last version of the manuscript

[ypriverol]

Summary by CodeRabbit

• Documentation
  • Updated the citation for the PRIDE database reference with revised title, author list, publication volume, pages, and year.
  • Adjusted in-text citation references to align with the new citation details across the documentation.

[coderabbitai]

Walkthrough

The pull request replaces an existing article entry in the bibliography file with a new one. The old entry (Perez-Riverol2022-ow) is removed and replaced by a new entry (Perez-Riverol2025-mo) with updated title, authors, abstract, journal volume, pages, and year. Additionally, citation references in the markdown file are updated to refer to the new citation key, ensuring consistency in the documentation.

Changes

File	Change Summary
paper/paper.bib	Replaced the old article entry (Perez-Riverol2022-ow) with a new one (Perez-Riverol2025-mo). Updated title, authors, abstract (including mentions of a new file transfer protocol and PRIDE chatbot), volume (50→53), pages ("D543--D552" → "D543--D553"), and year (2022→2025).
paper/paper.md	Updated citation references from [@Perez-Riverol2022-ow] to [@Perez-Riverol2025-mo] in two instances.

Poem

I'm a rabbit with a hop so spry,
Scanning updates that catch my eye,
A bib file revamped, a markdown rhyme,
New keys and data ahead in time,
Hopping through change with a joyful cheer 🐰,
Celebrating updates, crisp and clear!

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📜 Recent review details

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Review profile: CHILL
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📥 Commits

Reviewing files that changed from the base of the PR and between 6ae6183 and 04c7b58.

⛔ Files ignored due to path filters (1)

• paper/paper.pdf is excluded by !**/*.pdf

📒 Files selected for processing (2)

• paper/paper.bib (1 hunks)
• paper/paper.md (1 hunks)

✅ Files skipped from review due to trivial changes (1)

• paper/paper.md

⏰ Context from checks skipped due to timeout of 90000ms (2)

• GitHub Check: build
• GitHub Check: build

🔇 Additional comments (1)

paper/paper.bib (1)

1-34: Verify the publication details for the future publication.

The article entry appears to be for a future publication (2025) which raises some concerns:

1. The volume number should be 54 for 2025 (current volume in 2024 is 52, as seen in the Thakur2024-zu entry)
2. Consider using a preprint citation if the article is not published yet

Let's verify the latest volume of Nucleic Acids Research:

✅ Verification successful

🌐 Web query:

What is the latest volume of Nucleic Acids Research journal in 2024?

💡 Result:

The latest volume of Nucleic Acids Research in 2024 is Volume 52, Issue D1, released in January 2024 as part of its annual database special issue[1][7][8]. This edition contains 180 papers covering new biological databases (90 papers), updates to existing resources (83 papers), and updates from databases previously published elsewhere (7 papers)[1][3][8]. Key updates include GenBank, JASPAR, and AlphaFold Protein Structure Database[1][7], while new databases like NMPFamsDB and OPIA are highlighted as Breakthrough Articles[1][8].

Citations:

• 1: https://pmc.ncbi.nlm.nih.gov/articles/PMC10767945/
• 2: https://academic.oup.com/nar/issue/53/4
• 3: https://pubmed.ncbi.nlm.nih.gov/38035367/
• 4: https://alliance-uoregon.primo.exlibrisgroup.com/discovery/fulldisplay?docid=cdi_proquest_miscellaneous_2896810102&context=PC&vid=01ALLIANCE_UO%3AUO&lang=en&adaptor=Primo+Central&tab=Rollup&query=null%2C%2C272%2CAND&facet=citedby%2Cexact%2Ccdi_FETCH-LOGICAL-c361t-79c4c5429619c56a909944b021abe8acd383acfdb5533619f122f20de7c978653&offset=0
• 5: https://academic.oup.com/nar
• 6: https://pubmed.ncbi.nlm.nih.gov/39658041/
• 7: https://academic.oup.com/nar/issue/52/D1?login=false
• 8: https://ouci.dntb.gov.ua/en/works/lDPXaBLl/
• 9: https://www.researchgate.net/publication/376082792_The_2024_Nucleic_Acids_Research_database_issue_and_the_online_molecular_biology_database_collection

---

Publication details for future entry need adjustments.

The web query confirms that the 2024 Nucleic Acids Research database issue is in Volume 52. In our bibliography, the 2025 entry is assigned Volume 53. By standard increment (one volume per year), the 2025 entry should likely be Volume 53, not Volume 54 as previously suggested. You may want to verify if the journal’s volume numbering follows a different pattern or if this entry is meant to reference a preprint. Otherwise, consider updating the entry accordingly.

• Reassess whether the future publication year (2025) and its volume (53) are intentional.
• Confirm if a preprint citation is more appropriate if the final publication details aren’t available yet.

---

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