docs: add "How to cite a SeqSet" section - #1094
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Documents how to actually obtain the citation text for a SeqSet: the 'Export / Cite' dialog offers BibTeX, MLA and APA, with a copy-to-clipboard button. Shows what each generated citation looks like, notes that the DOI must be generated before copying (otherwise the citation points at the mutable SeqSet page URL), and that the generated text carries no author field. Emphasises that the DOI has to appear as an entry in the manuscript's References section rather than only being mentioned in the text, since only reference-list entries are indexed by Crossref and therefore discoverable as citations. Cross-links the new section from the SeqSets concept page, the citation requirements page, and the existing "Exporting a SeqSet" section. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
corneliusroemer
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Aug 5, 2026
Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>
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Pull request overview
Adds end-user documentation for obtaining and using the automatically generated SeqSet citation text (BibTeX/MLA/APA), and cross-links it from related documentation pages so users can find the guidance when creating or citing SeqSets.
Changes:
- Added a new “How to cite a SeqSet” section to the SeqSet how-to page, including steps and example outputs.
- Updated existing SeqSet docs to reference the new citation section (including the “Export / Cite” dialog and Crossref indexing note).
- Added cross-links from the SeqSet concept page and the “Citing Data from Pathoplexus” page.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.
| File | Description |
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| monorepo/website/src/pages/docs/how-to/generate-seqset.mdx | Adds the new “How to cite a SeqSet” section and links to it from related sections. |
| monorepo/website/src/pages/docs/concepts/seqset.mdx | Adds a direct link to the new citation section. |
| monorepo/website/src/pages/about/citation.mdx | Adds a reference to the new citation section from citation requirements guidance. |
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| Pathoplexus generates a ready-made citation for you, so you don't have to assemble one by hand. | ||
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| **Generate the DOI first.** The citation is built around the SeqSet's DOI, so create the DOI (see [above](#adding-a-doi)) before copying a citation. If you copy a citation from a SeqSet that has no DOI yet, it will point at the SeqSet's web page instead — that page can change over time and cannot be tracked as a citation. The DOI appears in the citation text as soon as it is generated, so you don't need to wait for the `doi.org` link to become resolvable before copying it. |
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| **Key point:** For publications and preprints, the DOI must be cited in your **References section** (as you would cite a paper), not just mentioned in the text. This ensures it is indexed by Crossref and linked to your manuscript. Pathoplexus imports these citations from Crossref and lists the citing publications on the sequence details page, so citing the DOI properly also gives credit back to the data generators. | ||
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| Pathoplexus generates the citation text for you in BibTeX, MLA, or APA style — you don't need to write the reference by hand. See [How to cite a SeqSet](/docs/how-to/generate-seqset#how-to-cite-a-seqset) for where to find it and what it looks like. |
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Quick draft based on discussion with @emmahodcroft - requires human editing to cut out the unnecessary AI edited stuff.
Documents how to actually obtain the citation text for a SeqSet: the
'Export / Cite' dialog offers BibTeX, MLA and APA, with a copy-to-clipboard
button. Shows what each generated citation looks like, notes that the DOI must
be generated before copying (otherwise the citation points at the mutable
SeqSet page URL), and that the generated text carries no author field.
Emphasises that the DOI has to appear as an entry in the manuscript's
References section rather than only being mentioned in the text, since only
reference-list entries are indexed by Crossref and therefore discoverable as
citations.
Cross-links the new section from the SeqSets concept page, the citation
requirements page, and the existing "Exporting a SeqSet" section.
Co-Authored-By: Claude Opus 5 (1M context) noreply@anthropic.com
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