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Preprint Open Access

10 Simple rules for design, provision, and reuse of persistent identifiers for life science data

McMurry, Julie; Blomberg, Niklas; Burdett, Tony; Conte, Nathalie; Dumontier, Michel; Fellows, Donal K; Gonzalez-Beltran, Alejandra; Gormanns, Philipp; Hastings, Janna; Haendel, Melissa A; Hermjakob, Henning; Hériché, Jean-Karim; Ison, Jon C; Jimenez, Rafael C; Jupp, Simon; Juty, Nick; Laibe, Camille; Le Novère, Nicolas; Malone, James; Martin, Maria J; McEntyre, Johanna R; Morris, Chris; Muilu, Juha; Müller, Wolfgang; Mungall, Christopher J; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Sariyar, Murat; Snoep, Jacky L; Stanford, Natalie J; Swainston, Neil; Washington, Nicole; Williams, Alan R; Wolstencroft, Katherine; Goble, Carole; Parkinson, Helen


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  <identifier identifierType="DOI">10.5281/zenodo.18003</identifier>
  <creators>
    <creator>
      <creatorName>McMurry, Julie</creatorName>
      <givenName>Julie</givenName>
      <familyName>McMurry</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Blomberg, Niklas</creatorName>
      <givenName>Niklas</givenName>
      <familyName>Blomberg</familyName>
      <affiliation>ELIXIR Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Burdett, Tony</creatorName>
      <givenName>Tony</givenName>
      <familyName>Burdett</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Conte, Nathalie</creatorName>
      <givenName>Nathalie</givenName>
      <familyName>Conte</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Dumontier, Michel</creatorName>
      <givenName>Michel</givenName>
      <familyName>Dumontier</familyName>
      <affiliation>Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Fellows, Donal K</creatorName>
      <givenName>Donal K</givenName>
      <familyName>Fellows</familyName>
      <affiliation>School of Computer Science, The University of Manchester, Manchester, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Gonzalez-Beltran, Alejandra</creatorName>
      <givenName>Alejandra</givenName>
      <familyName>Gonzalez-Beltran</familyName>
      <affiliation>Oxford e-Research Centre, University of Oxford, Oxford, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Gormanns, Philipp</creatorName>
      <givenName>Philipp</givenName>
      <familyName>Gormanns</familyName>
      <affiliation>Institute of Experimental Genetics, Helmholtz Centre Munich -German Research Center for Environmental Health (GmbH), Neuherberg, Germany </affiliation>
    </creator>
    <creator>
      <creatorName>Hastings, Janna</creatorName>
      <givenName>Janna</givenName>
      <familyName>Hastings</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Haendel, Melissa A</creatorName>
      <givenName>Melissa A</givenName>
      <familyName>Haendel</familyName>
      <affiliation>Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health &amp; Science University, Portland, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Hermjakob, Henning</creatorName>
      <givenName>Henning</givenName>
      <familyName>Hermjakob</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Hériché, Jean-Karim</creatorName>
      <givenName>Jean-Karim</givenName>
      <familyName>Hériché</familyName>
      <affiliation>European Molecular Biology Laboratory, Heidelberg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Ison, Jon C</creatorName>
      <givenName>Jon C</givenName>
      <familyName>Ison</familyName>
      <affiliation>Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark</affiliation>
    </creator>
    <creator>
      <creatorName>Jimenez, Rafael C</creatorName>
      <givenName>Rafael C</givenName>
      <familyName>Jimenez</familyName>
      <affiliation>ELIXIR Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Jupp, Simon</creatorName>
      <givenName>Simon</givenName>
      <familyName>Jupp</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Juty, Nick</creatorName>
      <givenName>Nick</givenName>
      <familyName>Juty</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Laibe, Camille</creatorName>
      <givenName>Camille</givenName>
      <familyName>Laibe</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Le Novère, Nicolas</creatorName>
      <givenName>Nicolas</givenName>
      <familyName>Le Novère</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom | Babraham Institute, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Malone, James</creatorName>
      <givenName>James</givenName>
      <familyName>Malone</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Martin, Maria J</creatorName>
      <givenName>Maria J</givenName>
      <familyName>Martin</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>McEntyre, Johanna R</creatorName>
      <givenName>Johanna R</givenName>
      <familyName>McEntyre</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Morris, Chris</creatorName>
      <givenName>Chris</givenName>
      <familyName>Morris</familyName>
      <affiliation>STFC, Daresbury Laboratory, Warrington, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Muilu, Juha</creatorName>
      <givenName>Juha</givenName>
      <familyName>Muilu</familyName>
      <affiliation>Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and Groningen Bioinformatics Center, University of Groningen, Groningen, Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Müller, Wolfgang</creatorName>
      <givenName>Wolfgang</givenName>
      <familyName>Müller</familyName>
      <affiliation>SDBV, HITS, Heidelberg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Mungall, Christopher J</creatorName>
      <givenName>Christopher J</givenName>
      <familyName>Mungall</familyName>
      <affiliation>Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Rocca-Serra, Philippe</creatorName>
      <givenName>Philippe</givenName>
      <familyName>Rocca-Serra</familyName>
      <affiliation>Oxford e-Research Centre, University of Oxford, Oxford, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Sansone, Susanna-Assunta</creatorName>
      <givenName>Susanna-Assunta</givenName>
      <familyName>Sansone</familyName>
      <affiliation>Oxford e-Research Centre, University of Oxford, Oxford, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Sariyar, Murat</creatorName>
      <givenName>Murat</givenName>
      <familyName>Sariyar</familyName>
      <affiliation>Institute of Pathology, Charite – University Medicine Berlin, Berlin, Germany | TMF – Technologie- und Methodenplattform e. V. Berlin, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Snoep, Jacky L</creatorName>
      <givenName>Jacky L</givenName>
      <familyName>Snoep</familyName>
      <affiliation>MIB, University of Manchester, Manchester, UK | Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa</affiliation>
    </creator>
    <creator>
      <creatorName>Stanford, Natalie J</creatorName>
      <givenName>Natalie J</givenName>
      <familyName>Stanford</familyName>
      <affiliation>School of Computer Science, The University of Manchester, Manchester, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Swainston, Neil</creatorName>
      <givenName>Neil</givenName>
      <familyName>Swainston</familyName>
      <affiliation>Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), University of Manchester, Manchester, UK.</affiliation>
    </creator>
    <creator>
      <creatorName>Washington, Nicole</creatorName>
      <givenName>Nicole</givenName>
      <familyName>Washington</familyName>
      <affiliation>Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Williams, Alan R</creatorName>
      <givenName>Alan R</givenName>
      <familyName>Williams</familyName>
      <affiliation>School of Computer Science, The University of Manchester, Manchester, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Wolstencroft, Katherine</creatorName>
      <givenName>Katherine</givenName>
      <familyName>Wolstencroft</familyName>
      <affiliation>Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Goble, Carole</creatorName>
      <givenName>Carole</givenName>
      <familyName>Goble</familyName>
      <affiliation>School of Computer Science, The University of Manchester, Manchester, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Parkinson, Helen</creatorName>
      <givenName>Helen</givenName>
      <familyName>Parkinson</familyName>
      <affiliation>European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom</affiliation>
    </creator>
  </creators>
  <titles>
    <title>10 Simple rules for design, provision, and reuse of persistent identifiers for life science data</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2015</publicationYear>
  <subjects>
    <subject>Identifiers</subject>
    <subject>Identifier design</subject>
    <subject>Reproducibility</subject>
    <subject>e-Science</subject>
    <subject>Big data</subject>
    <subject>Accessions</subject>
    <subject>Databases</subject>
    <subject>Interoperability</subject>
    <subject>Synthesis research</subject>
    <subject>Standards</subject>
    <subject>Open science</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2015-05-26</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Preprint</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/18003</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPreviousVersionOf">10.5281/zenodo.31765</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.610288</relatedIdentifier>
  </relatedIdentifiers>
  <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;In the life sciences, problems with identifiers impede the flow and integrity of information. This is especially challenging within &amp;ldquo;synthesis research&amp;rdquo; disciplines such as systems biology, translational medicine, and ecology. Implementation-driven initiatives such as ELIXIR, BD2K, and others have therefore been actively working to understand and address underlying problems with identifiers.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Good, global-scale, persistent identifier design is harder than it appears, and is essential for data to be Findable, Accessible, Interoperable, and Reusable (Data FAIRport principles). Here, we build on emerging conventions and existing general recommendations &amp;nbsp;and summarise the identifier characteristics most important to optimising the utility of life-science data. We propose actions to take in the identifier &amp;lsquo;green field&amp;rsquo; and offer guidance for using real-world identifiers from diverse sources.&lt;/p&gt;</description>
    <description descriptionType="Other">ORCIDs corresponding to the authors are:
http://orcid.org/0000-0002-9353-5498
http://orcid.org/0000-0003-4155-5910
http://orcid.org/0000-0002-2513-5396
http://orcid.org/0000-0002-1010-3121
http://orcid.org/0000-0003-4727-9435
http://orcid.org/0000-0002-9091-5938
http://orcid.org/0000-0003-3499-8262
http://orcid.org/0000-0001-9823-1621
http://orcid.org/0000-0002-3469-4923
http://orcid.org/0000-0001-9114-8737
http://orcid.org/0000-0001-8479-0262
http://orcid.org/0000-0001-6867-9425
http://orcid.org/0000-0001-6666-1520
http://orcid.org/0000-0001-5404-7670
http://orcid.org/0000-0002-0643-3144
http://orcid.org/0000-0002-2036-8350
http://orcid.org/0000-0002-4625-743X
http://orcid.org/0000-0002-6309-7327
http://orcid.org/0000-0002-1615-2899
http://orcid.org/0000-0001-5454-2815
http://orcid.org/0000-0002-1611-6935
http://orcid.org/0000-0002-9533-5684
http://orcid.org/0000-0002-1034-5171
http://orcid.org/0000-0002-4980-3512
http://orcid.org/0000-0002-6601-2165
http://orcid.org/0000-0001-9853-5668
http://orcid.org/0000-0001-5306-5690
http://orcid.org/0000-0002-5595-689X
http://orcid.org/0000-0002-0405-8854
http://orcid.org/0000-0003-4958-0184
http://orcid.org/0000-0001-7020-1236
http://orcid.org/0000-0001-8936-9143
http://orcid.org/0000-0003-3156-2105
http://orcid.org/0000-0002-1279-5133
http://orcid.org/0000-0003-1219-2137
http://orcid.org/0000-0003-3035-4195</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/284209/">284209</awardNumber>
      <awardTitle>Building data bridges between biological and medical infrastructures in Europe</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/601043/">601043</awardNumber>
      <awardTitle>DIACHRON – Managing the Evolution and Preservation of the Data Web</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/312455/">312455</awardNumber>
      <awardTitle>Infrastructure for Systems Biology - Europe</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/211601/">211601</awardNumber>
      <awardTitle>European Life-science Infrastructure for Biological Information</awardTitle>
    </fundingReference>
  </fundingReferences>
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