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Creating a citable workflow

Workflows registered in https://workflowhub.eu/ that are public can be assigned a DOI (Digital Object Identifier) so that they can more easily be cited in academic work. WorkflowHub DOIs are registered with DataCite using the DataCite Metadata Schema, meaning that the metadata joins the scholarly knowledge graphs DataCite Commons PID Graph and OpenAIRE Research Graph (example).

  • You can assign DOIs for workflows you have registered and that you have been given write access to.
  • You are not able to make DOIs for other people’s workflows.
  • Each version of the workflow must be registered separately.
  • You can create a new version of a workflow that has been assigned a DOI, without needing to assign a DOI to the new version.

Creating a DOI

1. Check metadata

Before you mint a DOI, make sure you check the correctness of the metadata for the workflow entry, and that it makes sense globally, as this will be part of the DataCite registration.

Use Actions -> Edit Workflow and Actions -> Manage workflow to fill in:

  • Title (is it specific enough)
  • Creators (you can include registered WorkflowHub users or others by name)
  • Status of workflow
  • Description
  • License

2. Freeze the workflow version

Before we can mint a DOI, we need to freeze the version of the workflow in WorkflowHub, so that its metadata stays consistent with the metadata used for the DOI registration with DataCite.

The next step towards a workflow DOI is shown in the Citation panel that appears on the right hand side of your workflow entry. In the image below, you can see that the next step is to Freeze the workflow version.

Freeze version

3. Publish the workflow

If your workflow is not public, the next step is to publish the workflow so that it is Public. You can do this by clicking the Publish button in the Citation panel (see below).

public

You can also check, and edit, sharing permissions by selecting Manage Workflow in the Actions drop down menu.

permissions

4. Generate a DOI

Now you can use the Citation panel to create a DOI.

Generate a DOI

A pop-up will remind you to revise the metadata and confirm.

Comfirm DOI

Finding DOIs

DOIs that have been minted for workflows are shown as part of the workflow entry:

doi in listing

Citing Workflows

You can generate a citation for a chosen journal style in the Citation box:

citation

Note that as this generated citation is based on the corresponding CSL styles, which may not include the DOI as part of its template for Software citations, or may append a . to the shown URL.

Therefore remember to add the DOI to the citation in your reference manager, for instance as a comment or URL.

Example:

Douglas Lowe and Genís Bayarri. 2021. “Protein Ligand Complex MD Setup Tutorial Using BioExcel Building Blocks (Biobb) (Jupyter Notebook).” WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.56.2

Retrieving DataCite metadata

You can look up the DataCite metadata of WorkflowHub DOI registrations using their programmatic APIs or the DataCite Commons.

For instance, from https://commons.datacite.org/doi.org/10.48546/workflowhub.workflow.56.2 we can download the metadata as DataCite XML, DataCite JSON, Schema.org JSON-LD, CiteProc JSON, BibTex, RIS.

Example of returned DataCite XML following DataCite Schema 4.3:

<?xml version="1.0" encoding="UTF-8"?>
<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.3/metadata.xsd">
  <identifier identifierType="DOI">10.48546/WORKFLOWHUB.WORKFLOW.56.2</identifier>
  <titles>
    <title xml:lang="en-gb">Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)</title>
  </titles>
  <descriptions>
    <description xml:lang="en-gb" descriptionType="Abstract"># Summary&#13;
&#13;
This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).&#13; 
      ....
  </descriptions>
  <creators>
    <creator>
      <creatorName>Lowe, Douglas</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org">https://orcid.org/0000-0002-1248-3594</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Bayarri, Genís</creatorName>
    </creator>
  </creators>
  <publicationYear>2021</publicationYear>
  <publisher>WorkflowHub</publisher>
  <resourceType resourceTypeGeneral="Workflow">Workflow</resourceType>
</resource>

Citing a workflow without a DOI

Note that if a workflow does not have a DOI, you can still cite it using the versioned WorkflowHub SEEK ID, e.g. https://workflowhub.eu/workflows/263?version=1

You will need to generate the metadata (e.g. title) yourself as it has not been verified for citation by the authors.