Citable workflows

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).

Assign a workflow DOI

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 necessarily giving the new version a DOI yet.

Note that DOI minting is only enable on the production instance https://workflowhub.eu/, although you can try the below instructions up to the “Publish” step on the sandbox instance https://dev.workflowhub.eu/.

Check metadata

Before you mint a DOI, make sure you check the correctness of the metadata of 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

For each of the registered users, it may be good to check that their ORCID identifier has been registered. This ensures that the people will be uniquely identified. Users can edit “My Profile” to link to ORCID.

Freezing the Workflow version

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

Freeze version

Publishing workflow

public

You need to check this workflow is Public. Either click the button as above, or edit under Manage Workflow:

permissions

Generate DOI

Now we can create a DOI:

Generate a DOI

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

Comfirm DOI

Finding DOI

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.

Note: The schema.org metadata rendered by DataCite may differ slightly from the more complete metadata embedded in a WorkflowHub entry’s HTML and RO-Crate.

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>

Tip: You can access these citations programmatically using DataCite’s content negotiation on resolving the DOI.

Citing a Workflow without a DOI

Note that if a workflow has not got 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.

Warning: As workflow versions without DOIs may not be frozen, it is also possible that the author later decides to withdraw the workflow from public view. Authors may subsequently edit the metadata of a given version, but not its downloadable content.