s11 Citation & Bibliography Style Guide

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

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:

First line lists all authors with full names as listed within article. No assumptions made about surnames.
After last author, add (year) in 4 digits, reflecting official publishing date, which may be before issue’s publication date. Terminated with : and newline.
Second line is title in bold. Hyperlinked to DOI - if open access. Final period . is not bold nor in hyperlink, followed by newline.
Third line is full journal name in italics with official captitalization. No acronyms, e.g. ~~J Chem Bio~~ -> Journal of Chemical Biology
Journal name immediately followed by volume number in bold. Optional (issue) and/or :article ID. Terminated with newline (no period as there is no sentence).
Page numbers are NOT included - welcome to the Internet. ..except for classic publications without DOI, then add: pp. 123–129.
Clickable DOI with prefix https://doi.org/ and any %2f within the DOI expanded to /

## Article/abstract in Conference proceedings

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 5 December 2016. https://doi.org/10.1109/BigData.2016.7840618 [preprint]

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:

Confirm that accessing the DOI gives an Open Access version of the article. You may have to click “PDF” or similar to find full text.
Ensure you don’t just have accidental institutional access, e.g. by using a Private Browser Window connected with your home ISP
Check on https://scholar.google.com/ you are citing the latest version - e.g. a bioRxiv preprint may have a later Open Access journal article with DOI.

### 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]/(http://users.ox.ac.uk/~oerc0033/preprints/research-objects.pdf)]

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

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

Tips:

Use https://unpaywall.org/ and https://scholar.google.com/ to find preprint versions.
Do not link to Sci-Hub!
Do not link to publisher PDFs at unaffiliated websites
Some article templates like IEEE will insert publisher copyright even in author’s version. If the DOI and journal issue is clearly missing, it is most likely the author’s version and not publisher’s version. Likewise, if they are both present it is likely the publisher’s version.
Archive non-DOI PDFs and their landing page using “Save Page Now” on WayBack Machine as websites are likely to change/break/disappear.
PubMed has both PMID and PMCID identifiers, prefer PMCID identifiers when available, e.g. https://identifiers.org/pmc/PMC2771753

Notes:

[preprint] may be replaced with hyperlinked preprint PIDs without [brackets], e.g. arXiv:2006.08589 or PMC2771753
Use the the commonly recognized term preprint even if the link technically goes to a later author-accepted version or postprint.
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:

Post preprint to Zenodo at submission time, before any copyright assignment. This is useful to get DOI for citing before publishing.
Post preprint to institutional repository (e.g. https://pure.manchester.ac.uk/) at submission time. This is useful for REF acceptance, as a legal backup, and as a way to gather forward links to later versions.
When accepted, update records in Zenodo and institutional repository. Check preprint policy of publisher if you are allowed to update preprint with the author-accepted version if changed following peer-review/editorial changes.
When accepted, list paper in personal/project/group bibliography.
When published, update all the above. If Gold OA you also have permission to re-publish the publisher’s version.
Add publisher’s DOI and journal details to Zenodo and institutional repository metadata.

### 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.

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 I can link to from our website/paper?

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

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!

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:

Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R Brinkman, Adam Michael Clark, Eric W Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M Hancock, Nigel W Hardy, Henning Hermjakob, Randall K Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novère, Jim Leebens-Mack, Suzanna E Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M Reecy, Donald G Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H Scheuermann, Daniel Schober, Barry Smith, Jason Snape, Christian J Stoeckert, Keith Tipton, Peter Sterk, Andreas Untergasser, Jo Vandesompele, Stefan Wiemann (2008): Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature biotechnology 26 https://doi.org/10.1038/nbt.1411 (No Open Access version available)