Portable Zotero

[Cristy Borovetz]

Ifyou still wish to use this workflow, most of it has not changed for Zotero 6; the only issue is that you will need to use the older version of zotfile - version 5.0.16 (available here) and disable updates on it.

Zotfile can manage your pdfs, rename them, extract annotations and store them wherever you want it to do that.

Zotero, Zotfile, and mdnotes also have hidden preferences, which I edit in part 3 of this workflow, with examples of different outputs for the various settings.

First, we want to create placeholders to add to the YAML Metadata that the Dataview plugin in Obsidian can read. For this, we create custom placeholders that are formatted according to the YAML-dataview requirements, meaning strings need to be in quotes, anything with multiple references (such as a book with more than one author) needs to be formatted with newline bullets for each such item. I have a set of custom placeholders and formats here that can be used.

(note: tags does not have a metadata field of its own and uses the field of collections. this is because dataview does not accept values of the first field entry of inline fields if there is more than one entry made, the latter field entries overwrite the previous ones. Since my collection and tag fields in zotero are both used to categorise subjects, I club them in the mdnotes template format).

(Side note - you might prefer to put highlights in blockquotes, but since this is a reference note, I assume that the default is a quote, and try to emphasise my thoughts on the note with the blockquote, since that is what I need to pay attention to while reviewing).

Mdnotes converts underlines to markdown headers. This makes sectioning in the annotations easy - Underlining headers in the PDF makes them sections. To facilitate this, I edit the underline to remove quotation marks and the citation link.

This is in the preference extensions.zotfile.pdfExtraction.colorCategories. The default value is a string of colors and hex codes: "Black": "#000000", "White": "#FFFFFF", "Gray": "#808080", "Red": "#FF0000", "Orange": "#FFA500", "Yellow": "#FFFF00", "Green": "#00FF00", "Cyan": "#00FFFF", "Blue": "#0000FF", "Magenta": "#FF00FF". The color names refer to a range of RGB points that will be read as that particular color category, the hexcode is the category name that zotfile can use instead. I edit this preference to read "Black": "", "White": "", "Gray": "[[Argument]]:", "Red": "[[Disagreement]]:", "Orange": "[[Idea]]", "Yellow": "", "Green": "- [ ] ", "Cyan": "[[Important]]", "Blue": "[[Confusion]]:", "Magenta": "[[Critique]]:"

to correspond with the labels I want it to use. I put some of these in backlinks for Obsidian.

"Black": "", "White": "", "Gray": "", "Red": "[[Important]]:", "Orange": "", "Yellow": "[[Author Point]]", "Green": "[[Disagreement]]:", "Cyan": "#pkbmk", "Blue": "[[Re-Read]]:", "Magenta": "- [ ] #litreview"

As I am on Windows, and so it might be different, but I was wondering how you get colours and blockquote to translate into Obsidian? Is it directly in your extracted notes after exporting it into markdown?

Although I think formatNoteTitle is for the title as it appears in the note since it includes HTML tags. HTML is not used in the note title as it appears in the screenshot above. (to my knowledge anyway, I could be wrong)

Highlights is the best way to read and annotate PDFs on your Mac, iPad and iPhone for free. Use the app to extract annotations, images, tables and citations and turn them into powerful notes you can export anywhere.

Zotero (/zoʊˈtɛroʊ/[7]) is free and open-source reference management software to manage bibliographic data and related research materials, such as PDF and ePUB files. Features include web browser integration, online syncing, generation of in-text citations, footnotes, and bibliographies, integrated PDF, ePUB and HTML readers with annotation capabilities, and a note editor, as well as integration with the word processors Microsoft Word, LibreOffice Writer, and Google Docs. It was originally created at the Center for History and New Media at George Mason University and, as of 2021, is developed by the non-profit Corporation for Digital Scholarship.

Zotero can also save a copy of the webpage, or, in the case of academic articles, a copy of the full text PDF. Users can then add notes, tags, attachments, and their own metadata. Items are organized through a drag-and-drop interface, and can be searched.

Selections of the local reference library data can later be exported as formatted bibliographies. Furthermore, all entries including bibliographic information and user-created rich-text memos of the selected articles can be summarized into an HTML report.[12]

Zotero users can generate citations and bibliographies through word processor plugins, or directly in Zotero, using Citation Style Language styles. The house styles of most academic journals are available in Zotero, and the bibliography can be reformatted with a few clicks. Zotero also allows users to create their own customised citation styles.

Zotero can import and export citations from or to many formats, including Wikipedia Citation Templates,[13] BibTeX, BibLateX, RefWorks, MODS, COinS, Citation Style Language/JSON, refer/BibIX, RIS, TEI, several flavours of RDF, Evernote, and EndNote.

Zotero has no institutional customer support service, but the Zotero website provides extensive information, including instructional screencasts, troubleshooting tips, a list of known issues, and user forums. Questions and issues raised in the forums are answered quickly, with users and developers suggesting solutions.[15] Many academic institutions provide Zotero tutorials to their members.

Most citation style and translator codes are written by volunteers from the community and, as open-source scripts, may be used by third-party tools as well, for example Wikipedia's Citoid citation generator.[16]

When using the Cita plugin, first released in 2021,[17] Zotero supports automated retrieval and sharing of citation network data from and to external sources, and local citation network visualization.[18] This further integrates Zotero to the Initiative for Open Citations ecosystem, including OpenCitations and Wikidata.[19]

Juris-M is a fork of Zotero with additional features supporting legal research and multilingual citations.[22][23][24] It allows for multilingual citations, and translations and transliterations of citation fields and provides additional support for needs of scholars in fields of law. It was created by Frank Bennett, an associate professor of comparative law at Nagoya University, who continues to maintain it.[25] Amongst the legal citation styles supported are the American Bluebook style, the UK OSCOLA style, and the Canadian McGill style. Many other European and Commonwealth jurisdictions are also supported.[22]

Zotero mobile apps are available for iOS (iPad and iPhone). Several apps not developed by Zotero for Android tablets and phones are available as well.[21] The iOS app is developed by the creators of the Zotero desktop app and was released in March 2022.[26] A Beta version of Zotero's own Android app by Zotero was released in December 2023.[27][28]

Synchronizing a library to zotero.org allows users to access and edit the library in the "web library" interface from any current web browser, including the mobile version of the website on a tablet or mobile phone.[21] Users can save new references to the web library using its "magic wand" button.[8]

In May 2018, Zotero's creators launched the web-based bibliography tool ZoteroBib (zbib.org), where users can generate bibliographies on the web without installing Zotero or creating a Zotero account.[29]

Development of Zotero has been funded by the Andrew W. Mellon Foundation, the Alfred P. Sloan Foundation, and the Institute of Museum and Library Services, as well as user donations. The storage subscriptions of individuals and institutions, which allow cloud syncing of attached files in users' libraries, fund Zotero's development and services.

The first release of Zotero, 1.0.0b2.r1, was made available in October 2006 as an add-on for the Firefox web browser. Development of Zotero 1.0.x continued until May 2009, when Zotero 1.0.10 was released.

The case was dismissed on June 4, 2009, due to a lack of jurisdiction.[35] Although the Virginia Supreme Court granted an appeal to Thomson Reuters in this case on December 18, 2009, the appeal was withdrawn on January 11, 2011. [citation needed]

Zotero 2.0, released in February 2010, added online features such as metadata and file syncing and group libraries, and included a license change from the Educational Community License to GPLv3.[36] Development of Zotero 2.0.x continued until October 2010, when Zotero 2.0.9 was released.

Zotero Standalone, first released in January 2011, allowed Zotero to be run as an independent program outside Firefox.[37] Using XULRunner, Zotero Standalone was made available for Windows, Linux, and macOS.[37] Browser connectors were available to use Zotero Standalone with the web browsers Safari and Chrome.[37]

Zotero 3.0, released in January 2012, includes the stable release of Zotero Standalone as well as several new major features, including overhauled Word and LibreOffice[38] integration and duplicate detection. Version 3.0 also introduced the Zotero bookmarklet for iOS[39] browsers, Android browser, Chrome for Android, Firefox mobile, and Opera mobile allowing uses to save reference data to their Zotero library when using mobile devices.[40]

Zotero 4.0, released in April 2013, includes new features such as automatic journal abbreviations, direct downloading of PDFs to Zotero Standalone from the Zotero Firefox plugin, a single save button on the Zotero browser plugin (which combines the functionality of the address bar icon and the "Create Web Page Item from Current Page" button), colored tags, and on-demand file syncing.[41]

Zotero 5.0, released in July 2017, did away with the Firefox plugin, replacing it with a Firefox connector for the new standalone product, which was now simply branded as the Zotero app.[42] This move was the result of Mozilla discontinuing its powerful extension framework on which Zotero for Firefox was based.[43] The Zotero Connectors for Chrome and Safari were also revamped, and given additional features.[44] A point update also introduced a new PDF recognizer, using a Zotero-designed web service that doesn't rely on Google Scholar, to retrieve metadata for PDF files.[45]

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