Human-oral

Mandatory Attributes Optional Attributes

Mandatory Attributes

Collection date

• Harmonized name: collection_date

• Description: the date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format

Broad-scale environmental context

• Harmonized name: env_broad_scale

• Description: Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020]

Local-scale environmental context

• Harmonized name: env_local_scale

• Description: Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]

Environmental medium

• Harmonized name: env_medium

• Description: Add terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Multiple terms can be separated by pipes e.g.: estuarine water [ENVO:01000301]|estuarine mud [ENVO:00002160]

Geographic location

• Harmonized name: geo_loc_name

• Description: Geographical origin of the sample; use the appropriate name from this list https://www.insdc.org/submitting-standards/geo_loc_name-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"

Host

• Harmonized name: host

• Description: The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".

Latitude and longitude

• Harmonized name: lat_lon

• Description: 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

NCBI Taxonomy ID

• Description: NCBI’s taxonomy identifier of the organism for this sample. The NCBI taxonomy ID can be found at https://www.ncbi.nlm.nih.gov/taxonomy/. Enter 32644 (which is a taxonomy ID for unidentified organisms) for the following or similar cases: (1) when NCBI taxonomy ID is not available because NCBI taxonomy does not yet cover the organism, (2) when metagenome or environmental sample was used, whose organismal composition is unknown in advance

• Example: 9606 (for Homo sapiens), 452680 (for Pseudomonas sp. UK4)

Organism

• Description: The most descriptive organism name for this sample (to the species, if possible). In the case of a new species, provide the desired organism name. In the case of unidentified species, choose the appropriate Genus and include ‘sp.’, e.g. “Escherichia sp.”. When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g. “Pseudomonas sp. UK4”

• Example: Homo sapiens, Pseudomonas sp. UK4

Sample name

• Description: A name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every sample name from a single submitter must be unique within a single BioProject

Optional Attributes

Chemical administration

• Harmonized name: chem_administration

• Description: 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

Collection method

• Harmonized name: collection_method

• Description: Process used to collect the sample, e.g., bronchoalveolar lavage (BAL)

Derived from

• Description: Indicates when one BioSample was derived from another BioSample. Value should include BioSample accession number(s)

• Example: SAMN00000001, KAS24095074

Ethnicity

• Harmonized name: ethnicity

• Description: ethnicity of the subject

Host age

• Harmonized name: host_age

• Description: Age of host at the time of sampling

Host body mass index

• Harmonized name: host_body_mass_index

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

Host body product

• Harmonized name: host_body_product

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

Host body temperature

• Harmonized name: host_body_temp

• Description: core body temperature of the host when sample was collected

Host diet

• Harmonized name: host_diet

• Description: 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

• Harmonized name: host_disease

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

Host family relationship

• Harmonized name: host_family_relationship

• Description:

Host genotype

• Harmonized name: host_genotype

Host height

• Harmonized name: host_height

• Description: the height of subject

Host last meal

• Harmonized name: host_last_meal

• Description: content of last meal and time since feeding; can include multiple values

Host occupation

• Harmonized name: host_occupation

• Description: most frequent job performed by subject

Host phenotype

• Harmonized name: host_phenotype

Host pulse

• Harmonized name: host_pulse

• Description: resting pulse of the host, measured as beats per minute

Host sex

• Harmonized name: host_sex

• Description: Gender or physical sex of the host

Host subject id

• Harmonized name: host_subject_id

• Description: a unique identifier by which each subject can be referred to, de-identified, e.g. #131

Observed host symbionts

• Harmonized name: host_symbiont

• Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host

Host tissue sampled

• Harmonized name: host_tissue_sampled

• Description: name of body site where the sample was obtained from, such as a specific organ or tissue, e.g., tongue, lung. For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON

Host total mass

• Harmonized name: host_tot_mass

• Description: total mass of the host at collection, the unit depends on host

Medication code

• Harmonized name: ihmc_medication_code

• Description: can include multiple medication codes

Isolation source

• Harmonized name: isolation_source

• Description: Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived.

Medical history performed

• Harmonized name: medic_hist_perform

• Description: whether full medical history was collected

Miscellaneous parameter

• Harmonized name: misc_param

• Description: any other measurement performed or parameter collected, that is not listed here

Negative control type

• Harmonized name: neg_cont_type

• Description: The substance or equipment used as a negative control in an investigation, e.g., distilled water, phosphate buffer, empty collection device, empty collection tube, DNA-free PCR mix, sterile swab, sterile syringe

Nose/mouth/teeth/throat disorder

• Harmonized name: nose_mouth_teeth_throat_disord

• Description: history of nose/mouth/teeth/throat disorders; can include multiple disorders

Omics Observatory ID

• Harmonized name: omics_observ_id

• Description: A unique identifier of the omics-enabled observatory (or comparable time series) your data derives from. This identifier should be provided by the OMICON ontology; if you require a new identifier for your time series, contact the ontology's developers. Information is available here: https://github.com/GLOMICON/omicon. This field is only applicable to records which derive from an omics time-series or observatory.

Organism count

• Harmonized name: organism_count

• Description: total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts

Oxygenation status of sample

• Harmonized name: oxy_stat_samp

• Description: oxygenation status of sample

Perturbation

• Harmonized name: perturbation

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

Positive control type

• Harmonized name: pos_cont_type

• Description: The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive

Reference for biomaterial

• Harmonized name: ref_biomaterial

• Description: Primary publication or genome report

Relationship to oxygen

• Harmonized name: rel_to_oxygen

• Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments, eg, aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe, missing, not applicable, not collected, not provided, restricted access

Sample collection device or method

• Harmonized name: samp_collect_device

• Description: Method or device employed for collecting sample

Sample material processing

• Harmonized name: samp_mat_process

• Description: Processing applied to the sample during or after isolation

Sample salinity

• Harmonized name: samp_salinity

• Description: the amount of salt dissolved within the collected sample

Sample size

• Harmonized name: samp_size

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

Sample storage duration

• Harmonized name: samp_store_dur

Sample storage location

• Harmonized name: samp_store_loc

Sample storage temperature

• Harmonized name: samp_store_temp

Sample volume or weight for DNA extraction

• Harmonized name: samp_vol_we_dna_ext

• Description: volume (mL) or weight (g) of sample processed for DNA extraction

Size fraction selected

• Harmonized name: size_frac

• Description: Filtering pore size used in sample preparation, e.g., 0-0.22 micrometer

Source material identifiers

• Harmonized name: source_material_id

• Description: 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.

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Time since last toothbrushing

• Harmonized name: time_last_toothbrush

• Description: specification of the time since last toothbrushing