Working with XML
We recommend manipulating EGA metadata using an XML editor, preferably one with the ability to validate against XML schemas.
Alternatively, XML can be edited in standard text editors and then checked using an XML validator, e.g. xmllint, a free unix-based XML validator.
General concepts: Aliases and center names
Every EGA object must be uniquely identified within the submission account using the alias attribute. The aliases can be used in submissions to make references between EGA objects. Please find more information about the use of aliases and center names below:
alias attribute: every object should have a name that is unique within your submission account. Once submitted successfully, every alias will be assigned an accession.
refname attribute: when an object references another by its alias, the alias goes into the refname attribute. For example, if a sample has the alias "sample1", and an experiment uses this sample, then the EXPERIMENT/SAMPLE/refname should be "sample1".
center_name attribute: The center_name attribute is required within the submission XML and will be propagated to all other XMLs if not individually provided. This element is the controlled vocabulary acronym or abbreviation that is provided to the account holder when the account is first generated for an institute. If the submitter is brokering a submission for another institute, the submitter should use their special broker account name in broker_name while the data centre acronym remains in center_name.
run_center attribute: Many submitting centres contract out the sequencing to another centre. In these cases, the sequencing centre should be acknowledged in the run_center attribute. Again, this is controlled vocabulary and the acronym should be sought from EGA before submitting.
Validating and submitting your EGA metadata objects
Log-in details should have been provided when you requested a submission account from the firstname.lastname@example.org.
New submitters are advised to use the Test service when submitting objects for the very first time. The test service is identical to the production service except that submissions are discarded on the following day.
Metadata objects can be validated against the test and production services by using the ‘VALIDATE’ action in the submission XML before submitting the object using the ‘ADD’ action to obtain th accessions for each object submitted.
<VALIDATE source="TODO: STUDY XML FILENAME" schema="study"/>
<ADD source="TODO: STUDY XML FILENAME" schema="study"/>