Human Associated
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 https://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 https://disease-ontology.org
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 https://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.