When there are many Experiment and Run objects, create metadata XMLs by
using the excel for the DRA metadata and the XML generator. The metadata
can be registered by uploading the Submission/Experiment/Run XMLs in
D-way. Please see Submit metadata by the excel for details.
-M 25: Minimum read length to output is 25 (default is 25)</li>
-E: No sequences starting or ending with >= 10N</li>
–skip-technical: Dump only biological reads</li>
–split-3: Legacy 3-file splitting for mate-pairs: first and second biological reads satisfying dumping conditions are placed in files *_1.fastq and *_2.fastq, respectively. If only one biological read is present, it is placed in *.fastq.</li>
-W: Apply left and right clips</li>
Reads are filtered and trimmed according to above dumping conditions, reads number of fastq is generally less than that of SRA file.Users can generate unfiltered and untrimmed fastq files by using following fastq-dump options.
Add the publication ID, Pubmed ID (recommended) or DOI, to the BioProject referenced by the DRA submission. Contact the BioProject team to add the publication ID.
GEA
Add the publication ID, Pubmed ID (recommended) or DOI, to the GEA metadata IDF by contacting the GEA team.
MetaboBank
Add the publication ID, Pubmed ID (recommended) or DOI, to the GEA MetaboBank IDF by contacting the MetaboBank team.
Please cite accession numbers according to instructions of submitting publications.
Example citation
Nucleotide sequence data reported are available in the DDBJ Sequenced Read Archive under the accession numbers DRXxxxxxx and DRXxxxxxx.
BioSample is descriptive information about the biological source materials, or samples, used to generate experimental data in any of primary data archives.
Please see Sample granularity.
Each SRA Experiment is a unique sequencing library and sequencing method for a specific sample.
Importantly, much of the descriptive information that is displayed in the public record of your data is captured at the level of the DRA Experiment.
SRA Runs are simply a manifest of data file(s) that should be linked to a given sequencing library – no information present in the Run is displayed on the public record of your project.
Note that all data files listed in a Run will be merged into a single SRA archive file (and fastq file for distribution).
MD5 checksums are used by DRA to verify integrity of transmitted data.
MD5 checksum is a 32-character alphanumeric string (example: bf4ac50dcd58bd2860dfac48c7fca348).
Please refer to the this page.
For instance, since DDBJ is a database for nucleotide sequences, we do
not prepare any specific item for amino acid sequence motifs.
However, you can describe such kind of information by using
misc_feature with /note qualifier.
DDBJ only accepts update requests from submitters of the data except publication reference update.
If you are not the submitter you will need permission from the submitter before requesting update.
See Rights and Duties of Submitter
We only accept the request from the original submitter of the entry.
Please contact us from contact form by selecting the item, “Updating Submitted Data” with accession numbers.
Barcoded data files should be demultiplexed prior to submission and a unique BioSample should be created for each barcoded sample; in other words, each BioSample must be linked to one or more unique data files.
If necessary, describe relationship between barcode sequences and samples in the Library Construction Protocol of Experiment as free-text.
Regarding 10x Genomics data in which samples tend to be large number,
please see the GEA Single-cell submission guide.
You can access the public DRA data through https/ftp and in the NIG supercomputer.
You can retrieve the filepath by searching accession numbers in the DDBJ Search.
If you are making update request for large number of entries, or many changes of features/locations/qualifiers due to sequence modification, see followings.
(1) Update information is in common of all entries.
Example: change reference or submitters information, postpone the hold-date, etc..
(2) Contents of corrections are different among entries.
Example: change each clone or gene name of all entries, etc..
(3) Extensive correction of data
Example: change more than 30 features due to the sequence update, etc..
In case of (2) or (3), we would like to know the number of entries, the correction item, etc. to specify the file format for your request.
Contact us in advance from contact form.
In general, we handle update requests within several days but for a large number of entries, it might take us time in updating the data.
Be sure to contact us beforehand when you request the release of data which accompanies correction.
DDBJ does not provide any procedure for a limited disclosure by the password authentication or else.
When you have to show your sequence data submitted with “Hold-Until-Published” status for only particular individuals, you can send as a text file including your sequences to them.
If the referee wish to confirm the condition and/or the descriptions of your sequence submission, you can choose either of the following two procedures;
a) Publish your sequences through DDBJ.
If you do not mind to open your sequences to the public, please send us your request to publicize your submitted sequences with all of accession numbers.
b) Send DDBJ flat files of your submission to the referee, directly
When the submitter requests to us, we send the text file including DDBJ flat files to the submitter. So, please send us your request with all of accession numbers to get DDBJ flat file(s) of your submission. Then, you can forward the text file to the referee.
For once published entries, we can restrict to use the data, if the conditions are right.
In case of the restriction, DDBJ will not include the data in its periodical release and remove from all services under DDBJ.
However, the data is permanently available on getentry queried with its accession number.
※ The rule is not applied, when the data is published by any mistake of INSD.
This policy is written in the document prepared by International Advisory Committee of INSD on Overview of International Nucleotide Sequence Databases Policies as follows;
All database records submitted to the INSD will remain an entry accessible as part of the scientific record. Corrections of errors and update of the records by authors are welcome and erroneous records may be removed from the next database release, but all will remain permanently accessible by accession number.
In addition, there are a number of databases constructed by occasionally using data from INSD.
DDBJ can not support to delete data from such databases. If you are to delete the cited data on other databases, you have to contact managing staff of each database, directly.
DDBJ does not accept any reservation for updating sequence data.
Therefore, in case of updating published data, the data will be
immediately re-distributed after update.
Please select either of following ways.
In this time, canceling the request for update, when you can publish
updated data, contact us again.
Submit the updated data as a new data with hold
date. When the new data is
published, the accession number of the old data will become a
secondary accession number for the new data.
# Please inform us during submitting the new data to link it to the
old data.
In principle, DDBJ can not restore any published data.
See also following item about access restriction.
In principle, you cannot remove your sequence data from DDBJ retrieval system: getentry, if it has already been open to the public (If DDBJ wrongly published your data because of any mistakes, the data should be removed as soon as possible.).
However, if there is some specific reason for removing your sequence data (i.e. some error is found, etc.), we can restrict access to your sequence data.
Please send your request from contact form with the following contents.
Accession numbers:
Reason in brief:
New hold-date: (e.g. 2019/06/25)
If we restrict access to your sequence data and remove it from the public view, then it will no longer be included in homology search services at DDBJ or distributed as a part of the next DDBJ periodical release. However, it may remain in other third party databases, and will still be retrievable in getentry by accession number based queries.
Moreover, our unified database may be copied and redistributed without permission at any other organizations. In case you need to withdraw your entry from such database, we ask you to make request directly to the organization which manages the database.
In principle, following two conditions are required to delete your
sequence data;
The sequence data has not yet been publicized
The accession number of the data has not yet been
published.
Please send your request from contact
form with the following contents in clear
English.
Accession numbers:
Reason in brief:
Just for information, we can restrict access to your sequence data that
have been open to the public, if the conditions are
right.
See also the following item.
It is getentry.
“getentry” is a system for data retrieval by accession numbers, etc.
In general, the sequence data will be available on getentry from the day after processed to release.
If you are not sure to which category your sequence data should be submitted, use Submission navigation.
See the following sites for detail and relationships of data types.
In general, we recommend to use NSSS.
However, since NSSS can not accept all types of sequence data, it may be required to use MSS for your data submission.
See Workflow of the data submission to DDBJ
In general, you can submit amino acid sequences by describing CDS feature for your nucleotide sequences.
However, DDBJ does not accept amino acid sequences only, i.e. without any nucleotide sequences.
In that case, please submit to UniProt, directly.
You can submit amino acid sequences to UniProt through SPIN.
Please contact to datasubs@ebi.ac.uk.
DDBJ can not accept only assembled EST sequences. However, DDBJ can accept EST assembled sequences as TSA with original (i.e. before assemble) sequence data. See also Data Submission form Transcriptome Project.
When original sequence data (primary entries) are generated from Next Generation Sequencers, submit to DDBJ sequence Read Archive (DRA), from traditional sequencers, submit as EST via Mass Submission System (MSS).
Then, DDBJ can accept assembled sequences (both de novo and reference mapping) as TSA through MSS.
In cases of sequences derived by direct molecular isolation from soil, sea water, etc. i.e. a bulk environmental DNA sample by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods, see What is ENV ? – environmental samples.
For description of organism qualifier, see 3. Environmental samples.
Though frequently confused, the term, ‘environmental samples’, does NOT mean “wild type”. If sequences are derived from isolated or cultured organisms, the sequence data are not classified into environmental samples.
Generally, DDBJ do not need any offprint to process your data.
Occasionally, DDBJ may contact the submitter of sequence data to ask sending an offprint, if necessary.
When you kindly describe about using DDBJ on academic papers etc., in
general, please use the latest article for
DDBJ on Nucleic Acids Res. Database issue
as a reference.
However, please note followings.
In case of citation for each sequence record
In general, it is enough to describe accession number for it in your publication.
If you discuss about the data in detail, please use primary
citation for the data as a reference.
In case of citation for each service provided at DDBJ
Basically, please submit every sequence that you have experimentally determined, whatever the resource of genome, mRNA or any others.
In principle, DDBJ accepts submission of experimentally determined sequence in its contiguous structure.
You can describe mRNA feature, CDS feature and so on as annotation for genomic sequence, however, descriptions of mRNA features do not mean “the mRNA sequence is experimentally determined.”, in general.
If you have read mRNA sequences, please submit mRNA sequences to DDBJ. See also Acceptable data for DDBJ.
Yes you can. It ought to be required at ‘instructions to authors’ of most of journals to submit sequence data to DDBJ (, EMBL-Bank or GanBank) before the paper submission.
During submission of sequence data, select status for your REFERENCE as follows.
“Unpublished”; In cases of preparing paper, during paper submission, or you do not prepare any publication.
“In Press”; When your paper is accepted and in press.
Regardless you are to publish academic paper or not, DDBJ accepts your submission of sequence data.
If you have no plan to paper publication, you have to fill following items of REFERENCE.
status: [Unpublished]
year: tentative year (this year), i.e. 2014
title: tentative title to explain your data
ab_name (authors): abbreviation of tentative author(s) (often the same as ab_name of SUBMITTER)
When you change your plan after sequence data submission, i.e. if you publish a paper, contact us from this form to send request with subject “Our paper was published”.
Though there is no requirement to submit sequence data to DDBJ (, EMBL-Bank or GenBank) on the journal, we strongly recommend to submit sequence data to DDBJ for improvement of data availability for readers of your paper.
DDBJ accepts updating requests only from the original submitter of the entry.
Basically, we strongly recommend to describe joint submitters more than two persons, e.g. at least a true worker and an adviser, to avoid lost communication in future.
When sequence data are published, the data will be shared among DDBJ, EMBL-Bank and GenBank. So, it is necessary and sufficient to submit sequence data to either of three data banks only once.
If you submit sequence data to GenBank after submission of the same data to DDBJ, the data will be duplicated. So, do not submit the same data to two or more data banks.
Though some journals instruct to authors to submit sequence data to GenBank, Accession Number is commonly used by all of DDBJ, EMBL-Bank and GenBank to construct INSD.
Nucleotide sequence data related to patent applications are transferred from Japan Patent Office to DDBJ.
So, usually, you do not have to submit such sequence data to DDBJ.
However, if you apply to any other Patent Office, or if you need to publish a paper during patent application, confirm at Patent Office whether you can submit the data to DDBJ or not.
Note that when the sequence data is published from DDBJ, the data becomes a part of the public domain, as “official notice”.
If you submit nucleotide sequence data to DDBJ, you can get NO priority for the data.
DDBJ takes no responsibility for any property or priority issues for patenting. For patent application, you should confirm JPO or some other Patent Offices.
DDBJ does not have any right for the gene nomenclature. Also, DDBJ does
not make any official collaboration with any committee of gene
nomenclature. If there is no particular incident, the descriptions
related to gene nomenclature are described as provided by submitter.
Even if you name a gene during your sequence data submission to DDBJ,
there is no guarantee that the gene name is accepted at research
communities.
In general, you can describe base substitutions by using
variation feature with
replace and
note qualifiers.
In case of using DDBJ Nucleotide Sequence Submission System, select
‘other’ for template.
About format of feature annotation, see F01) polymorphism and
variation at Example of
Submission.
Though you can submit sequence data including SNP (Single Nucleotide Polymorphisms) to DDBJ, the data will not automatically reflect to dbSNP. dbSNP is an independent database from INSDC, operated by NCBI.
For SNP data, we recommend you to submit to dbSNP.
For instance, when the length of sequence is 199035 bp and a CDS feature
is located in the range from 199001 to 100, you should describe the
location of CDS feature as
join(199001..199035,1..100)
See also Description of Location in detail.
At first, please confirm whether The Genetic
Code is appropriately selected or not.
Generally, if /transl_table
qualifier is appropriately described with a number of the genetic code,
the nucleotide sequence is automatically translated to amino acid
sequence according to the genetic code.
In exceptional cases of specific codons (selenocysteine etc.) that is
not followed the genetic codes, describe
/transl_except qualifier,
appropriately.
In case of rare initiation of translation, staring with an amino acid
other than methionine, describe the location of
CDS feature with starting from “<”, operatively indicating 5’end not
complete. And describe brief explanation about the translation mechanism
in /note qualifier.
See Contact person.
If your affiliation was changed after sequencing or when you belong two or more institutes, please describe the most responsible one as a representative.
We cannot answer necessary days to issue accession number(s) because it depends on the contents of your submission.
If you do not receive any email from DDBJ after 5 working days, please contact us from contact form.
In case of using DDBJ Nucleotide Sequence Submission System, please confirm whether you have received a mail from DDBJ with “DDBJ: Web submission completed” in its subject or not. This mail is automatically sent to contact person, when DDBJ accepts your sequence data via Nucleotide Sequence Submission System.
If you have NOT received the mail,
your submission is not yet finished, so, please complete your submission.
If you have received the mail,
please contact us from contact form with contact person E-mail address and Submission ID of your data.
If you have specific ID for your data other than accession number, such as EntryID or any, contact us from contact form with ID and E-mail address of contact person.
In case of uncertain, tell us following items as far as you know, then we will search your data.
Your name
Your affiliation at the time of submission
Your current affiliation
Your mail address at the time of submission
Your current mail address
The date, month and/or year, when you submit your data
Tool that you used to submit your sequence
Your sequence(s) (if many, just a few representatives)
Biological feature of your sequence
When we can not find your data, we will ask you to submit your data as new one.
In general, see the rule of the journal (i.e. Instructions to Authors), and follow it.
At INSDC, we recommend you to describe accession numbers in the footnote on the title page of your paper as following;
Note: Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number(s)—-‘.
It indicates that this data is directly submitted from the submitter. The term is the antonym to “journal scan”. REFERENCE 1 is the information of submitter(s), not general reference.
So, do not describe “Direct Submission” in the title for literature in REFERENCE 2 or after.
If the information of contact person is old or invalid, we may be unable to acknowledge publication of your data or any other important announcement.
Contact us from this form to send request by selecting the subject, “Change the contact person, belonging, institution, etc..”.
In general, you can find accept date
in JOURNAL line of REFERENCE 1 on
DDBJ flat file.
Please note that some old data do not have the description of accept
date.
In case of the meantime of data distribution:
The data may be on the process of data distribution. If you are
unable to retrieve the data longer than a week, please send us an
inquiry including the accession number from contact
form.
In case of not yet confirmed the accession number is published
on a paper or others:
Please let us know the paper or other media in which the accession
number is described.
In case of the data submitted BEFORE January 1, 1998:
The sequence data be still unpublished after hold
date.
In case of 3 or 4, we will check and support it.
Please contact us from contact form by
selecting the item, “Updating Submitted Data” with accession numbers.
See “Why is the hold-date required?”. Please specify the date.
Though DDBJ does not restrict the date, we strongly recommend to specify the date within two years.
If not specified, the data will be published, immediately.
After data submission, you can change the hold date as needed.
Contact us from this form by selecting “Change the hold-date” in [Subject].
DDBJ is functioning as one of the international nucleotide sequence
databases, including EMBL-Bank/EBI in Europe and
GenBank/NCBI in the USA as the two other members.
When DDBJ releases the submitted data, EMBL-Bank and GenBank will load
the data into their own services, respectively.
See Sequence Data Transition.
Note that the data are converted into EMBL-Bank or GenBank format.
In general, the data released from EMBL-Bank or GenBank are loaded into DDBJ services and published from DDBJ within their released date.
The data released from DDBJ are loaded into ENA/EBI and GenBank and published from them within a few days.
However, the data release processes at all three databases may be delayed, because of system maintenance, troubles on the network, or any other reasons. So, we can not specify the temporal differences among them.
The amino acid sequence for CDS feature will be automatically translated from nucleotide sequence according to location and other items, and reflected into /translation qualifier. So, in general, do not enter it.
Nucleotide Sequence Submission System (NSSS) is an interactive application to enter all of items required for your submission on step by step basis.
To use Mass Submission System (MSS), submitters have to make submission files by themselves.
However, since NSSS can not accept all types of sequence data, it may be required to use MSS for your data submission.
You can use Mass Submission System (MSS) not only for many sequences but also for one long sequence with many features (i.e. complete genome with annotation).
There is no limit of the number of sequences to use MSS and, in some cases, it is required to use of MSS by factors other than the number of sequences.
Use Submission navigation.
See Workflow of the data submission to DDBJ
At 6. Template, a) select
‘other’ and click [Input annotation] or b) Click [Upload annotation
file].
Then, you can describe two or more features for each sequence as
follows.
Click [Select Qualifier], check qualifiers in the dialog as needed
and click [Save] button.
Then, you can find input fields for qualifiers on
7.Annotation.
Related to this issue, in case of selecting “other” on 6.
template, you have to specify
some features other than source. So, click [Add feature] and
select some feature on the list.
These errors mean amino acid translation for CDS (protein coding sequence) feature is not appropriate in the 5’ or 3’ end, respectively.
When the CDS feature is not complete (i.e. partial) at 5’ and/or 3’ ends, its location is required to include flag for ‘not complete’.
According to rules on Description of Location, partial sequences should be appropriately specified with flags for 5’ end not complete, “<”, and/or for 3’ end not complete, “>” on its feature location.
location
condition
<1..295
[not start with initiation codon] and [stop with termination codon]
1.. >295
[start with initiation codon] and [not stop with termination codon]
<1.. >295
[not start with initiation codon] and [not stop with termination codon]
For example: partial CDS feature in the range, 1..295
This error message is outputted, because you select
/translation for CDS
feature by dialog of [Select Qualifier]
button.
Generally, since /translation qualifier is automatically created
according to items under CDS feature, do not enter any amino acid
sequence.
So, you can fix the error by removing /translation qualifier.
For your information, /translation qualifier is required only in case
describing with /exception
qualifier.
Typically, /exception qualifier indicates “RNA editing” is occurred on
mRNA. In that case, conceptual amino acid translation of genome sequence
is different from protein product of real mRNA molecules.
For your information, in case of a previously reported organism, the genetic code is automatically specified, by describing Scientific name (/organism qualifier) and /organelle qualifier. If your sequence is derived from an organelle other than nuclei, you have to specify /organelle qualifier to set the genetic code for mitochondrion, chloroplast or some, appropriately.
At first, please save the URL of the page of Nucleotide Sequence
Submission System.
Then, clear cache of the browser and reopen the saved URL.
It is likely to resolve the condition.
If not resolved, confirm if you use either of browsers
Firefox or
Chrome that we recommend to use.
If not, change to Firefox or Chrome and reopen the URL.
If you still have any problem, please contact us with followings from
contact form by selecting the item,
“DDBJ Nucleotide Sequence Submission System”.
You may enter incorrect values for Location
and/or /codon_start of
CDS feature.
If the value of /codon_start is either of “2” or “3”, the location of
CDS feature should be 5’ end not complete.
See Description of Location and modify the
location with flag for “5’ end not complete”, for an example, from
“1..300” to “<1..300”.
When the CDS feature is started with an initiation codon, correct
/codon_start with “1”.
You can modify your inputs on any pages before finishing your submission.
You can go back to each page by clicking either of 1.Contact person, 2.Hold date, 3.Submitter, 4.Reference, 5.Sequence, 6.Template or 7.Annotation in progress bar at upside of pages.
※Caution
After inputting feature annotation on 7.Annotation, if you do either of followings, feature annotation will be removed.
On 5.Sequence, input all of your sequences in multi-FASTA format. We will assign consequent accession numbers for your sequences.
Moving to 7.Annotation, you can enter feature annotation for each sequence at once. Caution
All of following items must be unified for all sequences. You can not specify thenm for each sequence.
Contact person
Hold date
Submitter
Reference
You can select only one template on 6.Template for all sequences. You can not select a template for each sequence.
Though you have not yet enter either
/organism or
/mol_type on annotation table, you
click [Confirm] button.
You must fill mandatory items of annotation (feature, location,
qualifier) before clicking [Confirm] button.
On 7.Annotation, click
[Select Qualifier] button beside ‘source’, and select qualifiers as
needed. Then, click [Edit] button beside entry name and input
/organism and others. Note that it is required to input at least one
feature other than source.
See also 7.Annotation – Organism
name.
If multiple entries are united to an entry, or if an entry is extensively modified after the submission, the responsible data banks may assign a new accession number to it. In these cases, the new accession number is called the primary accession number, and the old accession number(s) is/are called the secondary accession number(s).
In the flat file, the primary accession number is indicated first, then the secondary accession number(s) follows.
Example
ACCESSION AB999999AB888888AB777777
AB999999 – primary accession number AB888888 AB777777 – secondary accession number
You can find the same updated entry with both the primary and the secondary accession numbers, in general.
However, if the old entry with secondary accession number has previously been open to the public, the old one is not removed. So, you can find the old record by getentry.
These three sample attributes describe environmental systems have influences on living organisms.
env_broad_scale
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]
env_local_scale
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]
env_medium
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]
Authentification is by using SSH key not by password.
A private key is pair of a public key registered in a D-way submission account.
A private key file has read permission.
A private key file permission is set as others cannot access. For example, rw——-.
A passphrase for private key is correctly entered.
When transferring data files by using a private key generated in the other operating system, please check format of a private key. Convert private key
Environments and private key formats:
Unix/Mac OS X: Use an OpenSSH-format key. Convert a key in the Windows PuTTY file format into the OpenSSH.
Windows WinSCP: Use a PuTTY-format key. Convert a key in the Unix/Mac OS X OpenSSH file format into the Windows PuTTY format.
When these are correct, because we do not support technical details regarding use of third-party softwares, please refer to websites of softwares or confirm your system administrators whether scp (port 22) is allowed or not.
If the private key access permission is too open, following error will be shown.
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: UNPROTECTED PRIVATE KEY FILE! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Permissions for './private-key-for-auth' are too open.
It is required that your private key files are NOT accessible by others.
This private key will be ignored.
Load key "./private-key-for-auth": bad permissions
test07@ftp-private.ddbj.nig.ac.jp: Permission denied (publickey,gssapi-keyex,gssapi-with-mic).
lost connection
Right-click the private key file and select the property.
Select detailed setting of the security tab.
Disable access permission entry inheritance to enable permission deletion.
Uploaded data files are processed per Run. All files under a Run are
merged into single binary SRA
file
by using SRA
toolkit.
During this conversion, length and format of all reads are checked.
Read names are editted and identifiers (DRR accession number + serial
number) are automatically inserted (example:
DRR000001).
Original read names should be unique in a Run.
A DRR accession number is used as a filename. If the
fastq is selected for the filetype,
read names are replaced with the DRR accession number + serial number. (example:
DRR030615).
When “PAIRED” is selected in Experiment, paired reads are grouped in a Run.
DRA generates fastq from SRA files by using SRA toolkit
and provide sequencing data in both file formats.
More than two fastq files are provided for paired reads. Paired reads
are divided into a file with “_1” (example, DRR000001_1.fastq.bz2) and
“_2” (example, DRR000001_2.fastq.bz2). Reads without pair are provided
in a file without “_1” nor “_2” (example, DRR000001.fastq.bz2).
The E value is computed using the following formula, in which l denotes
the length of the query string, n denotes the number of strings stored
in the database, and S is a score that measures the homology between
nucleic acids or between amino acids. Note that k and m are positive
constants.
E=k*l*n*exp^(－mS)
If the BLAST output results computed using this formula are displayed in
the form 1E-X, this means that the quantity has the value
10-X.
BLAST search results are displayed in descending order of homology score.
There is no way to assign priorities to strings with identical scores, so there is no particular regularity to the order in which such strings are displayed.
If the number of search results shown is fewer than the number specified for the options “Number of Search Results to Display” and “Number of Alignments to Display,” you may increase the number of displayed results by increasing the value of the “Expectation value” under the “Advanced settings” field.
In such a case, try setting the expectation value to an extremely large number such as 10,000.
Note that, if the string is too short (a sequence length of 10 or so), BLAST will frequently be unable to find matches.
The sequence that you
entered was filtered by the BLAST program.
The filtering has the effect
of replacing regions of your input sequence of low structural complexity
with “N” (or “X” for amino-acid sequences). For details on filtering,
see the section “[FILTER](/services/blast-e.html#filter)” in the BLAST HELP. To
disable filtering, select the OFF radio button in the “FILTER” option in
the lower portion of the Settings screen.
Note with caution that setting
this option to “OFF” may result in search times that are longer than
normal.
Search results are displayed in the following order.
1. Precedence table of sequences with high homology scores
1. Homologous sequences and their alignment
1. Parameters and statistics
Note that the symbol “|” in the BLAST search results for nucleotide sequences indicates agreement between nucleotide sequences.
For amino-acid sequences, matching amino acids will be displayed.
The symbol “+” is used to indicate similarities between amino acids.
For further details, refer the original papers on BLAST.
[BLAST Reference](/blast-e.html#reference)
Search results may be accessed via the following URL, which contains a Request ID field.
: http://blast.ddbj.nig.ac.jp/blast/r/**Request ID**
Request ID
: Note that the Request ID will be displayed in the window that appears after transmitting the input. Make sure to note down this.
The format differs from journal to
journal; please ask the publisher.
In your publications, please cite the
original papers for the appropriate tools and state that you used DDBJ
software for searching and analyzing gene sequence data.
Please see the DDBJ home page [References](/services/references-e.html)
about the original papers and other related papers on the DDBJ search
and analysis software.
The DDBJ/EMBL/GenBank data banks share
the sequences stored within each data bank, and in principle all three
data banks should contain the same data. However, due to time delays in
the inter-data-bank sharing of data released by individual data banks,
as well as delays between the time at which data are entered into a data
bank and the time at which the data are reflected in the corresponding
search service, searches conducted using different services at the
similar time on the same day may yield slightly different results. If
you do not obtain the search results that you were expecting, time
delays of this sort are the most likely culprit; however, for cases
requiring a more detailed investigation, please contact the DDBJ via the
“Other general questions” section of the contact portal. In this case,
make sure to specify the following information:
- The name of the search program and/or the URL that you used to
conduct the search.
- The search conditions that you used.
- The date and time at which you conducted the search.
- Accession number of the entry that should have been found.
- URL of the search results.
- Any other relevant information.
Also, please see the sections of this document corresponding to the
following questions.
- [Can not find the sequence data, though the accession number cited
on a
paper.](/faq/en/cannot-find-accession-number-cited-paper-e.html)
- [I am having trouble finding an accession number that should be
publicly available.](/faq/en/cannot-find-data-already-published-e.html)
“Newly arrived DDBJ data (new data that have arrived after a scheduled DDBJ release)” are data made publicly available on the next day of the deadline or after for the most recent DDBJ release. The deadlines for the most recent releases are listed in the text of [the release notes](https://ddbj.nig.ac.jp/public/ddbj_database/ddbj/ddbjrel.txt). For example, if the most recent release were Release 67, then the deadline would be 8/25/2006, as stated below; thus, in this case, “newly arrived DDBJ data” would be data made publicly available after 8/26/2006.
The present release contains the newest data prepared by the DNA Data Bank ofJapan (DDBJ), GenBank (\*), and European Molecular Biology Laboratory/EuropeanBioinformatics Institute (EMBL/EBI) as of August 25, 2006. (This statement comes from the release notes for Rel. 67; the remainder of that discussion is omitted here.)
The services that exist for communicating information about DDBJ are as follows.
Choose whichever resource is most appropriate for your purposes.
- [Official Sites on Social Media](/policies-e.html#third-party-sites )
- [RSS feed](/data-feed-e.html )
- [DDBJ Mail Magazine](/subscribe-ddbj-e.html )
While no limitations are placed on information citations from the DDBJ website, DDBJ is not responsible for websites that cite information from DDBJ or how the cited information is displayed.
When citing information from this website, please clearly indicate that the information has been taken from the DDBJ website.
If possible, please let us know the following information from [contact form](/contact-ddbj-e.html#to-ddbj)
- The website on which the information will be cited (or where image(s) will be reproduced)
- The URL or the image(s) that will be cited
The DDBJ is a database center of nucleotide sequences, so it does not
distribute any clones.
Please contact the submitter of the clone sequence directly.
When all sequencing data files listed in the Run metadata are uploaded to the DRA server, the "Validate data files" button becomes clickable and users are able to start the validation process.If the button remains inactive after submitting metadata ("metadata_submitted"), check the following points.
- Have all data files listed in the Run metadata been uploaded?
- Doesn't data files contain spaces?
- Aren't uploaded files contained in sub-directories?
It is necessary for submitters [to contact the BioSample team](/contact-ddbj-e.html) to request updates and withdrawals as necessary.
You can confirm updated samples by downloding the [attribute tsv](/submission.html#update-biosample) (example, SSUB000001.txt) in the ATTRIBUTES of the D-way BiSample submission page.
Upper limit
: If the sequence is really observed, there is no upper limitation of the sequence length to submit to DDBJ.
However, we can not accept any operationally joined sequence, for example, joining chromosomes. We accept each chromosome sequence, respectively.
For whole genome scale sequences, submit by using [Mass Submission System (MSS)](/ddbj/mss-e.html ) instead of [Nucleotide Sequence Submission System (NSSS)](/ddbj/web-submission-e.html ).
See [Workflow of the data submission to DDBJ](/ddbj/submission-e.html#workflow )
Lower limit
: Since June 2021, when the sequence is less than 100 bp in its length, we will refuse the sequence data submission.
References
: [Is there any case to reject submission to DDBJ?](/faq/en/reject-submission-e.html)
: [Acceptable data for DDBJ](/documents/data-categories-e.html#accept)
: [Not acceptable sequences](/ddbj/sequence-e.html#not_acceptable )
At DDBJ, we do not provide any official services to accept SNV, CGH analysis, microarray, variation and so on.
We assume that you can submit your data at NCBI or EBI.
Please submit to some of followings. If you have any questions, please ask each database, directly.
- [NCBI](http://www.ncbi.nlm.nih.gov/): [Gene Expression Omnibus (GEO)](http://www.ncbi.nlm.nih.gov/geo/), [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/), [dbVar](http://www.ncbi.nlm.nih.gov/dbvar), [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/)
- [EBI](http://www.ebi.ac.uk/): [ArrayExpress](http://www.ebi.ac.uk/arrayexpress/), [European Variation Archive (EVA)](http://www.ebi.ac.uk/eva/), [Database of Genomic Variants archive (DGVa)](http://www.ebi.ac.uk/dgva)
If your data are derived from human subjects, it may be required to submit your data to either of following [controlled access databases](/policies-e.html#human).
- [The database of Genotypes and Phenotypes (dbGaP)](http://www.ncbi.nlm.nih.gov/gap)
- [European Genome-phenome Archive (EGA)](http://www.ebi.ac.uk/ega/)
- [Japanese Genotype-phenotype Archive (JGA)](/jga/index-e.html)
References
: - [After submission of SNP data to DDBJ, will it automatically reflect to dbSNP?](/faq/en/submit-snp-reflect-dbsnp-e.html)
- [How to submit sequence data related to DNA polymorphism?](/faq/en/how-to-submit-dna-polymorphism-e.html)
To get a FASTA format of WGS, TSA, or TLS entries, please use (http://getentry.ddbj.nig.ac.jp/top-e.html)[getentry], specifying the following values.
- ID : Specify the Accession Number.
- Output format : Select **"total nt seq FASTA"** for the result.
- Result : Select one from the following filetype for the output.
- html
- text
- compress (gz)
- Limit : Set an upper limit number of the result.When you specify the Limit "0", there is no upper limit of the data acquisition.
For more information about each value, please see [getenry HELP](/services/getentry-e.html).
In the JGA submission, fields including the Subject ID and Gender are required.
Specifically, that the main variable (e.g., heart disease) and co-variates (e.g., age, weight) used in the analysis are submitted to JGA so that other people can reproduce the information in your publication.
The goal is to include the data that would be required for another researcher to be able to reproduce the published analysis.
For DDBJ nucleotide sequence submission system([NSSS](/ddbj/web-submission-e.html)), you must input nucleotide sequence(s) in FASTA format (for 1 sequence only) or in multi-FASTA format (for 2 or more sequences).
Related page: [Format of the nucleotide sequences that you can paste or
upload](/ddbj/web-submission-help-e.html#flow-5-1)
You must insert the end flag (//) at the end of each sequence when you use MSS for the submission. Please see the page, ["How to Make Sequence File"](/ddbj/file-format-e.html#sequence).
See also [Wikipedia, FASTA format](https://en.wikipedia.org/wiki/FASTA_format)
**Subject** ： Select from the following items.
- Our paper was publishied
- Our paper was accepted
- Change the hold-date
- Change discription about the contact person
**To** ： [Data updates /
Corrections](mailto:ddbjupdt@ddbj.nig.ac.jp) (click the service name to
send an e-mail)
**Body** :(\* Required)
\[For all subjects\]
: Applicant Name\*
: Applicant Email address\*
: Contact person Name（When you are not contact person, please input
this item.）
: Contact person Email address（When you are not contact person, please
input this item.）
: Accession Numbers\*
\[Our paper was publishied\]
: Paper Title \*
: Paper All authors \*
: Paper Journal \*
: Paper Volume
: Paper Issue
: Paper Start page - End page
: Paper Year
: Paper URL
: Paper PubMed ID
: Paper DOI
\[Our paper was accepted\]
: Paper Title \*
: Paper All authors \*
: PaperJournal \*
: Paper Volume
: Paper Issue
: Paper Start page - End page
: Paper Year
: Paper URL
: Paper PubMed ID
: Paper DOI
: When will you release the data?（Select from the following
items.）\*
- Release immediately
- Specify the hold-date → Please specify the hold-date
\[Change the hold-date\]
: New hold-date（Select from the following
items.）\*
- Release immediately
- Specify the hold-date → Please specify the hold-date
\[Change discription about the contact person\]
: Name ( Current )
: Name ( Update )
: Email address( Current )
: Email address( Update )
: Institution ( Current )
: Institution ( Update )
: Address ( Current )
: Address ( Update )
: Phone ( Current )
: Phone ( Update )
: FAX ( Current )
: FAX ( Update )
\[For all subjects\]
: Message
Mutual data exchange between [NCBI
GEO](https://www.ncbi.nlm.nih.gov/geo/) and
[ArrayExpress](https://www.ebi.ac.uk/arrayexpress/) is not realized so
GEA data are not shared with GEO. ArrayExpress had been imported GEO
data, however, this import was suspended.
BioProject and BioSample registered during GEA submission are exchanged
with NCBI/EBI in the framework of INSDC.
No. Both annotation and sequence files are necessary for an MSS submission.
Please visit the following sites for detailed instructions to prepare submission files.
- [Sequence file](/ddbj/file-format-e.html#sequence)
- [Annotation file](/ddbj/file-format-e.html#annotation)
- [Sample annotation file](/ddbj/file-format-e.html#sample)
By using the [GEA reviewer access](/gea/reviewer-access-e.html), you can provide metadata, microarray data and NGS processed data to reviewers.
Reviewer access services are not available in [DRA](/dra/index-e.html), [DDBJ](/ddbj/index-e.html) and [JGA](/jga/index-e.html).
For DDBJ, see ['On the process of submission of a paper to a journal, we have to show the referee our nucleotide sequence submitted as "Hold-Until-Published" status'](/faq/ja/paper-show-referee-e.html).
For DRA, you may send a metadata summary list attached to the accession number notification e-mail. For sequencing data, download [archived fastq files](/dra/overview-e.html#fastq-sra-files) and provide them to reviewers through access-controlled file sharing services or servers.
For JGA, we can not offer the reviewer access service due to [the policy](https://humandbs.biosciencedbc.jp/faq#faq-20).
For open-access GEA/DRA/DDBJ/MetaboBank, if you make your data public, all users including reviewers can access the data.
Confirm the following points.
- Authentification is by using SSH key not by password.
- A private key is pair of a public key registered in a D-way account. [Manual](/account-e.html#enable-dra-submission-in-account)
- Make sure to specify a private key for authentification and not a private key for dataset encryption/decryption. [Manual](/jga/download-e.html#data-use-approval-download)
- A private key file has read permission.
- A private key file permission is set as others cannot access. For example, rw-------.
- A passphrase for private key is correctly entered.
- The ssh connection with the port number 443 is allowed in your network (Please ask your network administrator)
When transferring data files by using a private key generated in the other operating system, please check format of a private key. [Convert private key](/account-e.html#convert-private-key)
- In Unix/Mac OS X: Convert a key in the Windows PuTTY file format into the OpenSSH.
- In Windows WinSCP: Convert a key in the Unix/Mac OS X OpenSSH file format into the Windows PuTTY format.
When these are correct, because we do not support technical details regarding use of third-party softwares, please refer to websites of softwares or confirm your system administrators whether ssh (in the case of JGA, port 443) is allowed or not.
Because the [DDBJ Trace Archive](/dta/index-e.html) will be integrated to SRA,
we do not accept sequencing traces (chromatograms).
Please submit fastq files (bases and quality values) to DRA by choosing a Genetic Analyzer series instrument in the DRA Experiment [Instrument Model](/dra/metadata-e.html#Instrument).
Please cite accession numbers according to journal instructions.
It is recommended to cite accession numbers assigned to your data submissions, e.g. the DDBJ nucleotide sequence or DRA Run accession numbers.
Please cite a BioProject accession to reference all data from the project. It is necessary that metadata are described to enable users understand relationship between data in the publication and in the databases.
## DDBJ {#ddbj}
Cite accession number(s) assigned to nucleotide sequence(s).
[Prefix Letter List](/prefix-e.html)
## DRA {#dra}
Cite Run accession number(s) (prefix DRR) assigned to sequencing reads. [Metadata](/dra/metadata-e.html)
Please cite a BioProject accession to reference all data from the project. It is necessary that metadata are described to enable users understand relationship between data in the publication and in the databases.
Because data cannot be added to existing DRA submission, more than one DRA submission accessions will be created after data addition ([Update](/dra/update-e.html)). Therefore, citing DRA submission accessions (prefix DRA) is not recommended. Instead, we recommend to cite a BioProject accession.
## GEA {#gea}
Cite Experiment accession "E-GEAD-n".
[GEA Accession](/gea/overview-e.html#acc)
## MetaboBank {#metabobank}
Cite Study accession "MTBKSn".
[MetaboBank Accession](/metabobank/submission-e.html#accession)
## BioProject {#bioproject}
If an individual BioProject needs to be referenced, state that "The data have been deposited with links to BioProject accession number PRJDBxxxxxx in the DDBJ BioProject database." along with the accession numbers assigned to the data submissions.
## BioSample {#biosample}
If an individual BioSample needs to be referenced, state that "BioSample metadata are available in the DDBJ BioSample database under accession number SAMDxxxxxxxx".
If you want to release your data, specify DDBJ/DRA/GEA/MetaboBank accession numbers to be released. When only BioProject accession is informed, only the BioProject record is released and related data are not released. Similarly, when only BioSample accession is informed, only the BioSample record is released and related data are not released.
DDBJ/DRA/GEA/MetaboBank data release triggers relase of referencing BioProject and BioSample.
FAQ: [How are linked BioProject/BioSample/sequence data released?](/faq/en/bp-bs-seq-release-e.html)
## DDBJ {#ddbj}
Inform accession number(s) of nucleotide sequence(s) to be released through the [update form](/ddbj/update-form-e.html).
## DRA {#dra}
Login D-way and [release DRA data by yourself](/dra/submission-e.html#change-hold-date).
## GEA {#gea}
Inform GEA Experiment accession number (E-GEAD-n) or Submission ID (e.g., ESUB000001) to be released through the [contact form](/contact-ddbj.html).
## MetaboBank {#metabobank}
Inform MetaboBank Study accession number (MTBKSn) to be released through the [contact form](/contact-ddbj.html).
## BioProject {#bioproject}
Inform BioProject accession number (e.g., PRJDB1) or Submission ID (e.g., PSUB000001) to be released through the [contact form](/contact-ddbj.html).
When only BioProject accession is informed, only the BioProject record is released and related data are not released.
## BioSample {#biosample}
Inform BioSample accession number (e.g., SAMD00000001) or Submission ID (e.g., SSUB000001) to be released through the [contact form](/contact-ddbj.html).
When only BioSample accession is informed, only the BioSample record is released and related data are not released.
For sequence data related to the [Barcode of Life project](https://ibol.org/), submit nucletide sequence(s) to [DDBJ](/ddbj/index-e.html).
Because all data in [Trace Archive](https://trace.ncbi.nlm.nih.gov/Traces/trace.cgi?view=list_arrivals) will be migrated to [SRA](https://www.ncbi.nlm.nih.gov/sra), [DDBJ Trace Archive](/dta/index-e.html) no longer accepts trace data.
You may submit fastq files from Sanger-type sequencers to [DRA](/dra/submission-e.html). Submit fastq files and select a Sanger-type sequencer in the Experiment [Instrument Model](/dra/metadata-e.html#Instrument).
### Header must be enter with sample name {#header}
If you upload an Excel file instead of a tab-separated text (tsv) file, an error will occur.
If you are uploading a tsv file, please fill in the sample information from the second line, one sample per line.
Please refer to the [example of BioSample submission files](https://docs.google.com/spreadsheets/d/1zVgr1JWDVsHwotDBfhhp32KCp8cKCv83UQ3Hygmcewg/edit#gid=726659595).
For other messages and validation rules, please see the [Validation rules page](/biosample/validation-e.html) and upload the revised file.
The BioProject/BioSample/DRA/GEA systems have been migrated to new supercomputer at 28th September 2021.
Due to this migration, access to ftp-private.ddbj.nig.ac.jp may be blocked by the remote host key identification warning.
```
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: POSSIBLE DNS SPOOFING DETECTED! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
The RSA host key for ftp-private.ddbj.nig.ac.jp has changed,
and the key for the corresponding IP address 133.39.224.111
is unknown. This could either mean that
DNS SPOOFING is happening or the IP address for the host
and its host key have changed at the same time.
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
SHA256:MQi8isve0moRNQj/9z73dZy6lBcprrd5p87ynoznZ3o.
Please contact your system administrator.
Add correct host key in /home/test07/.ssh/known_hosts to get rid of this message.
Offending RSA key in /home/test07/.ssh/known_hosts:11
remove with:
... snipped ...
RSA host key for ftp-private.ddbj.nig.ac.jp has changed and you have requested strict checking.
Host key verification failed.
lost connection
```
Delete a line where "ftp-private.ddbj.nig.ac.jp" or the IP address "133.39.224.111" are recorded from the known_hosts file under your home directory (for example, test07).
/home/test07/.ssh/known_hosts
You may know the line number to be deleted from the warning message (example below is 11).
```
Offending RSA key in /home/test07/.ssh/known_hosts:11
```
After deleting the line of the known_hosts file, access to the server.
Because the access is regarded as a first time access, you are asked whether record the server key or not. Please select "yes" and access the server.
Use the following taxonomy IDs for non-organism samples commonly used for metabolomics experiments.
* [blank sample (taxid: 2582415)](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2582415)
* [unidentified (taxid: 32644)](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32644)
We have stopped to generating fastq files from mirrored NCBI/ENA SRA data to save storage spaces since 11th December 2019. We have generated and will generate fastq files of DRA data.
* NCBI SRA: sra file only
* ENA SRA: sra and fastq files
* DDBJ SRA: Before 10th December 2019, sra and fastq files. After 11th December 2019, fastq of DRA only.
| Archive | sra files | NCBI SRA fastq | ENA SRA fastq | DDBJ SRA fastq |
|---|
| NCBI SRA | O | X | X | X |
| ENA SRA | O | O | O | O |
| DDBJ SRA | O | X (since 2019-12-10) | X (since 2019-12-10) | O |
For NCBI/ENA SRA data whose fastq files are not generated, you may obtain the fastq as follows.
### Download from ENA {#ena}
If ENA has generated fastq of the Run of your interest (for example, ERR3350433), you may download the fastq from ENA.
[ERR3350433](https://www.ebi.ac.uk/ena/browser/view/ERR3350433?show=reads)
Download fastq from ENA
### Generating fastq from DRA mirrored sra file {#dra}
Search the Run in [DDBJ Search](https://ddbj.nig.ac.jp/search?query=%22ERR3350433%22).
Example; [ERR3350433](https://ddbj.nig.ac.jp/resource/sra-run/ERR3350433)
Download the sra file from DRA
sra filepath;
* https://ddbj.nig.ac.jp/public/ddbj_database/dra/sralite/ByExp/litesra/ERX/ERX337/ERX3374941/ERR3350433/ERR3350433.sra
* ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/ERX/ERX337/ERX3374941/ERR3350433/ERR3350433.sra
Please see [How to use prefetch and fasterq-dump to extract FASTQ-files from SRA-accessions](https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump) regarding how to generate fastq from sra.
If you decrypt JGA data by using a PuTTY-format private key, an "Unable to load Private Key" error will be shown.
[Convert a PuTTY-format private key into an OpenSSH-format key](/account-e.html#convert-private-key) and use the OpenSSH-format private key.
Both OpenSSH and PuTTY format public keys can be registered in NBDC data use applications, you do not need to convert the registered public key format.
It is common to analyze non-living material samples in metabolomics experiments. For these samples, choose an appropriate name from [metagenomes](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock) of NCBI Taxonomy (please think excluding metagenome). Here are a few examples.
* food sample: [food metagenome](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870726&lvl=3&lin=f&keep=1&srchmode=1&unlock)
* soil sample: [soil metagenome](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=410658&lvl=3&lin=f&keep=1&srchmode=1&unlock)
For some non-living samples, please use names other than [metagenomes](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock).
* blank measurement: "[blank sample](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=blank+sample)"
* reference compound: "[unidentified](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=32644)"
### Samples are metabolically labeled by isotopes
When samples are labeled by metabolically uptaking stable isotopes (metabolic isotope labeling), describe isotope-labeled compounds in the “isotope_labeled_compound” attributes of BioSample records. Stable isotopes are described in the “isotope” attributes.
* isotope_labeled_compound=[U-13C]-glucose
* isotope=13C
In the SDRF rows correspond to the samples, describe the compounds and isotopes in the Characteristics columns.
|Characteristics[isotope_labeled_compound]|Characteristics[isotope]|
|[U-13C]-glucose|13C|
In this case, isotopes are described at sample-level, so the Labeled Extract Name and Label column values can be left empty.
### Extracted metabolites are chemically labeled by isotopes
When samples are chemically labeled by isotopes (chemical isotope labeling), describe isotopes in the SDRF Label column and isotope-labeled compounds in the Comment[isotope_labeled_compound] column.
|Labeled Extract Name|Label|Comment[isotope_labeled_compound]|
|human urine sample 1 12C|12C|12C-dansyl chloride|
|human urine pooled sample 13C|13C|13C-dansyl chloride|
In this case, isotopes are described at the extract-level, so BioSample records may not contain attributes for isotopes.
If a public SRA Run is replaced by a new Run, the previous accession will be a secondary accession of the new one to track replacement.
For example, when DRR046787 was replaced by DRR049544,
DRR049544 became primary and DRR046787 became secondary accession (below is the DRR049544 Run XML).
```
DRR049544DRR046787454 GS Junior sequencing of SAMD00041397
```
DRR049544 is displayed when searching DRR046787 at NCBI SRA ([https://ncbi.nlm.nih.gov/sra/DRR046787](https://ncbi.nlm.nih.gov/sra/DRR046787)) .
In the NCBI SRA Run Browser, the secondary DRR046787 is displayed in small characters with the primary DRR049544 ([DRR049544](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=DRR049544&display=metadata)).
Here is an example of how to find an appropriate attribute to describe "transplant recipient tissues".
### NCBI BioSample
If you have some idea, you may grasp the overview by seeing attribute name and their numbers in the NCBI BioSample [Advanced Search Builder](https://www.ncbi.nlm.nih.gov/biosample/advanced).
Select "Attribute Name" for the field name and input "transplant", then names and their numbers are displayed. You may find most used name. If you want to see BioSample records using the name, select the name and search.
{% include image.html url="faq/ncbi-bs-advanced.jpg" caption="Advanced Search Builder" class="w600" %}
### BioSample dump file
Download the BioSample XML file which contains all public records.
```
wget https://ddbj.nig.ac.jp/public/ddbj_database/biosample/biosample_set.xml.gz
```
Search attribute names and values by using grep.
```
grep "attribute_name=\"transplant" biosample_set.xml
intertidalsubtidalsubtidalintertidalnon-targeting scramble shRNA control MLL-AF9 primary AMLnon-targeting scramble shRNA control MLL-AF9 primary AMLCdkn1b specific shRNA expressing MLL-AF9 primary AML
...
```
For ancient DNA samples, the location and date reported depends on when the sample was collected with the intention of sequencing.
If the sample was from a museum, the location of the museum and time of collection should be provided. This indicates the sample collection event with the intention of sequencing. In this case, if known, the original geographic location and original collection date can optionally also be provided.
If the sample was from an archaeological site, the location of the site and the time of that collection event should be provided.
This is considered a valid exemption as we recognise that some consortia will have agreements that pre-date the new standard and you can report this as a reason that the metadata are missing.
In this case, during initial sample registration you would report:
* geo_loc_name (or /country) = missing: data agreement-established pre-2023
* collection date = missing: data agreement-established pre-2023
Submissions can be updated at a later date to include the missing metadata.
We recognise there may be valid exemptions for this which are included for missing value reporting. For example, you may have collected a control sample from a collection instrument to sequence a negative control. In this case, the location of where you collected that control is not applicable to report as it was prepared in a lab but you could report the date in which you collected the control sample.
In this case, you would report:
* geo_loc_name (or /country) = missing: control sample
* collection date = 2020-05-25
You should report the collection date in the format year-month-day followed by the time in ISO8601 standard format. Collection times must be in Coordinated Universal Time (UTC). You should report the country and the region in an related field. For example:
* geo_loc_name (or /country) = Japan:Shizuoka
* collection date = 2023-05-05T05:12:55
For species originating elsewhere to where the sample was physically collected for sequencing e.g. species in a museum, zoo, aquaculture, botanic garden or farm, the collection location is still useful information and the collection date and geographic location (country and/or sea) provided should reflect the collection event when the sample was collected for sequencing purposes. This means that for these kinds of samples, the location of the museum, zoo, aquaculture, botanic garden or farm should be provided. In these cases, if there is a known origin elsewhere, submitters should also report the origin of the sample with the fields original geographic location and original collection date.
The minimum requirement is the name of the ocean/sea (or country) of the collection event and date to the nearest year. In this case, as you know the ocean and the year of collection, there is no reason that you can not share these metadata. You would report:
* geo_loc_name (or /country) = Pacific Ocean
* collection_date = 2010
