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Published October 2, 2015 | Version v2
Preprint Open

10 Simple rules for design, provision, and reuse of identifiers for web-based life science data

  • 1. European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
  • 2. ELIXIR Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
  • 3. Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
  • 4. School of Computer Science, The University of Manchester, Manchester, United Kingdom
  • 5. Oxford e-Research Centre, University of Oxford, Oxford, United Kingdom
  • 6. Institute of Experimental Genetics, Helmholtz Centre Munich -German Research Center for Environmental Health (GmbH), Neuherberg, Germany
  • 7. Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, USA.
  • 8. European Molecular Biology Laboratory, Heidelberg, Germany
  • 9. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
  • 10. European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom | Babraham Institute, Cambridge, United Kingdom
  • 11. STFC, Daresbury Laboratory, Warrington, United Kingdom
  • 12. Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and Groningen Bioinformatics Center, University of Groningen, Groningen, Netherlands
  • 13. SDBV, HITS, Heidelberg, Germany
  • 14. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • 15. Institute of Pathology, Charite – University Medicine Berlin, Berlin, Germany | TMF – Technologie- und Methodenplattform e. V. Berlin, Germany
  • 16. MIB, University of Manchester, Manchester, UK | Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
  • 17. Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), University of Manchester, Manchester, UK.
  • 18. Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands

Description

Life science data is evolving to be ever larger, more distributed, and more natively web-based. However, our collective handling of identifiers has lagged behind these advances. Diverse identifier issues (for instance “link rot” and “content drift”) have hampered our ability to integrate data and derive new knowledge from it. Optimizing web-based identifiers is harder than it appears and no single scheme is perfect:  Identifiers are reused in different ways for different reasons, by different consumers. Moreover, digital entities (e.g., files), physical entities (e.g., biosamples), and descriptive entities (e.g., ‘mitosis’) have different requirements for identifiers. Nevertheless, there is substantial room for improvement throughout the life sciences and several other groups have been converging on identifier standards that are broadly applicable.

Building on these efforts and drawing on our experience, we focus on the use case of large-scale data integration: we outline the identifier qualities and best practices that we feel are most important in this context. Specifically, we propose actions that providers of online databases (repositories, registries, and knowledgebases) should take when designing new identifiers or maintaining existing ones (Rules 1-9). In Rule 10, we conclude with guidance to data integrators and redistributors on how best to reference identifiers from these diverse sources. This article may also be useful to data generators and end users as it offers insight into the issues associated with data provision in a web environment. We call upon data providers to take a long-term view of their entities’ scope and lifecycle, and to consider existing identifier platforms and services. 

Rule 1.  Use established identifiers

Rule 2.  Design identifiers for use by others

Rule 3.  Help local identifiers travel well: document Prefix and Namespace

Rule 4.  Opt for simple durable web resolution

Rule 5.  Avoid embedding meaning

Rule 6.  Make URIs clear and findable

Rule 7.  Implement a version management policy

Rule 8.  Do not re-assign or delete identifiers

Rule 9.  Document the identifiers you issue and use

Rule 10. Reference responsibly

Notes

This manuscript is a revision of doi:10.5281/zenodo.18003 and was recently resubmitted to PLoS Computational Biology

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Additional details

Related works

Is new version of
10.5281/zenodo.18003 (DOI)

Funding

BIOMEDBRIDGES – Building data bridges between biological and medical infrastructures in Europe 284209
European Commission
ELIXIR – European Life-science Infrastructure for Biological Information 211601
European Commission
DIACHRON – DIACHRON – Managing the Evolution and Preservation of the Data Web 601043
European Commission
ISBE – Infrastructure for Systems Biology - Europe 312455
European Commission