Clinical or host-associated pathogen

Mandatory Attributes Organism Group Attributes Optional Attributes

Mandatory Attributes

Biomaterial provider

• Description: Name and address of the lab or PI, or a culture collection identifierr. If a value cannot be provided, submitters are asked to use one of the accepted missing value reporting terms

• Example: Korean Collection for Type Cultures(KCTC), Korean Cell Line Bank(KCBL), Dr. Gildong Hong from Seoul National University

Collected by

• Description: Name of persons or institute who collected the sample

Collection date

• Description: The date (or date and time) on which the sample was collected. If a value of an expected format cannot be provided, submitters are asked to use one of the accepted missing value reporting terms

• Format: Use ISO 8601 standard on date and time. For date, use the formats “YYYY”, “YYYY-MM”, “YYYY-MM-DD”. For date and time, use the format “YYYY-mm-ddThh:mm:ssZ”. In this format, time is in Coordinated Universal Time (UTC), otherwise known as Zulu time, the letter “T” is added between date and time, and the letter “Z” (indicating Zulu) is added after time. For a range of two date and time values, use the forward-slash character “/” as the delimiter

• Example: 1990-10-30, 1990-10, 1990, 1952-10-21/1953-02-15, 2015-10-11T17:53:03Z

Geographic location

• Description: Geographical origin of the sample. If a value of an expected format cannot be provided, submitters are asked to use one of the accepted missing value reporting terms

• Format: Use the appropriate name from the list shown in geo_loc_name_qualifier_vocabulary. Use a colon to separate the country or ocean from more detailed information about the location

• Example: “South Korea: Seoul”, “Canada: Vancouver”, “Germany: halfway down Zugspitze, Alps”

Host

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

• Example: Homo sapiens

Host disease

• Description: Name of relevant disease

• Format: Controlled vocabulary from (1) Human Disease Ontology or (2) MeSH

• Example: Salmonella gastroenteritis

Isolation source

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

Latitude and longitude

• Description: The geographical coordinates of the location where the sample was collected. When the information is lacking or specification of location is not appropriate, submitters are asked to use one of the accepted missing value reporting terms

• Format: Specify as degrees latitude and longitude in format “d[d.dddd] N|S d[dd.dddd] W|E”

• Example: 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

Specimen voucher

• Description: Identifier for the physical specimen. When the information is not available or not applicable, submitters are asked to use one of the accepted missing value reporting terms

• Format: Use the format “[<institution-code>:[<collection-code>:]]<specimen_id>”, in which collection-code is optional, along with a controlled vocabulary provided at http://www.insdc.org/submitting-standards/controlled-vocabulary-specimenvoucher-qualifier/

• Example: KCLB:30082, KCTC:6910, KACC:44679

• Note: The institution-code can be found in the institution-code list file provided by NCBI

Organism Group Attributes

Isolate

• Description: Identification or description of the specific individual from which this sample was obtained

• Example: Stage 3 lung cancer patient #17, 2-year-old Panax ginseng

Strain

• Description: Microbial or eukaryotic strain name

Optional Attributes

Culture collection

• Description: Name of source institute and unique culture identifier

• Format: See http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier for the description for the proper format and list of allowed institutes

Derived from

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

• Example: SAMN00000001, KAS24095074

Description

• Description: Description of the sample

Genotype

• Description: Observed genotype

Growth protocol

• Description: Protocol for growth

• Example: 30 min egg collections of OreR and yw flies at 25 degree Celsius were aged at room temperature (RT) according to the different temporal classes T0-T4

Host age

• Description: Age of host at the time of sampling

Host description

• Description: Additional information not included in other defined vocabulary fields

Host disease outcome

• Description: Final outcome of disease

• Example: death, chronic disease, recovery

Host disease stage

• Description: Stage of disease at the time of sampling

Host health state

• Description: Information regarding health state of the individual sampled at the time of sampling

Host sex

• Description: Gender or physical sex of the host

• Possible value: Select on from the controlled vocabulary

• Controlled Vocabulary: "male", "female", "pooled male and female", "neuter", "hermaphrodite", "intersex", "not determined", "missing", "not applicable", "not collected"

Host subjected id

• Description: A unique identifier by which each subject can be referred to, de-identified

• Example: #131

Host tissue sampled

• Description: Type of tissue the initial sample was taken from

• Format: Controlled vocabulary from BRENDA Tissue and Enzyme source Ontology

Passage history

• Description: Number of passages and passage method

Pathotype

• Description: Some bacterial specific pathotypes

• Example: Escherichia coli - STEC, UPEC

Sample size

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

Serotype

• Description: Taxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties

• Example: serotype=“H1N1” in Influenza A virus CY098518

Serovar

• Description: Taxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Sometimes used as species identifier in bacteria with shaky taxonomy

• Example: Leptospira, serovar saopaolo S76607 (65357 in Entrez)

Subgroup

• Description: Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate

Subtype

• Description: Used as classifier in viruses

• Example: HIV type 1, Group M, Subtype A

Treatment

• Description: Describes how the sample was treated

• Example 1: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0.7% NaCl, 0.04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL)

• Example 2: The rats were treated with 150 mg phthalate per bodyweight kilogram for each day for 13 weeks.

Other characteristics

• Description: Other characteristics needed to describe sample characteristics, which can be useful to enter the information on experimental factors. Do not enter this field if there are no other characteristics that are needed to describe the sample

• Format: This field consists of a pair of two sub-fields: otherCharacteristics_key and otherCharacteristics_value, which correspond to the name of the factor and its value, respectively. Fill out the two sub-fields in a pair. For multiple characteristics, use “;” as a delimiter to enter in the Excel template.

• Example 1: BRCA 1 mutation - Yes

• Example 2: BRCA1 mutation status;Chemotherapy dosage - Yes;High

• Example 3: BRCA1 mutation status;Chemotherapy dosage;Weight in kg - Yes;High;65