I then sorted the entries by read status and assigned xxx to all the ones I’ve read. So instead I sorted all my entries in BibDesk by rating, selected all the 5 star ones and added a zzzzz tag, selected all the 4 star ones and added a zzzz tag, and so on (so that 1 star entries got a z) tag. I considered making some sort of programmatic solution and writing a script to convert all the rating and read fields to keywords, but that seemed like too much work-many entries have existing keywords and parsing the file and concatenating ratings and read status to the list of keywords would be hard. I decided to treat these as Zotero tags, which BibDesk calls keywords. Internally, BibDesk stores this data as entries in the raw BibTex: I’ve used these fields for years and find them super useful for keeping track of how much I like articles and for remembering which ones I’ve actually finished. To make Zotero work nicely with a pandoc-centric writing workflow, and to make file management and tag management easier, I installed these three extensions:īibDesk allows you to add a couple extra metadata fields to entries for ratings and to mark them as read. Preparing everything for migration meant I had to make a ton of edits to the original references.bib file, so I made a copy of it first and worked with the copy. references.bib file to Zotero was a relatively straightforward process, but it required a few minor shenanigans to get everything working right. It supports all kinds of entry types and fields, beyond what BibTeX supports. It was the first program to adopt CSL (way back in 2006!). Zotero follows the CSL standard that pandoc uses. Zotero treats collections like iTunes/Apple Music playlists-just like songs can belong to multiple playlists, bibliographic entries can belong to multiple collections. Editing an item in one collection updates that item in all other collections. You can create a Zotero collection for specific projects, and items can live in multiple collections. It’s also far easier to maintain a master list of references. For one of my reading-intensive class, I’ve even created a shared Zotero group library that all the students can join and cite from, which is neat. When I started my PhD in 2012, something revolutionary happened: the characters in the. R Markdown hadn’t been invented yet and I still hadn’t discovered pandoc, so living in a mostly LaTeX-based world was fine. I kept using my MultiMarkdown + LaTeX output system throughout my second master’s degree, and my references.bib file and PDF database slowly grew. BibDesk is a wonderful and powerful program with an active developer community and it does all sorts of neat stuff like auto-filing PDFs, importing references from DOIs, searching for references on the internet from inside the program, and just providing a nice overall front end for dealing with BibTeX files. I stored all my bibliographic references in a tiny little references.bib BibTeX file that I managed with BibDesk. I didn’t know about pandoc yet, so I only ever converted to PDF, not HTML or Word. I did all my writing for my courses and my thesis in Markdown and converted it all to PDF through LaTeX using MultiMarkdown. Markdown itself had been a thing for 4 years, and MultiMarkdown-a pandoc-like extension of Markdown that could handle BibTeX bibliographies-was brand new. When I started my first master’s degree program in 2008, I decided to stop using Word for all my academic writing and instead use plain text Markdown for everything. My longstanding workflow for writing, citing, and PDF management
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