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

Julie McMurry; Navtej Juty; Niklas Blomberg; Anthony Burdett; Tom Conlin; Nathalie Conte; Melanie Courtot; John Deck; Michel Dumontier; Donal Fellows; Alejandra Gonzalez-Beltran; Philipp Gormanns; Jeffrey Grethe; Janna Hastings; Henning Hermjakob; Jean-Karim Heriche; Jon Ison; Rafael Jimenez; Simon Jupp; John Kunze; Camille Laibe; Nicolas Le Novere; James Robert Malone; Maria-Jesus Martin; Jo McEntyre; Chris Morris; Juha Muilu; Wolfgang Mueller; Philippe Rocca-Serra; Susanna-Assunta Sansone; Murat Sariyar; Jacky Snoep; Natalie J Stanford; Stian Soiland-Reyes; Neil Swainston; Nicole Washington; Alan Williams; Sarala Wimalaratne; Lilly Winfree; Katy Wolstencroft; Carole Goble; Christopher Mungall; Melissa Haendel; Helen Parkinson

doi:10.1101/117812

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

Julie McMurry, Navtej Juty, Niklas Blomberg, Anthony Burdett, Tom Conlin, Nathalie Conte, Melanie Courtot, John Deck, Michel Dumontier, Donal Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Henning Hermjakob, Jean-Karim Heriche, Jon Ison, Rafael Jimenez, Simon Jupp, John KunzeCamille Laibe, Nicolas Le Novere, James Robert Malone, Maria-Jesus Martin, Jo McEntyre, Chris Morris, Juha Muilu, Wolfgang Mueller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky Snoep, Natalie J Stanford, Stian Soiland-Reyes, Neil Swainston, Nicole Washington, Alan Williams, Sarala Wimalaratne, Lilly Winfree, Katy Wolstencroft, Carole Goble, Christopher Mungall, Melissa Haendel, Helen Parkinson

Research output: Working paper / Preprint › Preprint

Abstract

In many disciplines, data is 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 ten 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 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.

Original language	English
Publisher	Cold Spring Harbor Laboratory - bioRxiv
Pages	1-27
DOIs	https://doi.org/10.1101/117812
Publication status	Published - 20 Mar 2017
Externally published	Yes

Access to Document

10.1101/117812Licence: Unspecified

1 Article

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D. K., Gonzalez-Beltran, A., Gormanns, P., Grethe, J. S., Hastings, J., Heriche, J-K., Hermjakob, H., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J., & 24 othersLaibe, C., Le Novere, N., Malone, J., Martin, M-J., McEntyre, J. R., Morris, C., Muilu, J., Mueller, W., Rocca-Serra, P., Sansone, S-A., Sariyar, M., Snoep, J. L., Soiland-Reyes, S., Stanford, N. J., Swainston, N., Washington, N. L., Williams, A. R., Wimalaratne, S. M., Winfree, L. M., Wolstencroft, K., Goble, C., Mungall, C. J., Haendel, M. A. & Parkinson, H., Jun 2017, In: Plos Biology. 15, 6, e2001414.
Research output: Contribution to journal › Article › Academic › peer-review

Open Access

Cite this

McMurry, J., Juty, N., Blomberg, N., Burdett, A., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D., Gonzalez-Beltran, A., Gormanns, P., Grethe, J., Hastings, J., Hermjakob, H., Heriche, J.-K., Ison, J., Jimenez, R., Jupp, S., ... Parkinson, H. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. (pp. 1-27). Cold Spring Harbor Laboratory - bioRxiv. https://doi.org/10.1101/117812

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abstract = "In many disciplines, data is highly decentralized across thousands of online databases (repositories, registries,and knowledgebases). Wringing value from such databases depends on the discipline of data science and onthe humble bricks and mortar that make integration possible; identifiers are a core component of thisintegration infrastructure. Drawing on our experience and on work by other groups, we outline ten lessons wehave 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 important considerations for those referencing identifiers invarious circumstances, including by authors and data generators. While the importance and relevance of eachlesson will vary by context, there is a need for increased awareness about how to avoid and manage commonidentifier problems, especially those related to persistence and web-accessibility/resolvability. We focusstrongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to otherdisciplines. ",

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McMurry, J, Juty, N, Blomberg, N, Burdett, A, Conlin, T, Conte, N, Courtot, M, Deck, J, Dumontier, M, Fellows, D, Gonzalez-Beltran, A, Gormanns, P, Grethe, J, Hastings, J, Hermjakob, H, Heriche, J-K, Ison, J, Jimenez, R, Jupp, S, Kunze, J, Laibe, C, Novere, NL, Malone, JR, Martin, M-J, McEntyre, J, Morris, C, Muilu, J, Mueller, W, Rocca-Serra, P, Sansone, S-A, Sariyar, M, Snoep, J, Stanford, NJ, Soiland-Reyes, S, Swainston, N, Washington, N, Williams, A, Wimalaratne, S, Winfree, L, Wolstencroft, K, Goble, C, Mungall, C, Haendel, M & Parkinson, H 2017 'Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data' Cold Spring Harbor Laboratory - bioRxiv, pp. 1-27. https://doi.org/10.1101/117812

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AU - Burdett, Anthony

AU - Conlin, Tom

AU - Conte, Nathalie

AU - Courtot, Melanie

AU - Deck, John

AU - Dumontier, Michel

AU - Fellows, Donal

AU - Gonzalez-Beltran, Alejandra

AU - Gormanns, Philipp

AU - Grethe, Jeffrey

AU - Hastings, Janna

AU - Hermjakob, Henning

AU - Heriche, Jean-Karim

AU - Ison, Jon

AU - Jimenez, Rafael

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AU - Snoep, Jacky

AU - Stanford, Natalie J

AU - Soiland-Reyes, Stian

AU - Swainston, Neil

AU - Washington, Nicole

AU - Williams, Alan

AU - Wimalaratne, Sarala

AU - Winfree, Lilly

AU - Wolstencroft, Katy

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