Updating XMLs

It is possible to update submitted objects. The only exception is that a run or analysis XML can't be made to point to different data files. To update an object you need a submission XML with MODIFY action pointing to XML files containing the updated objects.

Preparing submission XML

To update objects, you must use the MODIFY action instead of ADD action in the submission XML  ... more information.

The MODIFY action should point to the XML files containing the objects to be updated.

Below is an example of a submission XML used to update sample objects stored in sample.xml file:

<?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 updated XML

Please note that submitted run or analysis objects can't be updated to point to different data files.

Checklist for preparing an object for update:

  • The XML for the object must either contain alias with center name or the assigned accession.
  • If you provide us with the alias then it must be given exactly as in the original submission. The alias is guaranteed to be an unique identifier for a given object type within the submission account.
  • If you provide us with the accession then 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 objects.

Below is an example of an 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>

 

Below is an example of an updated sample XML with an 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>

 

Below is an example of an updated sample XML with an 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>

 

Preparing updated XML using the ENA Browser

If you are unable to create the updated XMLs from scratch you can retrieve the latest public XMLs using the ENA Browser. Please note that you will need to substitute the ROOT element in the returned XMLs with STUDY_SET, SAMPLE_SET, EXPERIMENT_SET, RUN_SET or ANALYSIS_SET element. 

Step by step instructions:

  1. Retrieve objects from ENA Browser.

    Single objects: 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

    Range of objects:
    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. Create a Submission XML to submit the amended XMLs ... more information.

  4. Submit the amended XMLs following instructions in ... more information.

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11 Oct 2017: Read data download issues resolved

Read data download issues previously affecting ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk services now resolved.

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