Metagenome or environmental

Mandatory Attributes Source Group Attributes Optional Attributes

Mandatory Attributes

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”

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

Source Group Attributes

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

Isolation source

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

Optional Attributes

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

Reference for biomaterial

• Description: Primary publication or genome report

• Format: PubMed ID, or DOI (Digital Object Identifier), or URL

Relationship to oxygen

• Description: Aerobic or anaerobic

• Possible value: Select on from the controlled vocabulary

• Controlled Vocabulary: "aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"

Sample collection device or method

• Description: Method or device employed for collecting sample

Sample material processing

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

Sample size

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

Sample type

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

Source material identifiers

• 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

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