Human vaginal

Here is a link to NCBI definition page for the human vaginal 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

birth_control

specification of birth control medication used

chem_administration

Descriptionlist 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

douche

date of most recent douche

ethnicity

ethnicity of the subject

gynecologic_disord

history of gynecological disorders; can include multiple disorders

host_age

Age of host at the time of sampling

host_body_mass_index

body mass index of the host, calculated as weight/(height)squared

host_body_product

substance produced by the host, e.g. stool, mucus, where the sample was obtained from

host_body_temp

core body temperature of the host when sample was collected

host_diet

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

host_disease

Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, https://bioportal.bioontology.org/ontologies/1009 or https://www.ncbi.nlm.nih.gov/mesh

host_family_relationship

host_genotype

host_height

The height of subject

host_last_meal

Content of last meal and time since feeding; can include multiple values

host_occupation

Most frequent job performed by subject

host_phenotype

host_pulse

Resting pulse of the host, measured as beats per minute

host_sex

Gender or physical sex of the host

host_subject_id

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

host_tissue_sampled

Type of tissue the initial sample was taken from. Controlled vocabulary, https://bioportal.bioontology.org/ontologies/1005)

host_tot_mass

Total mass of the host at collection, the unit depends on host

hrt

Whether subject had hormone replacement theraphy, and if yes start date

hysterectomy

Specification of whether hysterectomy was performed

ihmc_medication_code

Can include multiple medication codes

medic_hist_perform

Whether full medical history was collected

menarche

Descriptiondate of most recent menstruation

menopause

Date of onset of menopause

organism_count

Total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts

oxy_stat_samp

Oxygenation status of sample

perturbation

Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

pregnancy

Date due of pregnancy

rel_to_oxygen

Aerobic or anaerobic

samp_collect_device

Method or device employed for collecting sample

samp_mat_process

Processing applied to the sample during or after isolation

samp_salinity

samp_size

Amount or size of sample (volume, mass or area) that was collected

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

sexual_act

Current sexual partner and frequency of sex

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.

temp

Temperature of the sample at time of sampling

urogenit_disord

History of urogenital disorders, can include multiple disorders

user_defined

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