Submitting Antibodies

This page provides instructions for adding antibody validation data to the ATLAS-D2K Data Explorer.

If you have any questions or feedback, please send them to your consortium’s help email: help@atlas-d2k.org

We also have the following training materials available:

• Webinar Slides
• Webinar Replay 12/11/2017 (37:08)

Overview

Adding antibody validation data involves the following steps:

• Make sure you are in the correct Globus authentication group (follow the instructions on this page), and that you are logged in.
• Search that antibody data already exists for your test.
• If it doesn’t, then create an antibody record.
• Create an antibody test record.
• Add distribution terms to your antibody test record.
• Add any images or other media.
• Add a test summary sheet.
• You may also ‘bulk add’ several test records if they are similar (ie, only the media type and outcome are different).

Schema

The Antibody schema contains two main tables:

• Antibodies: General product information about each antibody, similar to what might be found on the manufacturer’s website.
• Antibody Tests: Information about researchers’ experience using each antibody.

Other related tables include:

• Antibody Media Files: Images and other media files related to antibody tests (slide images, summary PDFs, etc.)
• Test Methods: Descriptions of the methods used in antibody tests.
• Various vocabulary tables.

0. Are you in the correct group? (Required)

Follow the instructions on this page. If you’re not sure which group you need to join, please contact help@atlas-d2k.org.

1. Search for the antibody you’re working on

• Go to https://www.atlas-d2k.org/chaise/recordset/#2/Antibody:Antibodies@sort(Protein_Target,RID) and log in.

• This will take you to the antibody search page, which you can use to find out if the antibody you’re working on is already listed in our database. Start typing the name of the antibody in the search field or use the filtering sidebar on the left to narrow down the results.

• If your antibody is there, you can go ahead and create the antibody test record (See next section). If not, move on to the next step below.

2. If you cannot find the antibody, create a new antibody record

If you did find the antibody, move on to the next step.

• From the navigation bar, click Internal > Antibody > Antibodies.

  The Create Antibodies Record form opens in a new browser tab.

  

• Select the values for each relevant field. The required fields are:
  • Company ID
  • Catalog Number
  • Host Species
  • Protein Target: Note that this list comes from the NCBI Gene List and should include all proteins. Also, you will soon be able to search on synonyms.
  • Curation Status: Choose either
    • In Preparation (still drafting),
    • PI Review (ready for internal approval), or
    • Submitted (ready for Hub review). Your data will not be viewable publicly until approved for Release by the Hub. For a complete description of the Curation Process, click here.
  • Consortium: Make sure you indicate whether this is from the ATLAS-D2K Consortium.
• When finished, click Submit Data to save your new antibody record. You can now close this tab.

What if my antibody is not from a vendor?

If your antibody is not from a vendor (ie, it’s a donated reagent), then you may choose a name for the Company ID (“Donated reagent from X Lab”) and use the RRID for the Catalog Number or some other unique identifier.

3. Create your new antibody test record

• From the navigation bar, click Internal > Antibody > Antibody Test.

  The Create Antibody Test Record form appears in a new browser tab.

  

• Select the values for each relevant field. The required fields are:
  • Antibody Product ID
  • Protein Target: Note that this list comes from the NCBI Gene List and should include all proteins. Also, you will soon be able to search on synonyms.
  • Curation Status: Choose either
    • In Preparation (still drafting),
    • PI Review (ready for internal approval), or
    • Submitted (ready for Hub review). Your data will not be viewable publicly until approved for Release by the Hub. For a complete description of the Curation Process, click here.
  • Principal Investigator: Choose the name of your project’s contact PI.
  • Consortium: Make sure you indicate whether this is from the ATLAS-D2K consortium.
• Note: If you are creating multiple antibody test records, you may click the + button (under the Submit Data button) to copy over the record form. Each time you click + will display a copy of the most recent form that you can edit as needed.

• When finished, click Submit Data to save your new antibody test record(s).

• If you are not finished with your submission, you may still save your work by clicking the Submit Data button. Then you may go back to the record, log in and click Edit to resume filling it out.

4. Add distribution terms to your antibody test record

• Scroll to the bottom of the antibody test record until you see a section labelled Distribution. This is our term for cell types / anatomical regions relevant to this antibody test.

• Click Add in the Distributions section.

This will bring up a Create Antibody Test Distribution Record window.

• Start typing the anatomical term in the search term to narrow your results.

• Click Select a value
• Click the checkmark to the left of your desired distribution value.
• Click Submit Data to add the distribution.
• Repeat for as many distributions as desired.

5. Add test summary sheets and images

Near the bottom of the newly-created antibody test record, you’ll see empty sections labelled Test Summary Sheets for PDF summaries of the test, and Test Images for slide images relevant to the test.

To add a test-related files:

• Click Add in the Test Images or Test Summary Sheets section.

This will bring up the Choose Antibody Media Files window.

• If the desired file has already been uploaded, select it.

• If not, upload your file:

  • Click the + at the top right-hand side of the Choose Antibody Media Files window.

  

  This will open a Create Antibody Media Files Record page in a separate browser tab.

  

  • Click on Select File to select a file from your computer. Either an image file if you’re adding a test image or a PDF for the test summary.

  

• Please use the Comment Field to paste in the summary of the test result doc from the PDF.

• Fill in the rest of the fields on the form. Required fields are: * Principal Investigator: Choose the name of the contact PI for your project. If their name isn’t available, please contact the Hub. * Curation Status: Choose either * In Preparation (still drafting), * PI Review (ready for internal approval), or * Submitted (ready for Hub review). Your data will not be viewable publicly until approved for Release by the Hub. For a complete description of the Curation Process, click here. * Data Provider: This is your lab’s institution. If you need to add an institution, please contact the Hub. * Consortium: Make sure you indicate whether this is from the ATLAS-D2K consortium. * Description: This is not required - however, this field is useful for test images if you want to describe what different colors represent, etc.

• Click Submit Data to complete the upload.

• Go back to the browser tab of your Antibody Test Record and select your newly-uploaded image from the Choose Antibody Media Files window.

• Click Submit Data to link your image or PDF to the antibody test. Note you may need to refresh the page to see the results.

<!–

6. Add additional tests by copying

If you’ve done several tests that are mostly the same (e.g., two tests that differ only by media type and outcome), you can save time by copying an existing test and modifying it.

• Start at the record you want to copy.

• Click Copy at the top of the page (if you don’t see the Copy button, you’re probably not logged in).

• Make the desired changes to the new record and click the Submit Data button. –>

6. Reviewing and Submitting Antibody Data

Note: By the hard launch of the new GUDMAP site in April, there will be dashboards and email notifications to make this process more straightforward. In the meantime, here is how a project’s PI or designated reviewer can find their project’s data with a Curation Status of “PI Review”

• Make sure you are logged in.

• From the navigation bar, click Data > Antibody Data > Antibody Tests.

• In the faceting sidebar on the left, scroll to Curation Status and choose PI Review. Note: Keep in mind that the data submitter may have forgotten to set the Curation Status field, in which case the status would still be In Preparation.

• In the faceting sidebar, scroll to Principal Investigator and choose your project’s PI. Now you should see the data you need to review.

• When your record is approved internally, change Curation Status to Submitted to send it to the Hub (click here for the full Curation Workflow).

7. Deleting Antibody Data

Before you can delete Antibody Test record, you must delete (unlink) any distributions, test summary sheets or test images associated with it.

To delete an antibody test record:

• In the ‘Distributions’ field, click the Edit link to the right and for each distribution, click the ‘x’ icon in the Actions column.

• Scroll down the record to the sections for ‘Test Summary Sheets’ and ‘Test Images’.

• In each of these sections, unlink the entries by clicking the ‘x’ icon in the Actions columns.

• Once all of the related records have been deleted (unlinked), then scroll up to the top of the record and click Delete.