Submit Genotype Data with XML

Submitting genotype data to PharmGKB via XML can be broken down into these five steps:

1. Create an XML file containing your data according to the PharmGKB XML schema.
2. Validate your XML file with the PharmGKB XML validator.
3. Submit your XML file to the PharmGKB Preview Site.
4. Verify the data on the PharmGKB Preview Site.
5. Approve (or reject) the submission.

Step 1: Create an XML file containing your data according to the PharmGKB XML schema.

The first step in submitting genotype data to PharmGKB is to format your data in XML so that it conforms to the PharmGKB XML schema. The documentation for the schema is embedded within the schema itself. Please note that while the schema defines all the elements that PharmGKB uses when exporting the data, not all of these elements are available to submitters. Elements constrained in this manner are all documented within the schema. For example, submitters may not define a gene symbol. PharmGKB maintains this information itself, and we will not accept submissions that attempt to override PharmGKB's definitions.

A list of Accession IDs of all genes in the PharmGKB: genes.zip (909 KB, last updated on 7/26/07)

Step 2: Validate your XML file with the PharmGKB XML validator.

Once you've created your XML file, you should validate it with the PharmGKB XML validator. This validator is a Java program that checks to make sure that your XML file conforms to the PharmGKB XML schema. Please download our XML Validator (Zip 9,128 kb) at http://preview.pharmgkb.org/schema/validator.zip.

Note that the PharmGKB XML validator is frequently updated and so it is best if the submitter downloads a new copy of the validator each time they want to validate a new batch of files.

Step 3: Submit your XML file to the PharmGKB Preview Site.

If your XML file passes the validator, submit it to the PharmGKB Preview Site. Click on the "Submit" tab, and you will be given the option to submit an XML file.

Once we receive your file, we will perform further validation. If the submission passes this second stage of validation, we will inform you via e-mail. You will be able to then view your data on the PharmGKB Preview Site. If the submission does not pass validation, you will be notified of the reasons via e-mail. PharmGKB will help you resolve the issues and resubmit the file.

Step 4: Verify the data on the PharmGKB Preview Site.

Once you have been notified via email that your submission is available for review, follow the link to the PharmGKB Preview Site.

If you do not have the email link or it does not work for some reason, you may find your submission page one of the following ways:

Click on the "Search" tab at the top of the page. Click on the "Submissions by project" link. Find your project and click on the number in the "Pending" column. Click on the submission ID (PS number) that you would like to review.
OR
If you know the submission ID of the submission you want to approve, type it into the search box at the top right corner of the page. A search page should come up listing that submission. Click that link to continue.

Please see our documentation regarding Review My Genotype Submissions.

Step 5: Approve (or reject) the submission.

After the data have been reviewed for accuracy, only project PIs and other pre-approved registered users are able to approve submissions. The user with approval permissions must login to the PharmGKB Preview Site and go to the submission page (see Step 4 above).

If the submission is satisfactory, click the "Approve Submission" button on the page. The submission will then be posted on the public PharmGKB website. If there is a problem with the submission, reject the submission by clicking on that button instead.

(Note that only project PIs and other pre-approved registered users are able to view the Approve and Reject buttons, because they are the only users allowed to approve or reject submissions.)