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Revised

Recognizing the value of software: a software citation guide

[version 2; peer review: 2 approved]

Previously titled: "The importance of software citation"

Daniel S. Katz ¹, Neil P. Chue Hong², Tim Clark³, [...] August Muench⁴, Shelley Stall⁵, Daina Bouquin⁶, Matthew Cannon⁷, Scott Edmunds⁸, Telli Faez⁹, Patricia Feeney¹⁰, Martin Fenner¹¹, Michael Friedman¹², Gerry Grenier¹³, Melissa Harrison¹⁴, Joerg Heber¹⁵, Adam Leary¹⁶, Catriona MacCallum¹⁷, Hollydawn Murray¹⁸, Erika Pastrana¹⁹, Katherine Perry²⁰, Douglas Schuster²¹, Martina Stockhause²², Jake Yeston²³

Daniel S. Katz ¹, Neil P. Chue Hong², [...] Tim Clark³, August Muench⁴, Shelley Stall⁵, Daina Bouquin⁶, Matthew Cannon⁷, Scott Edmunds⁸, Telli Faez⁹, Patricia Feeney¹⁰, Martin Fenner¹¹, Michael Friedman¹², Gerry Grenier¹³, Melissa Harrison¹⁴, Joerg Heber¹⁵, Adam Leary¹⁶, Catriona MacCallum¹⁷, Hollydawn Murray¹⁸, Erika Pastrana¹⁹, Katherine Perry²⁰, Douglas Schuster²¹, Martina Stockhause²², Jake Yeston²³

PUBLISHED 12 Jan 2021

Author details Author details

¹ University of Illinois at Urbana-Champaign, Urbana, IL, USA
² EPCC, University of Edinburgh, Edinburgh, UK
³ University of Virginia, Charlottesville, VA, USA
⁴ American Astronomical Society, Washington, DC, USA
⁵ American Geophysical Union, Washington, DC, USA
⁶ Harvard-Smithsonian Center for Astrophysics, Cambridge, MA, USA
⁷ Taylor & Francis Group, Oxford, UK
⁸ GigaScience Press, BGI Hong Kong, Hong Kong, Hong Kong
⁹ Elsevier, Amsterdam, The Netherlands
¹⁰ Crossref, Lynnfield, MA, USA
¹¹ DataCite, Hannover, Germany
¹² American Meteorological Society, Boston, MA, USA
¹³ Publishing Technology, IEEE, Piscataway, NJ, USA
¹⁴ Production, eLife, Cambridge, UK
¹⁵ PLOS, San Francisco, CA, USA
¹⁶ Oxford University Press, Oxford, UK
¹⁷ Open Science, Hindawi, London, UK
¹⁸ F1000Research, London, UK
¹⁹ Springer Nature, New York, NY, USA
²⁰ Product Management, Wiley, Boston, MA, USA
²¹ National Center for Atmospheric Research, Boulder, CO, USA
²² German Climate Computing Center (DKRZ), Hamburg, Germany
²³ AAAS, Washington, DC, USA

Daniel S. Katz
Roles: Conceptualization, Methodology, Project Administration, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing

Neil P. Chue Hong
Roles: Conceptualization, Methodology, Project Administration, Writing – Original Draft Preparation, Writing – Review & Editing

Tim Clark
Roles: Conceptualization, Methodology, Project Administration, Writing – Original Draft Preparation, Writing – Review & Editing

August Muench
Roles: Conceptualization, Methodology, Project Administration, Writing – Original Draft Preparation, Writing – Review & Editing

Shelley Stall
Roles: Conceptualization, Methodology, Project Administration, Writing – Original Draft Preparation, Writing – Review & Editing

Daina Bouquin
Roles: Conceptualization, Writing – Review & Editing

Matthew Cannon
Roles: Conceptualization, Writing – Review & Editing

Scott Edmunds
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Telli Faez
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Patricia Feeney
Roles: Writing – Review & Editing

Martin Fenner
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Michael Friedman
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Gerry Grenier
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Melissa Harrison
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Joerg Heber
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Adam Leary
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Catriona MacCallum
Roles: Conceptualization, Writing – Review & Editing

Hollydawn Murray
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Erika Pastrana
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Katherine Perry
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Douglas Schuster
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Martina Stockhause
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

Jake Yeston
Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing

OPEN PEER REVIEW

REVIEWER STATUS

This article is included in the Research on Research, Policy & Culture gateway.

Abstract

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

Keywords

Software citation, publishing, scholarly communication, guidelines, bibliometrics

Corresponding author: Daniel S. Katz

Competing interests: Authors include representative and editors from: Journal of Open Source Software (Open Journals), Journal of Open Research Software (Ubiquity Press), AAS Journals, AGU Journals, Taylor & Francis, GigaScience Press, Elsevier, DataCite, American Meteorological Society, IEEE Publications, eLife, PLOS, Oxford University Press, Hindawi, F1000Research, Springer Nature, Wiley, Science Magazine. Hollydawn Murray is the Head of Data and Software Publishing at F1000 Research, but was not involved in the processing of this article.

Grant information: The author(s) declared that no grants were involved in supporting this work.

Copyright: © 2021 Katz DS et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Katz DS, Chue Hong NP, Clark T et al. Recognizing the value of software: a software citation guide [version 2; peer review: 2 approved]. F1000Research 2021, 9:1257 (https://doi.org/10.12688/f1000research.26932.2) First published: 19 Oct 2020, 9:1257 (https://doi.org/10.12688/f1000research.26932.1) Latest published: 12 Jan 2021, 9:1257 (https://doi.org/10.12688/f1000research.26932.2)

Revised Amendments from Version 1

In response to reviewer feedback, and an additional comment from a reader, we have made the following changes to this article:

A new title to better reflect the content and purpose
At the end of the first section, an added sentence and two references to recognize previous work in data citation and the differences between software and data
In the software citation essentials section, updated text on software versions and the software concept (the set of all versions).
Also in that section, added text to explain the software publication date.
Also in that section, updated text to emphasize citing the software itself citing an article about the software.
The usage note about hardware requirements has been removed as confusing and beyond the scope of the article.

See the authors' detailed response to the review by Gianmaria Silvello
See the authors' detailed response to the review by Ludo Waltman

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. Books and journal articles have long benefited from an infrastructure that makes them easy to cite, a key element in the process of research and academic discourse in all disciplines. We believe that software (including computational code, scripts, models, notebooks and libraries) should be cited in the same way that other sources of information, such as articles and books, are cited.

Citing software helps further research and provides the means for other researchers to access software in order to:

support proper attribution and credit (similar to that of papers, data, etc.);
enable peer-review, validation, and reproducibility of findings;
support collaboration and reuse; and
encourage building on the work of others.

Software citation elevates software to the level of a first-class object in the digital scholarly ecosystem, consistent with its immense actual present-day significance.

FORCE11 has been developing guidance for software citation. The Software Citation Principles (Smith et al., 2016) were written to encourage broad adoption of a consistent policy for software citation across disciplines and venues. The Software Citation Checklist for Authors (Chue Hong et al., 2019a) and Software Citation Checklist for Developers (Chue Hong et al., 2019b) provide more practical information for those seeking to improve their practice. This work has been influenced by prior work on Data Citation (Data Citation Synthesis Group, 2014), while recognizing that software is not the same as data in the context of citation (Katz et al., 2016).

Software citation essentials

This article is aimed at authors citing software. This includes software developed by others, as well as software developed by any or all of the authors. Making software citable is a critical developer-led step, which is briefly detailed in the next subsection, "Making Software Citable".

The use of persistent identifiers (PIDs) and core descriptive metadata are essential elements of software citation. This is because they are the mechanism used to index and track citations. We recognise that the challenges associated with software deposit and publication vary across disciplines, and we encourage research communities to develop citation systems that work well for them. We also recognise that the citation style formats used vary between disciplines and journals. Independent of the style of any citation, we recommend certain essential metadata elements should always be captured.

There are multiple use cases for citing software. These include referring to the software used in deriving the results of an article or discussing algorithms, general features, or concepts provided by a piece of software. If you used the software directly in the research described in your article (e.g., in the Methods section), then we recommend citing the specific version used (and the authors and publication date for that version). When discussing software more broadly, we recommend citing the software as a concept (project).

Our recommended format for software citation is to ensure the following information is provided as part of the reference:

Creator(s): the authors or project that developed the software.
Title: the name of the software.
Publication venue: the publication venue of the software, preferentially, an archive or repository that provides persistent identifiers.
Date: the date the software was published. This is the date associated with a release or version of the software, or “n.d.” if the date is unknown.
Identifier: a resolvable pointer to the software, preferentially, a PID that resolves to a landing page containing descriptive metadata about the software, similar to how a Digital Object Identifier (DOI) for a paper that points to a page about the paper rather than directly to a representation of the paper, such as the PDF. DOIs are preferable, and other examples of PIDs include Handles, RRIDs, ASCL IDs, swMath IDs, Software Heritage IDs, ARKs, etc. If there is no PID for the software, a URL to where the software exists may be the best identifier available.

It may also be desirable, and depending upon the publisher, may be required, to include information about two optional properties (as appropriate):

Version: the identifier for the version of the software being referenced. If the version is unidentified or unknown, the date of access should be used.
Type: some citation styles (e.g., APA), require a bracketed description of the citation (e.g., Computer software) to be included.

If an article exists that describes the software, it should be cited as an additional reference, as well as citing the software itself. Do not cite the article instead of the software.

Making software citable

Authors should consult the Software Citation Checklist for Developers (Chue Hong et al., 2019b) for information on how to obtain a PID or choose a software license for software they have developed. That document contains a set of steps that developers can take to ensure that they are following good practices. We strongly recommend that journals provide such information to their authors, either by referring to that document, or using text from it or similar text. Example guidance would include instructing authors to version their software, choose a license for their software, perhaps by linking to the information at choosealicense.org, record metadata about the software as part of the repository, deposit their software in a preservation repository that provides a PID, and advertise the recommended citation in the repository. In particular, guidance should explicitly mention that Creative Commons licenses (including CC-BY) must not be used for software, and an open source license should be used.

Software citation examples

The following examples show how software can be cited in one common citation style, APA. The general format for downloaded software, from Section 10.10 of (2020) Publication Manual of the American Psychological Association (Seventh Edition) is:

Developer, A. A., Developer, B. B., & Developer, C. C. (yyyy)¹. Title of the software: Subtitle (Version #.#)² [Computer software]³. Publisher⁴, https://URL⁵

If no version number or version string exists, we (the FORCE11 Software Citation Implementation Working Group) modify this to:

Developer, A. A., Developer, B. B., & Developer, C. C. (yyyy). Title of the software: Subtitle [Computer software]. Archive Name. Retrieved Month dd, yyyy, from https://URL

The following are examples of software citations.

Ideal citations to the specific version of the software, where all recommended information is present (the first demonstrates a large author list; the second demonstrates a project team as the author):

Coon, E., Berndt, M., Jan, A., Svyatsky, D., Atchley, A., Kikinzon, E., Harp, D., Manzini, G., Shelef, E., Lipnikov, K., Garimella, R., Xu, C., Moulton, D., Karra, S., Painter, S., Jafarov, E., & Molins, S. (2020, March 25). Advanced Terrestrial Simulator (ATS) v0.88 (Version 0.88) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.3727209
Lab For Exosphere And Near Space Environment Studies. (2019, March 20). lenses-lab/LYAO_RT-2018JA026426: Original Release (Version 1.0.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.2598836

Citation referencing software that is preserved in a software archive (e.g. Software Heritage)⁶:

Delebecque, F., Gomez, C., Goursat, M., Nikoukhah, R., Steer, S., & Chancelier, J.-P. (1994). Scilab (Version 1.1) [Computer software]. Software Heritage, swh:1:dir:1ba0b67b5d0c8f10961d878d91ae9d6e499d746a;origin=https://hal.archives-ouvertes.fr/hal-02090402
Di Cosmo, R. & Danelutto, M. (2020). The Parmap library: Core mapping routine (Version 1.1.1) [Computer software]. Software Heritage, swh:1:cnt:43a6b232768017b03da934ba22d9cc3f2726a6c5;lines=192-228;origin=https://github.com/rdicosmo/parmap

A citation for software that does not have a PID but does have a version and identifier (URL), where authorship is assigned to the project as a whole:

Dataverse Project (2020). Dataverse (Version 4.20) [Computer software] https://github.com/IQSS/dataverse/releases/tag/v4.20

A citation for software where there is no version identified and where the publishing date is unknown:

Thomas, J. & Daujotas, G.⁷ (n.d.). is-thirteen [Computer software]. GitHub. Retrieved June 17, 2020 from https://github.com/jezen/is-thirteen

A citation for a software concept (all versions):

BLAS team (n.d.), BLAS (Basic Linear Algebra Subprograms) [Computer software]. Netlib. http://www.netlib.org/blas/

A citation for software where little information is available, perhaps where only the executable program is available. For commercial software, a link to information about availability for purchase is helpful, as shown in the example below.

IBM Corp. (2017). IBM SPSS Statistics for Windows (Version 25.0) [Computer software]. IBM Corp. https://www.ibm.com/products/spss-statistics

In-text referencing

Two examples of how the citations above would be referenced in the text of a paper according to APA style⁸, the first in the methodology section and the second in a related work section:

We used version 0.88 of Advanced Terrestrial Simulator (Coon et al., 2019) and version 25.0 of IBM SPSS Statistics for Windows (IBM Corp., 2017) to carry out the analysis of the data in this paper.
In the field of bibliometrics, a different approach is taken by BLAS (BLAS team, n.d).

Usage note

This document provides generic guidance about software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce different versions of this document with software examples and citation styles that are appropriate for their intended audience. We request that those documents refer back to (or cite) this one. This document can be cited (in APA 7th Ed. style) as:

Katz, D. S., Chue Hong, N. P., Clark T., Muench, A., Stall, S., Bouquin, D., Cannon, M., Edmunds, S., Faez, T., Farmer, R., Feeney, P., Fenner, M., Friedman, M., Grenier, G., Harrison, M., Heber, J., Leary, A., MacCallum, C., Murray, H., … Yeston, J. (2020) Recognizing the value of software: a software citation guide. F1000 Research. https://doi.org/10.12688/f1000research.26932.2

Data availability

No data is associated with the article.

Acknowledgements

This article is based in part on data citation guidance published by DataCite (Datacite), and on related publications from FORCE11 working groups (Cousijn et al., 2018; Fenner et al., 2019). It was initially drafted by Neil Chue Hong, and further developed by Daniel S. Katz, Neil Chue Hong, Tim Clark, August Muench, and Shelley Stall, along with many participants in the FORCE11 Software Citation Implementation Working Group’s Journals Task Force. We also acknowledge useful advice from Kevin Swanson, Taylor & Francis.

Footnotes

¹The year is required, or “n.d.” if not identifiable.

²The version is optional but preferred. Note that the version may be a token/string that is not a semantic version (https://semver.org/) and that must be exactly preserved, such as a commit hash (e.g., a149dbc00fe8b0e8260f7c2d39c77692683e7fa4), a semi-numeric tagged release (e.g., v0.4-alpha01), or date string (e.g., 2020-02-20).

³APA style includes additional information that is helpful for software citation (e.g. it requires the [Computer software] bracketed description). Although this is not part of our guidance above, we recommend following APA style and including these elements. Other styles may not use this extra information.

⁴If the software is downloaded or if the developer is the same as the publisher, the publisher name is omitted.

⁵In APA style, the URL is used for both URLs and DOIs or other PIDs, e.g., a DOI is expressed as https://doi.org/DOI.

⁶This example is analogous to citing the preserved version of a webpage on archive.org, rather than the webpage directly.

⁷The README for the is-thirteen software says “A helpful tool by Jezen Thomas with helpful help from Gytis Daujotas and many fine folk.”; therefore our citation tries to take the developers intentions around authorship into account.

⁸American Psychological Association. (2020). Publication manual of the American Psychological Association (7th ed.). American Psychological Association. https://doi.org/10.1037/0000165-000

Faculty Opinions recommended

References

Chue Hong NP, Allen A, Gonzalez-Beltran A, et al.: Software Citation Checklist for Authors (Version 0.9.0). Zenodo. 2019a. Publisher Full Text
Chue Hong NP, Allen A, Gonzalez-Beltran A, et al.: Software Citation Checklist for Developers (Version 0.9.0). Zenodo. 2019b. Publisher Full Text
Cousijn H, Kenall A, Ganley E, et al.: A data citation roadmap for scientific publishers. Sci Data. 2018; 5: 180259. PubMed Abstract | Publisher Full Text | Free Full Text
Data Citation Synthesis Group: Joint Declaration of Data Citation Principles. Future of Research Communication and e-Scholarship (FORCE11). 2014. Publisher Full Text
DataCite: DataCite - Cite Your Data. Reference Source
Fenner M, Crosas M, Grethe JS, et al.: A data citation roadmap for scholarly data repositories. Sci Data. 2019; 6(1): 28. PubMed Abstract | Publisher Full Text | Free Full Text
Katz DS, Niemeyer KE, Smith AM, et al.: Software vs. data in the context of citation. PeerJ Prepr. 2016; 4: e2630v1. Publisher Full Text
Smith AM, Katz DS, Niemeyer KE, et al.: Software Citation Principles. PeerJ Comput Sci. 2016; 2: e86. Publisher Full Text

Comments on this article Comments (1)

Version 2

VERSION 2 PUBLISHED 12 Jan 2021

Revised

Reader Comment 15 Jan 2021

Oliver Bertuch, Forschungszentrum Jülich GmbH, Jülich, Germany

15 Jan 2021

Reader Comment

A very well written overview about how to make research software more important to research and researchers. If my comment below is out of scope for this doc, please feel ... Continue reading A very well written overview about how to make research software more important to research and researchers. If my comment below is out of scope for this doc, please feel free to disregard.

In many conversations with RDM people, there seem to form two "schools" of depositing software and making it citable. One is fostering bundles of software and data together in one package/container, the other encourages making seperate deposits. There are pros and cons in both approaches.

In my humble opinion it would help scientists to make an informed decision when this aspect is picked up in articles and guides like this. Maybe this is better suited for the checklist etc to explain all pesky details, yet a hint about taking care and where to find more information would be perfect.
A very well written overview about how to make research software more important to research and researchers. If my comment below is out of scope for this doc, please feel free to disregard.

In many conversations with RDM people, there seem to form two "schools" of depositing software and making it citable. One is fostering bundles of software and data together in one package/container, the other encourages making seperate deposits. There are pros and cons in both approaches.

In my humble opinion it would help scientists to make an informed decision when this aspect is picked up in articles and guides like this. Maybe this is better suited for the checklist etc to explain all pesky details, yet a hint about taking care and where to find more information would be perfect.
Competing Interests: No competing interests were disclosed. Close
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