Human

Mandatory Attributes Optional Attributes

Mandatory Attributes

Age

• Description: Age at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees. For samples such as cell lines in which age is not applicable, enter not applicable. For samples where an exact age is unknown, such as when only the range of age values is known, enter missing:not collected in this field, then use the “other characteristics“ field to enter the range of age values

• Example: 28 years, 2.5 months, 13 weeks, 3 days, 10 embryo age

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

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”

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”

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

Sex

• Description: Physical sex of sampled organism

• 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"

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

Tissue

• Description: Type of tissue the sample was taken from

• Example: liver, plasma, urine, leaf, root

Optional Attributes

Cell line

• Description: Name of the cell line

Cell subtype

• Description: Subtype of a cell

Cell type

• Description: Type of cell of the sample or from which the sample was obtained

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

Development stage

• Description: Developmental stage at the time of sampling

• Example: adult, embryo, fetal, hatching stage, infant, juvenile, larva, newborn, pluripotency, pupa, R3 growth stage, seedling, vegetative stage

Disease

• Description: Name of diseases diagnosed

• Format: Can include multiple diagnoses. Controlled vocabulary from (1) Human Disease Ontology or (2) MeSH

Disease stage

• Description: Stage of disease at the time of sampling.

Ethnicity

• Description: Ethnicity of the subject

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.

Health state

• Description: Health or disease status of sample at time of collection

Karyotype

• Description: Karyotype

Phenotype

• Description: Phenotype of sampled organism.

• Format: Controlled vocabulary from Phenotypic Quality Ontology (PATO)

Population

• Description: Applicable for human and plants. Population is a summation of all the organisms of the same group or species, which live in a particular geographical area, and it can also indicate filial generation, number of progeny, or genetic structure

Race

• Description: Race of the subject

Sample type

• Description: Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly

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