit}

tissue

Type of tissue the sample was taken from.

tot_mass

The total mass of the host at collection, the unit depends on host.

format: {float} {unit}

travel_out_six_month

The specification of the countries travelled in the last six months; can include multiple travels.

format: {text}

twin_sibling

The specification of twin sibling presence.

format: {boolean}

urine_collect_meth

The specification of urine collection method.

format: [, 'clean catch', 'catheter']

urogenit_tract_disor

The history of urogenitaltract disorders; can include multiple disorders.

format: {text}

weight_loss_3_month

The specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss.

format: {boolean};{float} {unit}

user_defined

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