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<h1 id="updating-information-on-genbank-">Updating Information on GenBank TSA submissions</h1>
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<p>The following information provides the different methods to submit updates for TSA records in order to ensure that your update is processed quickly and correctly. Updates provided in an incorrect format will delay processing. All update files should be saved as plain text. If you are updating multiple records, send a list of all accessions to be updated at the top of your request.</p>
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<p>Please check the status of your submission in the TSA Submission Portal before preparing an update and follow the instructions below. Update formats for <a href="#Queued">Queued</a>, <a href="#Queued">Processing</a>, and <a href="#Proc">Processed</a> submissions are provided below.</p>
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<h2 id="update-formats">Update Formats</h2>
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<h3 id="Queued">[1] Queued or Processing Status</h3>
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<p>[a] Updating Source Information:</p>
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<p>If you are changing the organism name then provide the following in an email to gb-admin@ncbi.nlm.nih.gov:</p>
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<ul>
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<li>TSA submission ID or accession number</li>
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<li>Revised organism name</li>
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<li>BioSample accession</li>
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<li>BioProject accession</li>
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</ul>
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<p>If you are updating source information other than the organism name then update your BioSample by sending an email to biosamplehelp@ncbi.nlm.nih.gov.</p>
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<p>[b] Updating Publication Information:</p>
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<p>Publication information can be sent in the text portion of an email to gb-admin@ncbi.nlm.nih.gov. Please provide the PubMedID, if one has been assigned. Otherwise, replace any non-ASCII characters (for example, characters with accents and umlauts) with the appropriate English letters and provide the journal name and paper title. Provide the authors in a 2-column table with the accession number in column 1 and the author names listed as " given_name middle_initial surname" in column 2, where the middle_initial is optional. For example:</p>
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<pre><code>GABC00000000 Thomas Smith, Robert T. Jones, Susan Zhu, Nature Genetics Transcriptome sequence of the ABCD organism
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</code></pre>
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<p>[c] Updating the Assembly:</p>
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|
<p>If you are updating sequences, removing/adding sequences, removing/adding annotation then send an email to gb-admin@ncbi.nlm.nih.gov with the TSA Submission Portal submission ID requesting the status be set to Error. You may then upload a revised file using the Fix button. You must resubmit the entire assembly not just the parts you are changing.</p>
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<h2 id="Proc">[2] Processed Status</h2>
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<p>[a] Updating Source Information:</p>
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|
|
<p>If you are updating the source information for a processed submission then you should send the revisions in the text portion of an email to gb-admin@ncbi.nlm.nih.gov. You should also include the BioSample and BioProject accession numbers in your update request. Send the updates in a multi-column tab-delimited table, See <a href="https://www.ncbi.nlm.nih.gov/Sequin/modifiers.html">https://www.ncbi.nlm.nih.gov/Sequin/modifiers.html</a> for a list of valid qualifiers. For example:</p>
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|
|
<pre><code>acc. num. strain geo_loc_name
|
|
XXXX00000000 82 USA
|
|
XXXX00000000 ABC Canada
|
|
</code></pre>
|
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|
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<p>[b] Updating Publication Information:</p>
|
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|
|
<p>Publication information can be sent in the text portion of an email to gb-admin@ncbi.nlm.nih.gov. Please provide the PubMedID, if one has been assigned. Otherwise, replace any non-ASCII characters (for example, characters with accents and umlauts) with the appropriate English letters and provide the journal name and paper title. Provide the authors in a 2-column table with the accession number in column 1 and the author names listed as " given_name middle_initial surname" in column 2, where the middle_initial is optional. For example:</p>
|
|
|
|
|
|
<pre><code>GABC00000000 Thomas Smith, Robert T. Jones, Susan Zhu, Nature Genetics Transcriptome sequence of the ABCD organism
|
|
</code></pre>
|
|
|
|
|
|
<p>[c] Adding contigs to an existing transcriptome:</p>
|
|
|
|
|
|
<p>If you are adding contigs to an existing assembly then create a new submission in the TSA Submission Portal. Please note that the new contigs must be derived from the same assembly. Please answer "Yes" to the Submission Portal inquiry "Is this an update of an existing submission?" on the General Information page. Please also explain why you are adding contigs to your previous assembly in the "Private comments to NCBI staff" field. Upload a file containing only the new contigs.</p>
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|
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<p>[d] A new assembly of the transcriptome:</p>
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|
|
|
|
<p>If you have generated a revised assembly using the same primary date, then create a new TSA submission in the TSA Submission Portal. Answer "Yes" to the submission portal inquiry "Is this an update of an existing submission?" on the General Information page. Also include a note that this is the next version of XXXX00000000 in the "Private comments to NCBI staff" field. Upload a file containing the complete revised assembly.</p>
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|
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<p>The pieces will be assigned new accession numbers and the master accession will increment to the next version, eg XXXX01000000 would update to XXXX02000000. For more information about TSA accession numbers see <a href="https://www.ncbi.nlm.nih.gov/genbank/tsa/">https://www.ncbi.nlm.nih.gov/genbank/tsa/</a>.</p>
|
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|
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<p>[e] Update features on an assembly without annotation:</p>
|
|
|
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|
|
<p>If the TSA submission has been released a new submission should be created in the submission portal. Please answer "Yes" to the Submission Portal inquiry "Is this an update of an existing submission?" on the General Information page and include the accession number as directed. In the "Private comments to NCBI staff" field explain that you are adding annotation to an existing submission. Your updated submission will be the 02 version of the TSA project and the new assemblies are given new accession numbers beginning with XXXX02000001.</p>
|
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|
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<p>[f] Update features on an assembly with annotation:</p>
|
|
|
|
|
|
<p>If you are updating many features of a record, let us know, and we can send you a tab-delimited 5-column Feature table with the current annotation for you to edit and return to us.</p>
|
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|
|
<p>Please contact us at <a href="mailto:gb-admin@ncbi.nlm.nih.gov">gb-admin@ncbi.nlm.nih.gov</a> if you have questions about updating your TSA submission.</p>
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