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Title: Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Abstract

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

Authors:
ORCiD logo [1];  [2];  [3];  [2];  [1];  [2];  [2];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [11];  [2];  [12];  [2];  [2];  [13] more »;  [2];  [10];  [2];  [2];  [2];  [14];  [15];  [16];  [7];  [7];  [17];  [18];  [6];  [6];  [19];  [20];  [6];  [2];  [1];  [21];  [6];  [20];  [1];  [2] « less
  1. Oregon Health & Science Univ., Portland, OR (United States). Dept. of Medical Informatics and Epidemiology
  2. European Molecular Biology Lab., Hinxton (United Kingdom). European Bioinformatics Inst.
  3. Wellcome Genome Campus, Hinxton (United Kingdom). ELIXIR Hub
  4. Univ. of California, Berkeley, CA (United States). Berkeley Natural History Museums
  5. Maastricht Univ. (Netherlands). Inst. of Data Science
  6. Univ. of Manchester (United Kingdom). School of Computer Science
  7. Univ. of Oxford (United Kingdom). Oxford e-Research Centre
  8. German Research Center for Environmental Health (Helmholtz Centre Munich) (Germany). Inst. of Experimental Genetics
  9. Univ. of California, San Diego, CA (United States). Center for Research in Biological Systems
  10. Babraham Inst., Cambridge (United Kingdom)
  11. European Molecular Biology Lab., Heidelberg (Germany)
  12. Technical Univ. of Denmark, Lyngby (Denmark). Center for Biological Sequence Analysis. Dept. of Systems Biology
  13. California Digital Library, Oakland, CA (United States)
  14. Daresbury Lab., Warrington (United Kingdom). Science and Technology Facilities Council
  15. Univ. of Groningen (Netherlands). Genomics Coordination Center. Dept. of Genetics. Univ. Medical Center Groningen. Groningen Bioinformatics Center
  16. Heidelberg Inst. for Theoretical Studies (Germany). Scientific Databases and Visualization
  17. Bern Univ. of Applied Sciences (Switzerland). Inst. for Medical Informatics. Engineering and Information Technology
  18. Univ. of Manchester (United Kingdom). Manchester Inst. of Biology; Stellenbosch Univ. (South Africa). Dept. of Biochemistry
  19. Univ. of Manchester (United Kingdom). Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals
  20. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
  21. Leiden Univ. (Netherlands). Leiden Inst. of Advanced Computer Science
Publication Date:
Research Org.:
Oregon Health & Science Univ., Portland, OR (United States); European Molecular Biology Lab., Hinxton (United Kingdom); Univ. of Oxford (United Kingdom); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Inst. of Health (NIH) (United States); European Commission (EC); Biotechnology and Biological Sciences Research Council (BBSRC) (United Kingdom)
OSTI Identifier:
1408440
Grant/Contract Number:
AC02-05CH11231; R24OD011883; U41HG007822; U24AI117966; U54AI117925; 675728; 312455; 654248; 601043; BB/L005069/1; BB/M013189/1; BB/K019783/1; BBS/E/B/000C0419; BB/M006891/1; BB/M017702/1; BB/L005050/1
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS biology (Online)
Additional Journal Information:
Journal Name: PLoS biology (Online); Journal Volume: 15; Journal Issue: 6; Journal ID: ISSN 1545-7885
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES; archives; internet; citation analysis; biodiversity; ontologies; colon; sequence databases; syntax

Citation Formats

McMurry, Julie A., Juty, Nick, Blomberg, Niklas, Burdett, Tony, Conlin, Tom, Conte, Nathalie, Courtot, Mélanie, Deck, John, Dumontier, Michel, Fellows, Donal K., Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Grethe, Jeffrey, Hastings, Janna, Hériché, Jean-Karim, Hermjakob, Henning, Ison, Jon C., Jimenez, Rafael C., Jupp, Simon, Kunze, John, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria Jesus, McEntyre, Johanna R., Morris, Chris, Muilu, Juha, Müller, Wolfgang, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L., Soiland-Reyes, Stian, Stanford, Natalie J., Swainston, Neil, Washington, Nicole, Williams, Alan R., Wimalaratne, Sarala M., Winfree, Lilly M., Wolstencroft, Katherine, Goble, Carole, Mungall, Christopher J., Haendel, Melissa A., and Parkinson, Helen. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. United States: N. p., 2017. Web. doi:10.1371/journal.pbio.2001414.
McMurry, Julie A., Juty, Nick, Blomberg, Niklas, Burdett, Tony, Conlin, Tom, Conte, Nathalie, Courtot, Mélanie, Deck, John, Dumontier, Michel, Fellows, Donal K., Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Grethe, Jeffrey, Hastings, Janna, Hériché, Jean-Karim, Hermjakob, Henning, Ison, Jon C., Jimenez, Rafael C., Jupp, Simon, Kunze, John, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria Jesus, McEntyre, Johanna R., Morris, Chris, Muilu, Juha, Müller, Wolfgang, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L., Soiland-Reyes, Stian, Stanford, Natalie J., Swainston, Neil, Washington, Nicole, Williams, Alan R., Wimalaratne, Sarala M., Winfree, Lilly M., Wolstencroft, Katherine, Goble, Carole, Mungall, Christopher J., Haendel, Melissa A., & Parkinson, Helen. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. United States. doi:10.1371/journal.pbio.2001414.
McMurry, Julie A., Juty, Nick, Blomberg, Niklas, Burdett, Tony, Conlin, Tom, Conte, Nathalie, Courtot, Mélanie, Deck, John, Dumontier, Michel, Fellows, Donal K., Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Grethe, Jeffrey, Hastings, Janna, Hériché, Jean-Karim, Hermjakob, Henning, Ison, Jon C., Jimenez, Rafael C., Jupp, Simon, Kunze, John, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria Jesus, McEntyre, Johanna R., Morris, Chris, Muilu, Juha, Müller, Wolfgang, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L., Soiland-Reyes, Stian, Stanford, Natalie J., Swainston, Neil, Washington, Nicole, Williams, Alan R., Wimalaratne, Sarala M., Winfree, Lilly M., Wolstencroft, Katherine, Goble, Carole, Mungall, Christopher J., Haendel, Melissa A., and Parkinson, Helen. Thu . "Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data". United States. doi:10.1371/journal.pbio.2001414. https://www.osti.gov/servlets/purl/1408440.
@article{osti_1408440,
title = {Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data},
author = {McMurry, Julie A. and Juty, Nick and Blomberg, Niklas and Burdett, Tony and Conlin, Tom and Conte, Nathalie and Courtot, Mélanie and Deck, John and Dumontier, Michel and Fellows, Donal K. and Gonzalez-Beltran, Alejandra and Gormanns, Philipp and Grethe, Jeffrey and Hastings, Janna and Hériché, Jean-Karim and Hermjakob, Henning and Ison, Jon C. and Jimenez, Rafael C. and Jupp, Simon and Kunze, John and Laibe, Camille and Le Novère, Nicolas and Malone, James and Martin, Maria Jesus and McEntyre, Johanna R. and Morris, Chris and Muilu, Juha and Müller, Wolfgang and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Sariyar, Murat and Snoep, Jacky L. and Soiland-Reyes, Stian and Stanford, Natalie J. and Swainston, Neil and Washington, Nicole and Williams, Alan R. and Wimalaratne, Sarala M. and Winfree, Lilly M. and Wolstencroft, Katherine and Goble, Carole and Mungall, Christopher J. and Haendel, Melissa A. and Parkinson, Helen},
abstractNote = {In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.},
doi = {10.1371/journal.pbio.2001414},
journal = {PLoS biology (Online)},
number = 6,
volume = 15,
place = {United States},
year = {Thu Jun 29 00:00:00 EDT 2017},
month = {Thu Jun 29 00:00:00 EDT 2017}
}

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