Updating XMLs

It is possible to update any SRA metadata object. The only exception to this rule is that submitted run objects can't be made to point to different data files. For updating an SRA object, you need a submission XML document with MODIFY actions pointing to the updated SRA objects.

Preparing Submission XML for update

To update SRA objects, you must use the MODIFY action instead of ADD action. The MODIFY action should point to XML documents containing SRA objects to be updated. When MODIFY action is given it is verified that the SRA objects being updated must already have been accessioned. This is done by comparing the SRA object alias and center name or the previously assigned accession number against SRA objects already submitted into SRA.

Below is an example of a Submission XML document used to update SRA sample objects stored in sample.xml document. Please note the use the MODIFY action and please retain the empty attribute target as this is required to validate the SRA Submission XML Schema.

<?xml version="1.0" encoding="UTF-8"?>
<SUBMISSION_SET>
   <SUBMISSION alias="anUpdate" center_name="YourCenterName">
	<ACTIONS>
   		<ACTION>
   			<MODIFY source="sample.xml" schema="sample"/>
   		</ACTION>
   	</ACTIONS>
   </SUBMISSION>
</SUBMISSION_SET>

 

Preparing SRA object for update

You can update any SRA object instead of Submission objects. Additionally, submitted run objects can't be updated to point to different data file.

Checklist for preparing an SRA object for update:

  • The XML for the SRA object must either contain alias and center_name or the assigned accession.
  • If you provide us with the alias and center_name they must be given exactly as in the original submission. The alias and center_name are guaranteed by the archive to constitute unique identifiers for the SRA objects.
  • If you provide us with the accession it must be the accession number assigned to the object during the original submission.
  • Either refname or accession are mandatory if references are made to other SRA objects.
  • In SRA Study objects, the INSDC project ID can't be updated to zero ('0') from an already-assigned non-negative value.
  • IN SRA Sample objects, INSDC taxonomy ID can't be updated to zero ('0') from an already-assigned non-negative value.

Update example

Original Sample XML

<SAMPLE accession="ERS000011" center_name="MyCenter"
        alias="Solexa sequencing of Saccharomyces paradoxus strain W7 random 200 bp library">       
    <SAMPLE_NAME>
        <TAXON_ID>580234</TAXON_ID>
        <COMMON_NAME>Saccharomyces paradoxus</COMMON_NAME>
    </SAMPLE_NAME>
    <DESCRIPTION>Solexa sequencing of Saccharomyces paradoxus 
	strain W7 random 200 bp library</DESCRIPTION>
</SAMPLE>

 

Updated Sample XML (using the assigned accession)

<SAMPLE accession="ERS000011" >
    <TITLE>Saccharomyces paradoxus W7</TITLE>
    <SAMPLE_NAME>
        <TAXON_ID>580234</TAXON_ID>
        <COMMON_NAME>Saccharomyces paradoxus</COMMON_NAME>
        <ANONYMIZED_NAME>Saccharomyces paradoxus</ANONYMIZED_NAME>
    </SAMPLE_NAME>
    <DESCRIPTION>Solexa sequencing of Saccharomyces
    paradoxus strain W7 random 200 bp library</DESCRIPTION>
    <SAMPLE_ATTRIBUTES>
        <SAMPLE_ATTRIBUTE>
            <TAG>strain</TAG>
    		<VALUE>W7</VALUE>
        </SAMPLE_ATTRIBUTE>
        <SAMPLE_ATTRIBUTE>
            <TAG>SAMPLE-TITLE</TAG>
		    <VALUE>Saccharomyces paradoxus W7</VALUE>
    	</SAMPLE_ATTRIBUTE>
	</SAMPLE_ATTRIBUTES>
</SAMPLE>

 

Updated Sample XML (using the alias and center name)

<SAMPLE center_name="MyCenter"
        alias="Solexa sequencing of Saccharomyces paradoxus strain W7 random 200 bp library">
    <TITLE>Saccharomyces paradoxus W7</TITLE>
    <SAMPLE_NAME>
        <TAXON_ID>580234</TAXON_ID>
        <COMMON_NAME>Saccharomyces paradoxus</COMMON_NAME>
        <ANONYMIZED_NAME>Saccharomyces paradoxus</ANONYMIZED_NAME>
    </SAMPLE_NAME>
    <DESCRIPTION>Solexa sequencing of Saccharomyces
    paradoxus strain W7 random 200 bp library</DESCRIPTION>
    <SAMPLE_ATTRIBUTES>
        <SAMPLE_ATTRIBUTE>
            <TAG>strain</TAG>
            <VALUE>W7</VALUE>
        </SAMPLE_ATTRIBUTE>
        <SAMPLE_ATTRIBUTE>
            <TAG>SAMPLE-TITLE</TAG>
            <VALUE>Saccharomyces paradoxus W7</VALUE>
        </SAMPLE_ATTRIBUTE>
    </SAMPLE_ATTRIBUTES>
</SAMPLE>

 

Step-By-Step Guide to Updating

  1. Decide which SRA objects (study, sample, experiment, run or analysis) need updating and obtain the latest XML for these objects. For public submissions, this can be done using the ENA Browser as instructed below. Please note that when creating XMLs for update submission you will need to remove the ROOT element from the XMLs returned by the ENA Browser and subtitute it with the correct root element: STUDY_SET, SAMPLE_SET, EXPERIMENT_SET, RUN_SET or ANALYSIS_SET. If your data is private please contact datasubs@ebi.ac.uk for further instructions.

    For a single object, http://www.ebi.ac.uk/ena/data/view/<accession>&display=xml&download&filename=<filename>
    E.g. http://www.ebi.ac.uk/ena/data/view/ERS000001&display=xml&download&filename=sample.xml

    For a range of objects, simply substitute the accession number with a comma separated list of ranges. In the example below there is only a single range.
    E.g. http://www.ebi.ac.uk/ena/data/view/ERS000001-ERS000001&display=xml&download&filename=sample.xml

  2. Edit the XML so that it contains the new/amended information.

  3. Generate a Submission XML used to submit the amended XMLs. Please note that a Submission XML containing MODIFY actions will be processed but no accession number will be assigned to the Submission object.

  4. Go to the SRA submission services page: https://www.ebi.ac.uk/ena/submit/drop-box/submit/

  5. Browse for your Submission XML and the updated XMLs.

  6. Enter your drop-box details and submit.

  7. If the update is successful the receipt will return true. If there was a problem, the receipt will return false. Please check the errors at the bottom of the page. If you cannot rectify the issues or understand the error message(s), please contact datasubs@ebi.ac.uk explaining the problem and attaching the XMLs and errors.

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18 Aug 2014: Changes to SRA XML 1.5
Small changes to Experiment XML, Analysis XML, EGA Dataset XML, EGA DAC XMLs were deployed on 11th of August 2014.

1 Jul 2014: ENA release 120
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23 May 2014: Change to date format for advanced search
From 16th June 2014, the date format used in the advanced search will be changed to ISO format (YYYY-MM-DD).

20 May 2014: Update to the ENA SAMPLE checklist
From 10th of June 2014 the ENA SAMPLE checklist XML will be updated and the older version will be deprecated.