Identifiers

The organism names (values of /organism qualifier) are required to submit your sequence data.
If you do not identify the species of the organisms, or if you need to submit a large number of sequences from the same species, it may be required to use some identifiers of the sample organisms for your sequence data.

For many cases of bacteria, yeasts, and other microorganisms, especially to submit whole genome sequences of the microorganisms, you may need to add identifiers of strains and/or culture collections for the organisms.
Further, when you propose a new species name, you have to deposit the organism to two or more culture collections.

Type of Idetifiers

There are two types of identifiers that are acceptable for us.

Assign to the Sample Organisms

In general, we expect you to use this type of identifier.
A typical case is to use the /strain qualifier. The other qualifiers would be /isolate, /culture_collection, /ecotype, /specimen_voucher, /cultivar, /bio_material, /cell_line, and so on.

Assign to the Sequences

This type of identifier is operatively described. In cases of your research purpose, you may need to use this type of identifier.

The typical ones are /clone and /submitter_seqid qualifiers.
Also, /isolate qualifiers for OTU of environmental samples, /bio_material qualifiers in some conditions would be assigned to the sequences.

For using every identical sequence, /haplotype qualifier is also corresponding to the case. For submitting data related to population genetics, see Representative submissions of identical sequences for variation studies.

Format of Identifiers

All sample identifiers must be distinct from each other.
Identical samples should be indicated with the same identifier.
In cases of commercial samples, model strains and any other official names, you should use them ‘as is’.
- For /bio_material, /culture_collection and /specimen_voucher qualifiers, we have the formats to enhance their traceability, so, please follow the formats.
When you isolate the sample organisms, please name them by yourself.
- Please note that “1”, “2”, “A”, “B” , or something like them are too simple to keep uniqueness among the data submitted from many researchers, in advance.
- For example, to make it easier keeping uniqueness by adding acronyms of geographical names of collection sites or the initials of the person who collected samples and the collected years to serial numbers,
  i.e. [serial number]-[acronym of geographical name]-[collected year], “1-MS-2021” etc.
- We strongly recommend that you do not include the name of an organism or the abbreviation of an organism name in the sample identifier.

Please note we do not systematically manage the identifiers of samples. So, at least, it is required to assign unique names within your submissions for your study.

In Detail about Identifiers

Situations where the identifiers not required

When your samples meet all of the following conditions, it is not required to use identifiers for your samples.
Please note we do not intend to prohibit using identifiers for your samples, so, we will accept the identifiers of your samples if you need.

Sequences derived from multicellular organisms
Aimed to study neither of identifying species, biogeography, epidemiology, population genetics or the like.
Aimed to study identifying and/or functional analysis genes/proteins and so on to describe general features of the subject organisms.

Bacteria or Archaea

Some identifiers are required regardless of the taxonomic identification level of the organisms or the number of sequences.

For the pure cultured lines that are expected to be genetically uniform, use /strain qualifier
For cultured strains deposited to or divided from culture collections, use /culture_collection qualifier
In cases difficult to call the pure cultured lines, use /isolate qualifier

Fungi

In cases of unicellular organisms like yeasts, some identifiers are required regardless of the taxonomic identification level of the organisms or the number of sequences.

For the pure cultured lines that are expected to be genetically uniform, use /strain qualifier
For cultured strains deposited to or divided from culture collections, use /culture_collection qualifier
In cases difficult to call the pure cultured lines, use /isolate qualifier

In cases of multicellular organisms like mushrooms, some identifiers may be required when the species is not identified or when you submit many sequences from multiple individuals of the same species.

For the identifiers of individuals, use /isolate qualifier
For specimens deposited to or divided from museum/collections, use /specimen_voucher qualifier
For the pure lines that are expected to be genetically uniform, /strain qualifier

Plants

In cases of unicellular organisms like algae, some identifiers are required regardless of the taxonomic identification level of the organisms or the number of sequences.

For the pure cultured lines that are expected to be genetically uniform, use /strain qualifier
For cultured strains deposited to or divided from culture collections, use /culture_collection qualifier
In cases difficult to call the pure cultured lines, use /isolate qualifier

In cases of multicellular organisms, some identifiers may be required when the species is not identified or when you submit many sequences from multiple individuals of the same species.

For the identifiers of individuals, use /isolate qualifier
For specimens deposited to or divided from museum/collections, use /specimen_voucher qualifier
For variants phenotypically/geographically distinguished, but not yet subspecies, use /ecotype qualifier
For cultivated varieties, use /cultivar qualifier
For the pure lines that are expected to be genetically uniform, use /strain qualifier

Animals

In cases of unicellular organisms like protists, some identifiers are required regardless of the taxonomic identification level of the organisms or the number of sequences.

For the pure cultured lines that are expected to be genetically uniform, use /strain qualifier
For cultured strains deposited to or divided from culture collections, use /culture_collection qualifier
In cases difficult to call the pure cultured lines, use /isolate qualifier

In cases of multicellular organisms, some identifiers may be required when the species is not identified or when you submit many sequences from multiple individuals of the same species.

For the identifiers of individuals, use /isolate qualifier
For specimens deposited to or divided from museum/collections, use /specimen_voucher qualifier
For breeded varieties, use /note qualifier with “breed:” prefix.
For pure or congenic lines of model organisms, use /strain qualifier
For mutated strains of model organisms, use /bio_material qualifier
For immortalised cell lines deposited to or divided from collections, /cell_line qualifier

Human Subjects

For the data derived from human subjects, description of individual identifiers may be needed to report polymorphisms or so.
Even in these cases, the identifiers must be anonymized. We prohibit using any personal names or any identifiers that enable inferring personal names.

For the identifiers of individuals, use /isolate qualifier
For immortalised cell lines deposited to or divided from collections, use /cell_line qualifier

Viruses

Usually, we recommend using /isolate qualifiers for viral data.
For frequently submitted pathogenic viruses like SARS-CoV-2 and Influenza virus, we strongly recommend you using /isolate qualifiers with the identifiers in the following format recommended by ICTV.

Format: [virus_type]/[host_common_name]/[locality_name]/[sample_identifier]/[year]
Example: SARS-CoV-2/human/Japan/A12/2021

`virus_type`	the abbreviated name, genotype or type of the virus
`host_common_name`	the common name of the viral host organism indicated in /host qualifier
`locality_name`	the name of country or region of the collection site indicated in /geo_loc_name qualifier
`sample_identifier`	any identifiers/numbers assigned by the submitters or the collectors
`year`	the year of the sampling date indicated in /collection_date qualifier

Though it is difficult for viruses to confirm the pure lines without culture by infected cells, we conventionally accepted /strain qualifiers for viral sequences.
However, we recommend using /isolate qualifiers.
Please note that a genotype (or genogroup etc.) is similar to species/lineage of virus, so, it cannot be sample identifiers.

Environmental Samples

In general, please describe /isolate qualifiers as names of individuals or OTUs.
You can not use /strain qualifiers for environmental samples.
When you have cloned the corresponding DNA samples, describe the clone names in /clone qualifiers.

Organism Names (/organism qualifier) and Identifiers

When you describe the organism names in species, subspecies, varieties or lower levels, it is not required to include any identifiers into the organism names.
However, please pay attention to the following cases.

Bacteria, Archaea, or Unicellular Fungi

In cases of unicellular organisms, it is not required to include any identifiers in organism names regardless of the taxonomic identification level.

When you propose a new species, it is recommended to include some identifier such as strain name in organism name.
In cases of cyanobacteria, it is required to include some identifiers such as strain names in organism names.
To submit whole-genome-scale sequences of microorganisms, etc., currently, if the species has not yet been identified, it is a general rule to include strain, etc. in the organism name.
Previously, regardless of species identification, it is required for genome-wide sequence submissions to include strain names, etc. in the organism names.

Animals, Plants, or Multicellular Fungi

In cases of multicellular organisms, it is required to include some identifiers in organism names when the species is not identified or when you propose new species.
The identifiers included in organism names do not have to be assigned to every individual, so you should assign an identifier in each unit that is considered to be the same species.

Viruses

Different from other domains, descriptions like scientific names can be accepted during species proposing.
In that case, we recommend to include some identifiers into the virus names.
By 2017, we used informal names for frequently submitted pathogenic viruses including their strain names and serotypes in the description of organism names. However, the rule has been discontinued for future submissions.

Environmental Samples

For most cases, the species names of the organisms can not be identified, however, it is not required to include any identifiers into the organism names.