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Add citation information following the citation file format #361

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sven1103 opened this issue Jul 27, 2019 · 20 comments · Fixed by #1663
Closed

Add citation information following the citation file format #361

sven1103 opened this issue Jul 27, 2019 · 20 comments · Fixed by #1663
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high-priority template nf-core pipeline/component template

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@sven1103
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Here at BOSC CodeFest, we got encouraged to use the human and machine-readable citation file format CFF, which provides citation metadata for software.

Please have a look at the current specification of CFF.

I want to bring this up here, so we can discuss if we want to incorporate this in our tools and pipeline repositories.

I know that @mkuzak and others are working on a Zotero browser plugin that reads CFF files to add it automatically in the bibliography. Changes are, that for other reference managers this will be possible too.

What do you think?

@ewels
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ewels commented Jul 28, 2019

Sounds good! How does this compare to .bib bibTex files? Those have been around forever and are supported everywhere.

Should probably be implemented as part of #236 - that one started to get a bit complicated and stalled..

@sven1103
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sven1103 commented Jul 28, 2019

I think the bibTex specification does not cover software as a native entry type: https://en.wikipedia.org/wiki/BibTeX#Entry_types

If you have a look at the current CFF core specification, it is targeted for software. Entries like:

  • license
  • copyright
  • repository
  • repository-code
  • repository-artifact
  • software-container
  • orcid
  • ....

are some i just cherry-picked which I found super useful. You can even reference a git commit hash!

@ewels
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ewels commented Jul 30, 2019

Nice! 👍

@maxulysse
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Should be easy enough to cover both, no?

@ewels ewels added the template nf-core pipeline/component template label Aug 18, 2019
@vsmalladi
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Have you guys checked the CSL style out: https://citationstyles.org/developers/

Used it for Manubot: https://github.com/manubot/manubot

@mkuzak
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mkuzak commented Sep 22, 2019

@vsmalladi if I understand correctly, CSL is another way to add citation information in a machine-readable way, it deas not address software citation per se. Is that correct?

@vsmalladi
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Yes that is correct. It’s a option so that we can store citation and export to journal specific format

@mkuzak
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mkuzak commented Sep 22, 2019

Alternative option is codemeta, it has a lot of crosswalks to other systems

@ewels
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ewels commented Jul 28, 2021

GitHub now has native support for this file type: https://twitter.com/natfriedman/status/1420122675813441540?s=21

@jfy133
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jfy133 commented Jul 28, 2021

Only issue is that with the GitHub native support it doesn't allow display/citation information for an actual publication - it only ever displays 'repository metadata'. This maybe an issue for pipelines that have been published

@sdruskat
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Only issue is that with the GitHub native support it doesn't allow display/citation information for an actual publication - it only ever displays 'repository metadata'. This maybe an issue for pipelines that have been published

FWIW, the GitHub feature was shipped very quickly, and the new CFF version (1.2.0) that we're currently in the process of finalizing will have a preferred-citation field for publications that aren't software publications (papers, etc.), so that you will be able to reference "actual publications".

Having said that, please note that good practice as laid out in the software citation principles includes that you should also cite the software itself, and you can provide metadata for software publications (e.g., on Zenodo with a DOI) in CFF, that's what it was created for 🙂.

@retorquere
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https://www.softwareheritage.org/2020/05/26/citing-software-with-style/ is working on software citation for bibtex

@sdruskat
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https://www.softwareheritage.org/2020/05/26/citing-software-with-style/ is working on software citation for bibtex

In a way. They've created a package for biblatex that can take care of different "slices" of software output to style them. They are also working on supporting CFF in the future: https://forge.softwareheritage.org/T3078.

@ggabernet
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@ewels
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ewels commented Jul 8, 2022

This should be ready to implement now. Both in the template (for all pipelines) and also in the core repos (tools, website, modules etc).

Example CFF files with syntax for specific publications here: https://github.com/ewels/MultiQC/blob/master/CITATION.cff

Publication that we want to cite: https://www.nature.com/articles/s41587-020-0439-x

@ErikDanielsson ErikDanielsson mentioned this issue Jul 8, 2022
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@ErikDanielsson ErikDanielsson linked a pull request Jul 8, 2022 that will close this issue
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@ErikDanielsson
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Closing due to merge of #1663.

@ewels ewels reopened this Jul 11, 2022
@ewels
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ewels commented Jul 11, 2022

Great! You did it in the root of tools but it should also be in the root of the pipeline template :)

Also nf-core/modules, nf-co.re and any other active core repos.

@ErikDanielsson
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Ok, I'll create a few more PRs then :)

@apeltzer
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apeltzer commented Jul 12, 2022

And I did my 🤠 duty there too 😆
☝🏻 but with proper reviews!

@ErikDanielsson
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ErikDanielsson commented Jul 12, 2022

Thanks @apeltzer! There are two more to be merged before we are done though: nf-core/configs#397 and nf-core/test-datasets#569

@ewels ewels closed this as completed Aug 18, 2022
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