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fix: clean up citations section + associated language #2610

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@jsstevenson jsstevenson commented Jun 14, 2024

a few possible changes -- let me know if they need to go through additional channels first:

  • Citation policy page
    • Fix wording, which refers to a "Cite" section on the ontology detail page (the header is actually "Publications")
    • Add blockquote formatting -- Jekyll wasn't properly converting these to bootstrap blockquotes and the result didn't help readability
  • OBO foundry papers page
    • Make formatting more consistent
  • Big "list of known publications" section
    • Reformat for readability
    • Update description. When I first saw it, I assumed it was totally ad-hoc and wanted to instead generate it from publication annotations from the ontology metadata -- then I looked at the code and realized that's what was already happening. So, I thought it might be helpful to give a brief explanation of where the list comes from.
    • Move it to a separate page (it's big)
  • Ontology detail page
    • add a linkable anchor to the "publications" header, so that the citation policy page can link to it directly
    • Fix bug where a blank "publications" section is shown if the publications metadata is an empty array instead of null. See eg here: http://obofoundry.org/ontology/fbcv.html
  • Give the citation pages their own sidebar TOC. Previously they reused the "about" section's TOC which is a little confusing, see eg http://obofoundry.org/docs/Citation.html

other possible todo's:

  • any other OBO publications to report/highlight under "Other papers about the OBO Foundry"?

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@matentzn matentzn left a comment

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LGTM

docs/Citation.md Show resolved Hide resolved
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jsstevenson commented Jun 17, 2024

Other TODO's

  • Fix navbar link to "other publications" anchor
  • Citations sidebar (currently gets the personnel sidebar for some reason) <- this should probably be a whole other issue

@matentzn matentzn marked this pull request as ready for review July 31, 2024 10:36
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I approve the changes (lgtm), but I am requesting the following change:

Once they have approved, I will too.

THANKS!

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@nataled nataled left a comment

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I approve, though I suggest that the phrase 'in a diversity of ways' be changed to 'in a variety of ways'.

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Looks good to me

@@ -1,46 +1,59 @@
---
layout: doc
layout: citation
title: OBO Citation and Attribution Policy
---

Open Biological and Biomedical Ontologies are used in a diversity of ways. The following guidelines are intended to promote proper attribution of the ontology creators and contributors, and to promote reproducibility in informatics applications.
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I agree with @nataled's suggestion to change "diversity" to "variety".

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Great! Just double checking -- is there anything that could be added under "other OBO foundry papers"?
Screenshot 2024-07-31 at 3 24 39 PM

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Not that I know of

@jsstevenson jsstevenson changed the title fix: clean up some language regarding citations fix: clean up citations section + associated language Aug 6, 2024
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Can this be squashed and merged?

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@nlharris strictly speaking, the GitHub review process wants me to re-attain Nico's approval, but I think it's implicit so I'd be happy to go ahead and squash

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It won't allow squash & merge until the requested change has been made (? I thought it already was) and 2 people approve.

@jsstevenson jsstevenson requested review from matentzn and removed request for matentzn August 20, 2024 19:17
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Ah, yeah, foiled by repository rules. We'll be able to once @matentzn is able to re-review.

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4 participants