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Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan; Stian Soiland-Reyes; Richard O. Sinnott; Andrew Lonie; Carole Goble; Michael R. Crusoe


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  <identifier identifierType="DOI">10.5281/zenodo.1966881</identifier>
  <creators>
    <creator>
      <creatorName>Farah Zaib Khan</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6337-3037</nameIdentifier>
      <affiliation>The University of Melbourne; Common Workflow Language project</affiliation>
    </creator>
    <creator>
      <creatorName>Stian Soiland-Reyes</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9842-9718</nameIdentifier>
      <affiliation>The University of Manchester; Common Workflow Language project</affiliation>
    </creator>
    <creator>
      <creatorName>Richard O. Sinnott</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5998-222X</nameIdentifier>
      <affiliation>The University of Melbourne</affiliation>
    </creator>
    <creator>
      <creatorName>Andrew Lonie</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2006-3856</nameIdentifier>
      <affiliation>The University of Melbourne</affiliation>
    </creator>
    <creator>
      <creatorName>Carole Goble</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1219-2137</nameIdentifier>
      <affiliation>The University of Manchester</affiliation>
    </creator>
    <creator>
      <creatorName>Michael R. Crusoe</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2961-9670</nameIdentifier>
      <affiliation>Common Workflow Language project</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>Provenance</subject>
    <subject>Common Workflow Language</subject>
    <subject>CWL</subject>
    <subject>Research Object</subject>
    <subject>RO</subject>
    <subject>BagIt</subject>
    <subject>Interoperability</subject>
    <subject>Scientific Workflows</subject>
    <subject>Containers</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-12-04</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Preprint</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1966881</alternateIdentifier>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.1109/BigData.2016.7840618</relatedIdentifier>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.5281/zenodo.51314</relatedIdentifier>
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    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/ro</relatedIdentifier>
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  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt; The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable &lt;strong&gt;A&lt;/strong&gt;utomation, &lt;strong&gt;S&lt;/strong&gt;caling, &lt;strong&gt;A&lt;/strong&gt;daption and &lt;strong&gt;P&lt;/strong&gt;rovenance support (&lt;strong&gt;ASAP&lt;/strong&gt;). However, there are still several challenges associated with the effective sharing, publication and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Results:&lt;/strong&gt; Based on best practice recommendations identified from literature on workflow design, sharing and publishing, we define a &lt;em&gt;hierarchical provenance framework&lt;/em&gt; to achieve uniformity in the provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realise this framework, we present &lt;a href="https://w3id.org/cwl/prov/"&gt;&lt;strong&gt;CWLProv&lt;/strong&gt;&lt;/a&gt;, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We utilise open source community-driven standards; interoperable workflow definitions in &lt;a href="https://www.commonwl.org/"&gt;Common Workflow Language&lt;/a&gt; (CWL), structured provenance representation using the &lt;a href="https://www.w3.org/TR/prov-overview/"&gt;W3C PROV&lt;/a&gt; model, and resource aggregation and sharing as workflow-centric &lt;a href="http://www.researchobject.org/"&gt;Research Objects&lt;/a&gt; (RO) generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of &lt;em&gt;CWLProv&lt;/em&gt; and evaluation using real-life genomic workflows developed by independent groups.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The underlying principles of the standards utilised by &lt;em&gt;CWLProv&lt;/em&gt; enable semantically-rich and executable Research Objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial re-runs, or reproduce the analysis to validate the published findings.&lt;/p&gt;</description>
    <description descriptionType="Other">Submitted to GigaScience (GIGA-D-18-00483)</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/730976/">730976</awardNumber>
      <awardTitle>Industrial Biotechnology Innovation and Synthetic Biology Accelerator</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/675728/">675728</awardNumber>
      <awardTitle>Centre of Excellence for Biomolecular Research</awardTitle>
    </fundingReference>
  </fundingReferences>
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