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Host Associated

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

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

blood_press_diast

The resting diastolic blood pressure, measured as mm mercury.

format: {float} {unit}

blood_press_syst

The resting systolic blood pressure, measured as mm mercury.

format: {float} {unit}

body_habitat

The original body habitat where the sample was obtained from.

format: {text}

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}

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

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}

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}

dry_mass

The measurement of dry mass.

format: {float} {unit}

elev

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

format: {float} {unit}

family_relationship

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

format: {text}; {text}

genotype

The observed genotype.

format: {text}

gravidity

Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used.

format: {boolean};{timestamp}

height_or_length

The measurement of height or length.

format: {float} {unit}

host_body_temp

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

format: {float} {unit}

host_color

The color of host.

format: {text}

host_growth_cond

The literature reference giving growth conditions of the host.

format: {PMID|DOI|URL}

host_shape

The morphological shape of host.

format: {text}

host_subject_id

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

format: {text}

host_taxid

NCBI taxonomy ID of the host, e.g. 9606

format: {integer}

infra_specific_name

The taxonomic information subspecies level.

format: {text}

infra_specific_rank

The taxonomic rank information below subspecies level, such as variety, form, rank etc.

format: {text}

last_meal

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

format: {text};{period}

life_stage

The description of life stage.

format: {text}

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}

phenotype

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

format: {term}

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']

substrate

The growth substrate of the host.

format: {text}

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}

user_defined

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