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Zotero: An open-source tool to help collect, organize, cite, and share research

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Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#161

Post by austinjp »

alexchamberlain wrote: post #138
austinjp wrote: post #132

Earlier quoted context omitted.

Genuine question: what do you do with Word docs sent back to you as email attachments with track changes and embedded comments? I'm slowly realising that my colleagues for whom this "works" are never going to change. Our shared folders are littered with "Copy of FINAL final + comments 2.7.18-my-copy.docx.docx". It doesn't matter how slick my git + markdown + pandoc workflow is when conversations go like this: "Just u…

Is your markdown to Word reversible? If so, accept all changes, convert back to Markdown and run git diff. I guess you're losing comments though.

Definitely worth a go.

Comments might be extractable, I'm not familiar with docx format but it's zipped X(?)ML type data so there will be parsers. Or a conversion to an intermediate format that's more amenable to computer processing, perhaps.

The problem remains in reverse, though: it's expected that I will produce Word docs full of track changes edits.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#162

Post by tiatia123 »

jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

That is definitely interesting. But I look for data of all kinds most of the time. And recoll has saved my life dozens of times. https://www.lesbonscomptes.com/recoll/

I don't like the standard configuration, I prefer the table view and a much smaller font. Play around with the settings.

Best thing: You can have it instructed to use tesseract to OCR all kinds of stuff in the background.

"Recoll will index an MS-Word document stored as an attachment to an e-mail message inside a Thunderbird folder archived in a Zip file (and more...). It will also help you search for it with a friendly and powerful interface, and let you open a copy of a PDF at the right page with two clicks. There is little that will remain hidden on your disk."

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#163

Post by nanna »

cpbotha wrote: post #158
nanna wrote: post #106

Earlier quoted context omitted.

Nah, not manual at all. I just call up RefTeX by hitting ctrl-x + (or "C-x +" in emacs parlance). This calls up a list of all possible references and a fuzzy search box which lets me narrow it down. When I've found my reference I have ten options, including: f1: Open associated pdf, url or doi f3: Insert the citation into my thesis and then be asked for what kind of note I want to add (footnote? Title? author name? Y…

I think what your OP was referring to is not adding a citation to a document that you're editing, but rather ingesting PDFs and bibliographic data from the web. I love Emacs (not as much as you do it seems ;) but Zotero is amazing for ingesting academic references including fulltext and bibliographic data from the web. One click of a button in your browser, and everything is ready to read and cite. (Source: Wrote qui…

Aha, apologies, my misunderstanding. Looks like I got a bit emaxcited 8)

So either you add them manually or you query Crossref, arXiv, DBLP or HAL (French open archive) within emacs and then can copy their bibtex entry from there. No pdf or web reference importer as far as I'm aware. Yet!

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#164

Post by geeio »

michaelmior wrote: post #86

I had tried Zotero before but I stuck with Mendeley for a long time. I ended up using Zotero a couple years ago to share some references with my advisor and since then I've grown to love it. One of the nice things about it being based on Firefox is that there's a lot of extensions written for it (which IMO, are not well-advertised). The API is also great and I've been using it to automatically sync PDFs of papers I w…

Do you like the reMarkable tablet?

I currently have an iPad Pro but I really don’t like reading PDFs on it. I’d love to stop printing out papers and an eink display would be nice.

EDIT: just read your review linked in the post

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#165

Post by michaelmior »

geeio wrote: post #164
michaelmior wrote: post #86

I had tried Zotero before but I stuck with Mendeley for a long time. I ended up using Zotero a couple years ago to share some references with my advisor and since then I've grown to love it. One of the nice things about it being based on Firefox is that there's a lot of extensions written for it (which IMO, are not well-advertised). The API is also great and I've been using it to automatically sync PDFs of papers I w…

Do you like the reMarkable tablet? I currently have an iPad Pro but I really don’t like reading PDFs on it. I’d love to stop printing out papers and an eink display would be nice. EDIT: just read your review linked in the post

One thing I'll add that has happened since the post was made is that the reMarkable team has been pretty good at churning out updates. The last firmware update adds table of contents and text search for PDFs and its incredibly fast.

My two biggest annoyances are currently:

1) No web app, so the only way to export PDFs is via the desktop app which is only available for Windows and Mac. The Android app is also pretty terrible. I think not starting with a web interface was a bad decision.

2) The PDFs exported from the desktop app are huge (a PDF that started out ~400KB ended up >100MB after export). Support tells me they're working on this.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#166

Post by yjftsjthsd-h »

tonyg wrote: post #48
innocenat wrote: post #11

Zotero really need more advertisement. I prefer Zotero over Mendeley, but Mandaley seems to advertise much more to university.

I have just recently switched away from Mendeley because of an insanely user-hostile thing they've just done to lock-in their users. Mendeley has started encrypting users' bibliography files (from version 19), claiming variously that encryption is required by GDPR (?!?!) and/or that it improves security on a multiuser system. (Neither of these excuses holds water.) The keys are not available to the users whose data w…

That sounds against GDPR: https://gdpr-info.eu/art-20-gdpr/

"The data subject shall have the right to receive the personal data concerning him or her, which he or she has provided to a controller, in a structured, commonly used and machine-readable format and have the right to transmit those data to another controller without hindrance from the controller to which the personal data have been provided [...]"

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#167

Post by tzm »

Excellent to see and plan to try it out. I almost exclusively use DEVONThink Pro for collecting, organizing and searching local documents and Web resources. It's a key part of my research workflow, but always open to testing (or creating) improved tooling.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#168

Post by jknz »

TsukiZombina wrote: post #154
jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

I tried to use the script but it just searches over the file names.

It seems that the pdftotext command does not go through. Create an issue on github if this still occurs.
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