s11 Citation & Bibliography Style Guide

In academic writing, the s11 House Rules recommend the following bibliography style:

First Author, Second Author, All Authors (year):
Title.
Event/Report, Venue volume(issue)
https://doi.org/10.1000/123456

Rationale:

  1. It should be possible to write the reference without a bibliography manager
  2. All authors SHOULD be credited. We have enough bytes left on the Internet, and et al. have high enough h-index already.
  3. Names around the world vary in how they order given name and surname, if they even have that concept. Respect each culture and don’t reshuffle name parts.
  4. Formatting and newlines help readability and to separate distinct pieces of information.
  5. The title is the most important information and should be highlighted, clearly different from author list or way of publishing.
  6. Publisher organization and location is not relevant, given a resolvable PID.
  7. You can cite any publicly available source. It does not have to be peer reviewed—you presumably reviewed the content before citing it?
  8. A persistent identifier (PID) or URL MUST be present. DOIs are included for any type of resource, where known.
  9. Anything cited should be accessible Open Access⁠—request or post a preprint if not.
  10. The bibliography is written primarily for human readers on the Web, not for print in 1960s style.
  11. The year of publication should be distinct from date of event.

Traditional bibliography styles (of which there are plenty) have several issues:

  1. Unnecessary information that only relate to printed press.
  2. Unnecessary shortening of author names and author list, which gives preference to surnames and lead authors.
  3. Double-comma lists of Surname, F, Surname, S, et al. are very hard to read.
  4. Finishing author list with the word and unncessarily emphasizes last author (articles should instead annotate contributor roles).
  5. Uneccessary abbreviation of journal names (Future Gener Comp Sy, New Engl J Med) is cryptic and assumes journal is well known to all readers.
  6. Uneccessary inclusion of page numbers which are then somehow mangled for continuations – did you really flip through pages 1213–20?
  7. Lack of hyperlinks1 and persistent identifiers makes it hard to navigate to the publication or to generate consistent metrics.
  8. Lack of formatting (e.g. difficult to differentiate authors, title or venue).
  9. Lack of findability details for online resources and standards. Readers should not need to Google the reference and hope for the best!
  10. Traditional style assume there is shortage of letters, using acrnms mke it dffclt to read. There are now sufficient spare pages on the Internet.
  11. Outdated bibliography managers (e.g. for LaTeX) deliberately mangle and remove information such as DOIs in order to emulate 1960s printing press practices.
  12. Bibliography manager outputs can’t easily be edited when the journal’s style is outdated or misleading. For instance, showing a temporary URL to a journal website from the url BibTeX field and ignoring the doi field.
  13. Bibliography managers have poor support for modern scholarly outputs, as they assume authors only cite outputs from a printing press. This makes it hard to cite software, websites, online proceedings.

The s11 bibliography style can be considered as a combination these citation styles:

s11 Citation Style Language

An experimental CSL definition s11.csl is available, but may require some final editing. Contributions welcome!.

Example usage with pandoc:

pandoc -i original.tex --bibliography references.bib --csl https://s11.no/2021/house-rules/s11-citation-style.csl -t gfm -o index.md

Journal article

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe (2019):
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.
GigaScience 8(11):giz095
https://doi.org/10.1093/gigascience/giz095

Notes:

  1. First line lists all authors with full names as listed within article. No assumptions made about surnames.
    For initials (e.g. middle name or unknown given name), use full punctuation: “C.J. Tunis”.
  2. Names are listed with regular comma , as separator, including for last name. No need for et al., and or &.
  3. After last author, add (year) in 4 digits, reflecting official publishing date (which may be before the issue’s publication date). Terminated with : and newline.
  4. Second line is title in bold. Hyperlink to DOI—only if open access. Final period . is not bold nor in hyperlink, followed by newline.
    If the landing page for a DOI does not show the full text, the hyperlink MAY go directly to HTML and PDF if the URI seem stable.
  5. Third line is full journal name in italics with official captitalization. No acronyms, e.g. J Chem Bio ⟶ Journal of Chemical Biology
  6. Journal name is immediately followed by volume number in bold. Optional (issue) and/or :article ID. Terminated with newline (no period as there is no sentence). Do not repeat (year) or month of issue, unless this is the official identifier.
  7. Page numbers are NOT included⁠—welcome to the Internet.
    ..except for publications without per-article DOI, then add: pp. 123–129 (that is en dash –, not hyphen - nor em dash ⁠—)
  8. Last line is literal URI, ideally DOI with prefix https://doi.org/ and any %2f within the DOI expanded to /
  9. Any optional links, e.g. [preprint] or [poster] (see below)

Tip: If you are using Markdown, use two spaces or \ at the end of line to force a <br /> newline.

Article/abstract in conference

Kyle Chard, Mike D’ Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W. Deutsch, Ivo Dinov, Nathan Price, Arthur Toga (2016):
I’ll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Datasets.
IEEE International Conference on Big Data 2016 (IEEE BigData 2016), Washington DC, USA, 2016-12-05
https://doi.org/10.1109/BigData.2016.7840618 [preprint]

Alasdair Gray, Carole Goble, Rafael Jimenez, Bioschemas Community (2017):
Bioschemas: From Potato Salad to Protein Annotation.
Proceedings of the ISWC 2017 posters & demonstrations and industry tracks co-located with 16th international semantic web conference (ISWC 2017), Vienna, Austria, .
CEUR Workshop Proceedings 1963
https://iswc2017.semanticweb.org/paper-579/ https://ceur-ws.org/Vol-1963/paper579.pdf

Notes:

  1. Conferences are often not consistent in what are their Full name, but usually have a consistent (SHRTNAME21). Do not italics the shortname as it’s not part of the full name.
  2. If the conference has already published proceedings, then prefer the book title rather than the conference website name. Do not include the editors of the proceedings (unless citing the whole of proceedings).
  3. Hyperlink to the conference/agenda from the shortname (or full name). As some conferences reuse the same website multiple years, or forget to renew their domain names, archive using Internet Archive’s Wayback Machine (tip: “Save outlinks” will on a good day archive the proceeding PDFs)
  4. Conferences sometimes don’t publish proceedings, or publish them a long time after, which could cause the published (year) to flip over. Optionally include the conference date in ISO-8601 format, it may differ from the published year. If a conference was delayed (e.g. in COVID-19 lockdown) then the shortname year may not match the conference dates.
  5. For some reason many conferences still do not publish Open Access. The biggest hint of paywalled conference content in my field is IEEE or Springer Lecture Notes… Make sure you add/ask for a [preprint].
  6. If the article is available as a PDF, but without a DOI, the URL may not survive the test of time. Archive specifically with Wayback Machine.
  7. Some citation software and websites may confusingly list the city of the proceeding publisher’s head quarters (e.g. Springer, New York, NY) instead of where the conference actually took place. If in doubt, remove the location, it is seldom relevant for international conferences. Some conferences are also online/hybrid.

Books and chapters

Lois Mai Chan (1995):
Library of Congress Subject Headings: Principles and Application, 3rd edition.
ISBN 9781563081910.

Barend Mons (2018):
Data Stewardship for Open Science.
ISBN 9781315351148

William Stallings (1990):
Handbook of computer-communications standards: The open systems (OSI) model and OSI-related standards, 2nd ed.
Sams.
ISBN 978-0-672-22697-7

Tim Berners-Lee, Mark Fischetti (1999):
Weaving the Web: The original design and ultimate destiny of the World Wide Web by its inventor.
ISBN 978-0-06-251586-5

Christian Bizer, Tom Heath, Tim Berners-Lee (2011):
Linked data: The story so far.
Semantic Services, Interoperability and Web Applications: Emerging Concepts, Amit Sheth (ed.)
ISBN 9781609605933 https://doi.org/10.4018/978-1-60960-593-3.ch008

Luiz Olavo Bonino Da Silva Santos, Mark D. Wilkinson, Arnold Kuzniar, Rajaram Kaliyaperumal, Mark Thompson, Michel Dumontier, Kees Burger (2016):
FAIR Data points supporting big data interoperability.
Enterprise interoperability in the digitized and networked factory of the future, Martin Zelm, Guy Doumeingts, Joao Pedro Mendonça (eds.).
iSTE Press.
ISBN 978-1-84704-044-2
[preprint]

  1. Check carefully if the book is actually a conference proceeding. You may need to navigate to the cover/introduction chapter.
  2. It can be hard to find preprints of text books, but some authors publish green open access versions of their book chapters.
  3. Include the ISBN number if known. Prefer the “electronic” issue. Use https://identifiers.org/isbn/ as prefix, removing any - and prefix 978 on shorter ISBN-10. Report any unknown ISBN to the resolver and link the ISBN to the publisher’s page (see iSTE example above).
  4. Cite as well the DOI of the book if available.
  5. Check you are citing the right (typically latest) edition – editors/authors may change.
  6. You may include the publisher name, particularly if there is no ISBN.
  7. Do not include the publisher’s address/city - no-one will go visit them.
  8. Include publisher name for older books which may not have an online landing page.
  9. If citing a chapter, use chapter title and book title similiar to as in proceeding; include editors unless equal to authors. You don’t need to include “In: " due to the use of italics.

W3C Standards

Luc Moreau, Paolo Missier (eds.), Khalid Belhajjame, Reza B’Far, James Cheney, Sam Coppens, Stephen Cresswell, Yolanda Gil, Paul Groth, Graham Klyne, Timothy Lebo, Jim McCusker, Simon Miles, James Myers, Satya Sahoo, Curt Tilmes (2013):
PROV-DM: The PROV Data Model.
W3C Recommendation 30 April 2013, World Wide Web Consortium
http://www.w3.org/TR/2013/REC-prov-dm-20130430/

Richard Cyganiak, David Wood, Markus Lanthaler (eds.), RDF Working Group (2014):
RDF 1.1 Concepts and Abstract Syntax.
W3C Recommendation 25 February 2014, World Wide Web Consortium
http://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/

Notes:

  1. Use the This Version versioned permalink. (Note: these are traditionally http:// even if they redirect to https://)
  2. Editors are listed first unless they are also in the author list. Some specifications don’t list authors, in which case you can add the working group, e.g.: RDF Working Group
  3. Include the document type and state as shown literally below title, e.g.: W3C Candidate Recommendation 05 March 2020
  4. For recommendations published only informally (e.g. github.io editor drafts), cite as a website.

RFCs and Internet Drafts

John A. Kunze, Justin Littman, Liz Madden, John Scancella, Chris Adams J. Kunze, J. Littman, E. Madden, J. Scancella, C. Adams (2018):
The BagIt File Packaging Format (V1.0).
Request for Comments RFC 8493, RFC Editor https://doi.org/10.17487/RFC8493

Stian Soiland-Reyes, Marcos Cáceres (2018):
The Archive and Package (arcp) URI scheme.
Internet-Draft draft-soilandreyes-arcp-03, Internet Engineering Task Force
https://datatracker.ietf.org/doc/html/draft-soilandreyes-arcp-03

Tips:

  1. Use https://datatracker.ietf.org/ to find the latest version and full author names under Bibtex link
  2. For Internet-Drafts, cite the versioned identifier, e.g. draft-soilandreyes-arcp-03

IEEE standards

Raja Mazumder, Vahan Simonyan (eds.) (2020):
IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication (2020).
IEEE Std 2791-2020.
ISBN 978-1-5044-6466-6.
https://research.manchester.ac.uk/en/publications/936de52b-ac53-4f0e-9927-77fd7073e88d
https://doi.org/10.1109/ieeestd.2020.9094416

  1. To find the title, editors and/or working group, search in standards.ieee.org
  2. Use IEEE Explore to find the DOI for the standard – this may appear later for new standards.
  3. It can be hard to find preprints of IEEE standards.

Websites and blogs

Cameron Neylon (2017):
As a researcher…I’m a bit bloody fed up with Data Management.
Science In The Open (2017-07-16)
https://cameronneylon.net/blog/as-a-researcher-im-a-bit-bloody-fed-up-with-data-management/ accessed 2021-12-23

Tips:

  1. You may have to do some research to find the full name of the author(s)
  2. Include full date in ISO-8601 format. You may have to use curl -I or View Source to find the publication date.
  3. Visit the front page to find the title of the blog/website. Fallback: Company name or domain name cameronneylon.net
  4. Make sure the URL does not include unnecessary ?tracker=1234 info.
  5. Archive using WayBack Machine and link to snapshot, e.g. accessed 2021-12-23

Personal Communication

Personal communication is now easier to cite, thanks to social media and forums.

Stian Soiland-Reyes (2022):
I deleted my Twitter account….
scholar.social, Mastodon (2023-09-19)
https://scholar.social/@soilandreyes/111093469588864194 [archived 2023-09-19]

Stian Soiland-Reyes (2020):
I am looking for which bioinformatics journals encourage authors to submit their code/pipeline/workflow supporting data analysis.
Twitter (2020-04-16)
https://twitter.com/soilandreyes/status/1250721245622079488 [archived 2021-05-05]

Gurvesh Sanghera (2021):
Guide to run CUDA + WSL + Docker with latest versions (21382 Windows build + 470.14 Nvidia).
NVidia Forums (2021-05-19)
https://forums.developer.nvidia.com/t/guide-to-run-cuda-wsl-docker-with-latest-versions-21382-windows-build-470-14-nvidia/178365

Tips:

  1. Social media commonly let you hover over ambigious times like “Yesterday” to reveal the exact timestamp
  2. Find “Share” permalinks to make sure you don’t use URLs that only work for your account
  3. Archive using WayBack Machine or https://archive.is/ if the communication is publicly accessible.
  4. For replies within a thread, use “Inspect Element” to find id="anchors" to append as #anchors in URI
  5. Note that some social media may require authentication or otherwise prevent public visibility.

Software

Resolution order for how to cite software:

  1. If they have a CITATION.cff files in a GitHub repository, click Cite this repository to find full list of authors
  2. Cite Journal of Open Source Software article if present. Search also relevant software journals.
  3. Use Zenodo DOIs for Software Release if available.
    Use the version-specific DOI if you used the software, or version-independent “Cite All Versions” DOI if you just reference the software.
  4. Cite their “Preferred citation” traditional journal article if website/repo indicates so. You may need to cite the (typically newer) release separately.
  5. Cite their main website. Make sure you find the page most specific to the software.
  6. Cite their open source repository – make a snapshot with Software Heritage and cite the SWHID (which may be made specific for version/filename if desired). For GitHub/GitLab, include owner/repositoryname in the title, as some repository names can be overly general.
  7. You may find it useful to combine several of the above, note that many journals will mangle this up anyway.
  8. Sorry, if it’s not publicly available or documented, I am not sure why you want to cite it!

For case 5/6 it can be difficult to find the author names. In some cases there may be an organization that can be listed (including GitHub owner).

Ghaith Arfaoui, Maroua Jaoua (2020):
RO-Crate RDA maDMP Mapper.
Zenodo
https://github.com/GhaithArf/ro-crate-rda-madmp-mapper
https://doi.org/10.5281/zenodo.3922136

Finn Bacall, Stian Soiland-Reyes, Marina Soares e Silva (2019):
eScienceLab: RO-Composer.
https://esciencelab.org.uk/projects/ro-composer/
https://github.com/ResearchObject/research-object-composer

Kostadin Belchev (2021):
KockataEPich/CheckMyCrate: A command line application for validating a RO-Crate object against a JSON profile.
GitHub.
https://github.com/KockataEPich/CheckMyCrate

Open Access by default

s11 strive to publish as Open Access (OA), or to provide Green Open access preprints where gold open access is not possible.

Likewise, in this style guide for citations, all bibliographic entries cited SHOULD be Open Access or otherwise MUST provide an alternative link to a Green Open Access preprint.

Check:

Article that is not Open Access

If the DOI for a citation do not resolve to an Open Access article, then add links to a [preprint] immediately after DOI:

Sean Bechhofer, Iain Buchan, David De Roure, Paolo Missier, John Ainsworth, Jiten Bhagat, Phillip Couch, Don Cruickshank, Mark Delderfield, Ian Dunlop, Matthew Gamble, Danius Michaelides, Stuart Owen, David Newman, Shoaib Sufi, Carole Goble (2013):
Why Linked Data is Not Enough for Scientists.
Future Generation Computer Systems 29(2)
https://doi.org/10.1016/j.future.2011.08.004 [preprint]

The preprint link should go to, in order of preference:

  1. Preprint server like arXiv, bioRxiv, linking to their landing page rather than PDF, e.g. arXiv:1310.6555
  2. Funder-supported preprint repository like Pubmed PMC or Europe PMC, linking to their landing page if full text is available, e.g. PMC2771753
  3. Public Repository like Zenodo, linking to their landing page (preferably by repository’s DOI), e.g. [preprint)
  4. Institutional repository by one of the authors, linking to their landing page, e.g. [preprint]
  5. PDF on conference/journal home page, e.g. [preprint
  6. PDF on author/project home page, e.g. [preprint]
  7. ResearchGate – only if full text is already uploaded by author!
  8. Wayback Machine archive of PDF previously found on above URLs

Tips:

Notes:

  1. [preprint] may be replaced with hyperlinked preprint PIDs without [brackets], e.g. arXiv:2006.08589 or PMC2771753 – if the preprint server has a DOI, use that as hyperlink, but do not include it as literal DOI unless the journal/proceedings did not itself assign DOIs.
  2. Use the commonly recognized term preprint even if the link technically goes to a later author-accepted version or postprint.
  3. If the link goes to a author-hosted PDF that is clearly the publisher’s version (technically not open access, but often allowed on author’s own site), then the link is called [pdf].

Posting your own preprint

If you are citing one of your own articles, you are responsible to make sure it is accessible Open Access!

If the article is yours (or you are the co-author), then you can usually post a preprint yourself on your institutional repository. Check in JISC’s Sherpa Romeo for journal preprint policies.

For conference submissions where you never signed away a copyright assignment you always have permission. Note that while a conference may have published your PDF on the web, conference websites are notoriously poorly maintained and not likely to remain available in 1, 2, 5, 10 years time.

Posting of preprints should follow the same preferences as above, but check the publisher’s guidelines if you have already signed copyright assignment. The best is to post the preprint before such signature.

Recommendations:

Requesting preprint

If no preprint is available, then contact authors to request one. Make sure you don’t request a PDF for yourself, but a web-hosted preprint you can link to, solving the access problem for the world instead of just yourself.

Example request:

I found your paper “A systematic review of foo bars” https://doi.org/10.13003/abcd which I quite enjoyed and want to cite.

I have/haven’t got access myself, but hope for a Green Open Access URL so that readers of our website/paper can also access your article.

Are you able to deposit an article preprint or postprint that I can link to from our website/paper?

For reference, IEEE’s preprint policies: https://www.ieee.org/publications_standards/publications/rights/authorrightsresponsibilities.html

You may include link to the preprint policies of the particular publisher. If they respond just with a PDF attachment or question of repository, you can recommend arxiv.org, Zenodo or their institutional repository.

Note: You are not allowed to post their preprint yourself, unless you are one of the co-authors or acting on their behalf in the same copyright holding institution.

Article without preprint

The first preference if the authors are unable to provide an Open Access preprint is do not cite the article! The radical rationale for this is: if the author didn’t want anyone to read it, why should you cite it?

However in some cases the article is fundamental and still needs to be cited. As a last resort, list it with a strong disclaimer about lack of Open Access:

Richard L. Grimsdale, Frank H. Sumner, C.J. Tunis, Tom Kilburn (1959):
A system for the automatic recognition of patterns.
Proceedings of the IEE - Part B: Radio and Electronic Engineering 106(26)
https://doi.org/10.1049/pi-b-1.1959.0392 (No Open Access version available)

  1. Although use of footnotes for URLs is easy to navigate (if hyperlinked!), used alone they also degrade Web resources as not being “proper” publications worthy of attribution and citation. ↩︎