Publishing in NDEx

Last updated: September 24th, 2017

The public NDEx site includes a number of features to promote and support publishing of data in network format. Although published networks will typically be associated with research articles, there are cases where authors will decide to publish network data independently from a canonical scientific journal article. For example, researchers generating networks from large datasets using automated analytic pipelines may wish to make their results available on an ongoing basis.

IMPORTANT NOTE: The screenshots in all our user manuals are for training purposes and might be different from the actual screen output you will obtain when working on the current NDEx version deployed to our public server.

Requesting a DOI

For reproducibility and long term data access, NDEx offers the possibility to request DOIs for any networks. Requesting a DOI for a network ensures that the network will become a stable, immutable resource and guarantees long term access to the underlying data. In addition, the DOI can be used in subsequent publications or to submit data to online repositories.

  • To initiate the request, click the "More" button in your network page and select "Request DOI":

  • In order to successfully submit a DOI request, your network must satisfy a number of criteria concerning its metadata annotation. The following list defines the minimum annotation requirements to qualify for a DOI request:
    • Title
    • Description
    • Version
    • Author
    • Rights
    • Rights holder
    • Reference (optional, can be added later)
  • Fill in all the DOI required field in the Network Properties Editor screen as shown in the image below:

  • Please note that each submitted requst will be accurately reviewed as the operation is not automated and that we might contact you to obtain additional information prior to assigning a DOI. Therefore, it is important to make sure you provide a valid contact email address when submitting your request. This same email address will also be used to notify you that the DOI has been assigned.

Rights: List of Available Licenses

One of the minimum annotation requirements to submit a DOI request, refers to the "Rights" metadata information. The NDEx user interface provides a number of standard licensing options you can choose from or lets you specify your own custom license in the form of a valid URL. The available options are listed below:

Reference: Adding Publication Information

Adding a publication reference to a network is not required to request a DOI; this operation can be performed by the author at a later time, usually after the article referencing the network has been officially accepted for publication.

Once a DOI has been issued, that network will become a stable, non-editable resource with the exception that the author may add one publication reference: after this has been done, the network will be permanently locked and its privacy changed to PUBLIC if not already so. No more changes or updates of any kind will be allowed on this network. Any subsequent versions/updates of the network content will be in new, separate networks. For example, the author or other user could generate an editable copy using the "Clone Network" function.