Online Submission

Overview

• An online submission interface has been developed to help with the submission of 4DN metadata.
• This web interface is especially useful for;
  • submitting one or a few experiments
  • editing the metadata for an existing experiment
  • understanding object dependencies in our metadata schemas (for example learning that every experiment needs a type and a biosample).
• The system has been developed as a submission wizard that allows both the stepwise creation of database objects and full submission of an entire experiment with all required associated objects.
• We do recommend you review the information on the Getting Started page to get some tips on important concepts like aliases and Replicate Sets.
• In order to submit, you will need submission privileges. Contact us at support@4dnucleome.org to let us know what you're submitting and we can set this up.

Creating New Items

There are several possible 'entry' points to a web submission

• You may want to start by entering metadata for an ExperimentSetReplicate object or an Experiment object of a particular type (eg. a Hi-C experiment or Microscopy experiment).
• You can start by creating experiments and then as a subsequent step associating multiple experiments with a Replicate Set.
• You can start your submission at a lower level item type (eg. Biosample) if that makes things easier for you.

To create a new item

1. Navigate to an item of the type for which you want to create metadata.

1. You can find Create and Edit links near the top of a page for most items in our system. NOTE You will not see one or both of these buttons if you lack permission to perform these operations, which may be due to the status of the item and/or your role in our system.
2. When you click Create the first thing you will be asked is to create an alias for your item. This is a lab specific unique identifier for this object taking the form of xxxx:xxxxx where the portion before the colon is a lab designation eg. 4dn-dcic-lab and the portion after is an identifier of your choice that is unique within your lab group (see section on using aliases here).

1. When you submit your alias, you will be brought to a page where you can start entering metadata. If another database Item needs to be linked to the current object, this can be done via 'Select existing' or 'Create new' buttons. If you make a mistake selecting an item, you can clear it with the red 'x' to the right of the field.

• Hovering your pointer over the i icon next to a field will cause an explanation of the field to pop up.

  • Some fields are marked as required and must be filled for an item to pass validation.
  • As you create or add linked Objects (with Select Existing or Create New buttons) you will see the Objects listed in the Navigation section change colors accordingly.
  • You can use the Navigation section on the left-hand side to review what you have submitted, validated and what remains to be added.

1. And finally when all your linked objects are submitted and validated (green) you can validate and submit the object to complete your submission.

WARNING: Be careful with the BACK and RELOAD buttons. Currently, if you choose to create a new linked object and then decide you actually don't want to or should have actually chosen an existing object you still should create the object with only the minimum information required, Validate and then Submit it. You will then be taken back to the previous form you were working on and be able to remove the unwanted object. If you try to navigate back to the previous page using your browser buttons you will lose the previously unsubmitted changes. We are working to improve this aspect of the interface.

Editing Existing Objects

• You can use the online submission interface to make edits to existing items providing you have permission to do so.
• If an object has been 'released' either to the 4DN project or to the public it can no longer be changed.
• If the object has an 'in review' status then you can make changes to fields provided you are the submitter of that object or a submitter for the lab that submitted the object.

WARNING: Please take care to be sure that the object you are editing is really the one you want to change.

1. Navigate to that object's page. If the object is editable, then you should see an Edit button.

1. After clicking the Edit button you will be brought to a page similar to that described above for creating a new item.
2. You will see the existing values, to which you can make changes as needed.
3. When finished, you can validate and submit to commit the changes to the system.