Thicket data repository for the EEG
anil.recoil.org
1{
2 "id": "https://ryan.freumh.org/bibliography-management.html",
3 "title": "Bibliography Management",
4 "link": "https://ryan.freumh.org/bibliography-management.html",
5 "updated": "2023-06-07T00:00:00",
6 "published": "2023-01-17T00:00:00",
7 "summary": "<div>\n \n <span>Published 17 Jan 2023.</span>\n \n \n <span>Last update 7 Jun 2023.</span>\n \n </div>\n \n \n\n <p><span>I recently received a request to outline my process\nfor managing bibliographies. Here’s a breakdown of my\napproach.</span></p>\n<h3>Bibliography Generation</h3>\n<p><span>I <a href=\"https://git.freumh.org/ryan/nixos/src/commit/19e643e3117d8d83dc86e5cf7a7cecc668f68a49/modules/personal/gui/extra.nix#L12\">use</a>\nthe <a href=\"https://www.zotero.org/\">Zotero</a> application as a\nreference manager. The Zotero Firefox <a href=\"https://www.zotero.org/download/connectors\">connector</a><a href=\"#fn1\">1</a> lets me add papers from URLs. Zotero\nis quite smart about grabbing the metadata from the URL or PDF\nitself.</span></p>\n<p><span>The view I have from Zotero\nis: <img src=\"./images/zotero.png\"></span></p>\n<p><span>While Zotero is great for\nstoring local copies of papers and generating bibliographies, I don’t\nfind it to be optimal for organisation and note-taking. Instead, I use\nthe <a href=\"https://retorque.re/zotero-better-bibtex/\">Zotero Better\nBibtex</a> plugin to export all the items in my library<a href=\"#fn2\">2</a>\ninto a <a href=\"https://ctan.org/pkg/biblatex\">BibLaTeX</a> file that I\nreference items in with another application.</span></p>\n<h3>Note-taking</h3>\n<p><span>I’m using <a href=\"https://obsidian.md/\">Obsidian</a> as a front-end into my Git\nrepository of notes as plaintext markdown files. I have Zotero exporting\nits bibliography into this directory as <code>references.bib</code>,\ntracked with version control, which I then interface with using the <a href=\"https://github.com/hans/obsidian-citation-plugin\">Obsidian\nCitations</a> plugin. This allows searching the bibliography in\nObsidian, referencing items in the bibliography in Obsidian notes, and\ncreating notes for bibliography items in Obsidian. I find this to be\nmuch more flexible than Zotero’s in-built note-taking functionality:\nnotes can be version controlled, can link to each other, and can other\nnotes can reference bibliography items.</span></p>\n<p><span>To organise references for a project, a\nnote associated with the said project can reference all relevant papers.\nAnd speaking of organisation, the plugin <a href=\"https://github.com/mgmeyers/obsidian-kanban\">Obsidian Kaban</a>\nprovides a convenient way to maintain a reading list.</span></p>\n<p><span>The graph view from Obsidian, with\nbibliography items notes in red, is: <img src=\"./images/obsidian.png\"></span></p>\n<h3>Conclusion</h3>\n<p><span>This approach is quite modular. Zotero\ncould be replaced with another reference manager that can generate a\nBibLaTeX file, or be omitted entirely and the file manually maintained.\nObsidian could also be replaced with another note-taking application\nthat can interface with a BiBLaTeX file, or indeed one that doesn’t if\nthe user doesn’t mind manually maintaining reference keys.</span></p>\n<p><span>However, with slightly tighter\nintegration we can get some benefits. Using the following Obsidian\nCitation plugin template:</span></p>\n<pre><code>title: {{title}}\nauthors: {{authorString}}\nyear: {{year}}\ncitekey: {{citekey}}\nDOI: {{DOI}}\nzoteroSelectURI: [{{zoteroSelectURI}}]({{zoteroSelectURI}})\nURL: {{URL}}\n\n---</code></pre>\n<p><span>We have not only a link to the URL (if\nit exists), but a clickable link to the local Zotero entry and the\nassociated PDF with <code>zoteroSelectURI</code>.</span></p>\n<p><span>There are still a few outstanding issues\nwith this approach, though:</span></p>\n<ul>\n<li>There is no way to generate a bibliography with only the items\nreferenced in a project note, e.g. for creating a\n<code>bibliography.bib</code> for a paper.</li>\n<li>There is no support for PDF annotations of papers. I’m currently <a href=\"../remarkable2\">using the reMarkable 2</a> to read and annotate\npapers, which is great while on the go and for saving paper. Currently,\nI’m <a href=\"../remarkable2/#syncing\">using rmfakecloud</a> to sync PDFs\nto the device and back up annotations. Some integration of annotated\nPDFs in this workflow could be useful.</li>\n<li>There isn’t a clear path to collaboration. One possibility would be\n<a href=\"https://www.zotero.org/groups/\">sharing a Zotero library\nout-of-band</a><a href=\"#fn3\">3</a> and then separately collaborating on\na shared Obsidian note repository. However, the Zotero library could\nbecome out of sync with the contents of the repository’s bibliography\nfile. Instead, perhaps managing separate bibliographies would be\nappropriate, and just committing sensible changes to the bibliography\nfile <code>references.bib</code> in the note repository. Another problem\nis that having a separate Obsidian note repository wouldn’t allow\nlinking to notes created here in a personal note repository. To remedy\nthis, using a git subtree of this shared repository in the user’s\npersonal note repository might make sense.</li>\n</ul>\n\n\n<p><span>Please get in touch if you have any\nsuggestions for improvement.</span></p>\n\n\n\n\n<ol>\n<li><p><span>Plugins are\navailable for other browsers.</span><a href=\"#fnref1\">↩︎</a></p></li>\n<li><p><span>One could also\nexport a subset of a Zotero library with a ‘collection’\n(folder).</span><a href=\"#fnref2\">↩︎</a></p></li>\n<li><p><span>Which is possible to <a href=\"https://github.com/foxsen/zotero-selfhost\">self-host</a>.</span><a href=\"#fnref3\">↩︎</a></p></li>\n</ol>",
8 "content": "<div>\n \n <span>Published 17 Jan 2023.</span>\n \n \n <span>Last update 7 Jun 2023.</span>\n \n </div>\n \n \n\n <p><span>I recently received a request to outline my process\nfor managing bibliographies. Here’s a breakdown of my\napproach.</span></p>\n<h3>Bibliography Generation</h3>\n<p><span>I <a href=\"https://git.freumh.org/ryan/nixos/src/commit/19e643e3117d8d83dc86e5cf7a7cecc668f68a49/modules/personal/gui/extra.nix#L12\">use</a>\nthe <a href=\"https://www.zotero.org/\">Zotero</a> application as a\nreference manager. The Zotero Firefox <a href=\"https://www.zotero.org/download/connectors\">connector</a><a href=\"#fn1\">1</a> lets me add papers from URLs. Zotero\nis quite smart about grabbing the metadata from the URL or PDF\nitself.</span></p>\n<p><span>The view I have from Zotero\nis: <img src=\"./images/zotero.png\"></span></p>\n<p><span>While Zotero is great for\nstoring local copies of papers and generating bibliographies, I don’t\nfind it to be optimal for organisation and note-taking. Instead, I use\nthe <a href=\"https://retorque.re/zotero-better-bibtex/\">Zotero Better\nBibtex</a> plugin to export all the items in my library<a href=\"#fn2\">2</a>\ninto a <a href=\"https://ctan.org/pkg/biblatex\">BibLaTeX</a> file that I\nreference items in with another application.</span></p>\n<h3>Note-taking</h3>\n<p><span>I’m using <a href=\"https://obsidian.md/\">Obsidian</a> as a front-end into my Git\nrepository of notes as plaintext markdown files. I have Zotero exporting\nits bibliography into this directory as <code>references.bib</code>,\ntracked with version control, which I then interface with using the <a href=\"https://github.com/hans/obsidian-citation-plugin\">Obsidian\nCitations</a> plugin. This allows searching the bibliography in\nObsidian, referencing items in the bibliography in Obsidian notes, and\ncreating notes for bibliography items in Obsidian. I find this to be\nmuch more flexible than Zotero’s in-built note-taking functionality:\nnotes can be version controlled, can link to each other, and can other\nnotes can reference bibliography items.</span></p>\n<p><span>To organise references for a project, a\nnote associated with the said project can reference all relevant papers.\nAnd speaking of organisation, the plugin <a href=\"https://github.com/mgmeyers/obsidian-kanban\">Obsidian Kaban</a>\nprovides a convenient way to maintain a reading list.</span></p>\n<p><span>The graph view from Obsidian, with\nbibliography items notes in red, is: <img src=\"./images/obsidian.png\"></span></p>\n<h3>Conclusion</h3>\n<p><span>This approach is quite modular. Zotero\ncould be replaced with another reference manager that can generate a\nBibLaTeX file, or be omitted entirely and the file manually maintained.\nObsidian could also be replaced with another note-taking application\nthat can interface with a BiBLaTeX file, or indeed one that doesn’t if\nthe user doesn’t mind manually maintaining reference keys.</span></p>\n<p><span>However, with slightly tighter\nintegration we can get some benefits. Using the following Obsidian\nCitation plugin template:</span></p>\n<pre><code>title: {{title}}\nauthors: {{authorString}}\nyear: {{year}}\ncitekey: {{citekey}}\nDOI: {{DOI}}\nzoteroSelectURI: [{{zoteroSelectURI}}]({{zoteroSelectURI}})\nURL: {{URL}}\n\n---</code></pre>\n<p><span>We have not only a link to the URL (if\nit exists), but a clickable link to the local Zotero entry and the\nassociated PDF with <code>zoteroSelectURI</code>.</span></p>\n<p><span>There are still a few outstanding issues\nwith this approach, though:</span></p>\n<ul>\n<li>There is no way to generate a bibliography with only the items\nreferenced in a project note, e.g. for creating a\n<code>bibliography.bib</code> for a paper.</li>\n<li>There is no support for PDF annotations of papers. I’m currently <a href=\"../remarkable2\">using the reMarkable 2</a> to read and annotate\npapers, which is great while on the go and for saving paper. Currently,\nI’m <a href=\"../remarkable2/#syncing\">using rmfakecloud</a> to sync PDFs\nto the device and back up annotations. Some integration of annotated\nPDFs in this workflow could be useful.</li>\n<li>There isn’t a clear path to collaboration. One possibility would be\n<a href=\"https://www.zotero.org/groups/\">sharing a Zotero library\nout-of-band</a><a href=\"#fn3\">3</a> and then separately collaborating on\na shared Obsidian note repository. However, the Zotero library could\nbecome out of sync with the contents of the repository’s bibliography\nfile. Instead, perhaps managing separate bibliographies would be\nappropriate, and just committing sensible changes to the bibliography\nfile <code>references.bib</code> in the note repository. Another problem\nis that having a separate Obsidian note repository wouldn’t allow\nlinking to notes created here in a personal note repository. To remedy\nthis, using a git subtree of this shared repository in the user’s\npersonal note repository might make sense.</li>\n</ul>\n\n\n<p><span>Please get in touch if you have any\nsuggestions for improvement.</span></p>\n\n\n\n\n<ol>\n<li><p><span>Plugins are\navailable for other browsers.</span><a href=\"#fnref1\">↩︎</a></p></li>\n<li><p><span>One could also\nexport a subset of a Zotero library with a ‘collection’\n(folder).</span><a href=\"#fnref2\">↩︎</a></p></li>\n<li><p><span>Which is possible to <a href=\"https://github.com/foxsen/zotero-selfhost\">self-host</a>.</span><a href=\"#fnref3\">↩︎</a></p></li>\n</ol>",
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