Symbiont-associated

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 dependence

• Harmonized name: host_dependence

• Description: Type of host dependence for the symbiotic host organism to its host., e.g., facultative, obligate

Host life stage

• Harmonized name: host_life_stage

• Description: Description: of host life stage

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

Symbiotic host organism life cycle type

• Harmonized name: sym_life_cycle_type

• Description: Type of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle, e.g., complex life cycle, simple life cycle

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

Altitude

• Harmonized name: altitude

• Description: The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

Duration of association with the host

• Harmonized name: association_duration

• Description: Time spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study

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)

Depth

• Harmonized name: depth

• Description: 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.

Derived from

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

• Example: SAMN00000001, KAS24095074

Elevation

• Harmonized name: elev

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

Gravidity

• Harmonized name: gravidity

• Description: whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used

Host age

• Harmonized name: host_age

• Description: Age of host at the time of sampling

Host body habitat

• Harmonized name: host_body_habitat

• Description: original body habitat where the sample was obtained from

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 cellular location

• Harmonized name: host_cellular_loc

• Description: The localization of the symbiotic host organism within the host from which it was sampled, e.g., intracellular, extracellular

Host color

• Harmonized name: host_color

• Description: the color of host

Host common name

• Harmonized name: host_common_name

• Description: The natural language (non-taxonomic) name of the host organism, e.g., mouse

Host dry mass

• Harmonized name: host_dry_mass

• Description: measurement of dry mass

Host family relationship

• Harmonized name: host_family_relationship

• Description:

Host genotype

• Harmonized name: host_genotype

Host growth conditions

• Harmonized name: host_growth_cond

• Description: literature reference giving growth conditions of the host

Host height

• Harmonized name: host_height

• Description: the height of subject

Host infra specific name

• Harmonized name: host_infra_specific_name

• Description: taxonomic information subspecies level

Host infra specific rank

• Harmonized name: host_infra_specific_rank

• Description: taxonomic rank information below subspecies level, such as variety, form, rank etc.

Host length

• Harmonized name: host_length

• Description: the length of subject

Host number individual

• Harmonized name: host_number

• Description: Number of symbiotic host individuals pooled at the time of collection

Observed coinfecting organisms in host of host

• Harmonized name: host_of_host_coinf

• Description: The taxonomic name of any coinfecting organism observed in a symbiotic relationship with the host of the sampled host organism, e.g. where a sample collected from a host trematode species (A) which was collected from a host_of_host fish (B) that was also infected with a nematode (C), the value here would be (C) the nematode {species name} or {common name}. Multiple co-infecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont

Host of the symbiotic host disease status

• Harmonized name: host_of_host_disease

• Description: List of diseases with which the host of the symbiotic host organism has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text

Host of the symbiotic host local environmental context

• Harmonized name: host_of_host_env_loc

• Description: For a symbiotic host organism the local anatomical environment within its host may have causal influences. Report the anatomical entity(s) which are in the direct environment of the symbiotic host organism being sampled and which you believe have significant causal influences on your sample or specimen. For example, if the symbiotic host organism being sampled is an intestinal worm, its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/)

Host of the symbiotic host environemental medium

• Harmonized name: host_of_host_env_med

• Description: Report the environmental material(s) immediately surrounding the symbiotic host organism at the time of sampling. This usually will be a tissue or substance type from the host, but may be another material if the symbiont is external to the host. We recommend using classes from the UBERON ontology, but subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483) may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS. Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g., air, water, blood) and not discrete, countable entities (e.g., intestines, heart)

Host of the symbiotic host family relationship

• Harmonized name: host_of_host_fam_rel

• Description: Familial relationship of the host of the symbiotic host organisms to other hosts of symbiotic host organism in the same study; can include multiple relationships

Host of the symbiotic host genotype

• Harmonized name: host_of_host_geno

• Description: Observed genotype of the host of the symbiotic host organism

Host of the symbiotic host gravidity

• Harmonized name: host_of_host_gravid

• Description: Whether or not the host of the symbiotic host organism is gravid, and if yes date due or date post-conception, specifying which is used

Host of the symbiotic host infra-specific name

• Harmonized name: host_of_host_infname

• Description: Taxonomic name information of the host of the symbiotic host organism below subspecies level

Host of the symbiotic host infra-specific rank

• Harmonized name: host_of_host_infrank

• Description: Taxonomic rank information about the host of the symbiotic host organism below subspecies level, such as variety, form, rank

Host of the symbiotic host common name

• Harmonized name: host_of_host_name

• Description: Common name of the host of the symbiotic host organism

Host of the symbiotic host phenotype

• Harmonized name: host_of_host_pheno

• Description: Phenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato

Host of the symbiotic host subject id

• Harmonized name: host_of_host_sub_id

• Description: A unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14

Host of the symbiotic host taxon id

• Harmonized name: host_of_host_taxid

• Description: NCBI taxon id of the host of the symbiotic host organism

Host of the symbiotic host total mass

• Harmonized name: host_of_host_totmass

• Description: Total mass of the host of the symbiotic host organism at collection, the unit depends on the host

Host phenotype

• Harmonized name: host_phenotype

Host sex

• Harmonized name: host_sex

• Description: Gender or physical sex of the host

Host shape

• Harmonized name: host_shape

• Description: morphological shape of host

Host specificity

• Harmonized name: host_specificity

• Description: Level of specificity of symbiont-host interaction, e.g., family-specific, generalist, genus-specific, species-specific

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

Host substrate

• Harmonized name: host_substrate

• Description: the growth substrate of the host

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 taxonomy ID

• Harmonized name: host_taxid

• Description: NCBI taxonomy ID of the host, e.g. 9606

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

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.

Miscellaneous parameter

• Harmonized name: misc_param

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

Mode of transmission

• Harmonized name: mode_transmission

• Description: The process through which the symbiotic host organism entered the host from which it was sampled, e.g., horizontal:castrator, horizontal:directly transmitted, horizontal:micropredator, horizontal:parasitoid, horizontal:trophically transmitted, horizontal:vector transmitted, vertical

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

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

Route of transmission

• Harmonized name: route_transmission

• Description: Description: of path taken by the symbiotic host organism being sampled in order to establish a symbiotic relationship with the host (with which it was observed at the time of sampling) via a mode of transmission (specified in mode_transmission), e.g., environmental:faecal-oral, transplacental, vector-borne:vector penetration

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 solution

• Harmonized name: samp_store_sol

• Description: Solution within which sample was stored, if any

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.

Host of the symbiont role

• Harmonized name: symbiont_host_role

• Description: Role of the host in the life cycle of the symbiotic organism, e.g., accidental, dead-end, definitive, intermediate, paratenic, reservoir, single host

Temperature

• Harmonized name: temp

• Description: temperature of the sample at time of sampling

Type of symbiosis

• Harmonized name: type_of_symbiosis

• Description: Type of biological interaction established between the symbiotic host organism being sampled and its respective host, e.g., commensalistic, mutualistic, parasitic