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Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

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Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#141

Post by maCDzP »

smukherjee19 wrote: post #111

As a grad student, Zotero is a lifesaver! Thanks to the people developing it! I use Google Drive for my pdf storage using some Zotfile acrobatics (awesome plugin btw) to manage my actual pdfs. I plan on switching to Zotero's cloud storage to support development as soon as I can. That being said, I wish I had a nice workflow for reading papers on my iPad like I do on PC (Windows specifically, I know there are software…

I use Zoteros cloud service and the PaperShipapp. It works really good even though the app hasn’t been updated in a while.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#142

Post by eesmith »

tomcam wrote: post #106
medimikka wrote: post #55

Earlier quoted context omitted.

Mendeley joined the Elsevier "Family." Elsevier is one of the big three making massive amounts of money by selling content they receive for free, paid for by the tax payer or non-profits. I strongly believe, that this has greatly contributed to the "Joe Roganization" of the pandemic, hiding true science and research, often created under the auspices of governmental research trusts, behind a paywall. Anyone not in aca…

> "Joe Roganization" of the pandemic Not sure what that means? Is he hiding true science and research?

My best guess is, the influence of non-specialists who do research on their own, without the training to understand which papers are meaningful, which are fluff, which are wrong, and which are fraudulent.

The most informative papers are often behind a paywall, so the non-paywalled papers are biased towards these other less-informative and even wrong papers.

If someone should point to paper X, in order to correct a mistaken belief discussed in a public form (like HN), and that paper X cost $50 to read, many fewer people will read it to examine the validity of the paper in the first place - even if were correct.

While if someone points to paper Y, which supports that belief due to subtly wrong assumptions, but that paper is free to read, then many more people are likely to look at it. And without the training or experience to identify the wrong assumptions.

None of this requires our "Joe Rogan" to hide true science and research - paywalls already do that.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#143

Post by medimikka »

mattkrause wrote: post #109
medimikka wrote: post #41

Earlier quoted context omitted.

Yes, Pages is, but the only citation manager integrating with it is EndNote, because Apple keeps the API locked down and expects quite the payment and revenue share to open it up. On the upside, no one with a little bit of academic cred would use Pages.

We've started doing the "final assembly" of preprints and other self-formatted things in Pages. Placing Figures is still annoying in Pages, but far, far less than in Word. LaTeX would be nicer but....biologists.

This is totally leaving the original topic, but how do you work figure and table management? In my "smaller" papers, I have 50+ figures (dose-response curves, antibody prevalence curves, etc.) and 10+ tables. Just referencing them based on a handwritten caption, the thought makes my skin crawl.

We've gone full in and do most papers in R Studio directly. R Markdown and R Latex work OK, Zotero is integrated, and for the slower members of the team we offer pandoc conversions of their docx and html. But Pages... it does not seem to be made for anyone doing science :(

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#144

Post by medimikka »

solarkraft wrote: post #118
dfraser992 wrote: post #56

Earlier quoted context omitted.

I forget why I didn't like Zotero - I am using iLibrarian [0]. It is positioned as a SaaS, but the source is available and you can host it yourself. But I can't speak to how it compares to other software as I am not continually using it. It seems I just like collecting scientific papers rather than actually reading them.... Maybe if I live to 150 will I manage to read them all. [0] https://i-librarian.net/ And I whol…

Oh damn. It looks extremely close to what I want (It's responsive and the PDF UI might even work on my e-reader), but it doesn't seem to support importing web pages?!?!?!?!?!?!?!?!?!?!?!?!?!?! What a massive and disappointing oversight. Otherwise I could've seen it becoming my new research manager.

It extracts the metadata, but not the body, yes. Retrieved websites are generally frowned upon in my field (medicine, virology), and that's why I never really needed this. We're pandoc-ing our internal MD files to PDF and attach them to the relevant HTML pages, which makes this somewhat a crutch but circumvents the "9 out of ten reviewers hate websites" problem.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#145

Post by jabl »

fjfaase wrote: post #137

I am doing research on a subject where almost all of the source material is in printed material, meaning that I have a lot of scans (photographs actually) that I want to reference. At first, I just extracted the facts, but then I discovered that I have to beter track the sources. What I would like is a process where I transcribe parts of the images, turn those text in some semantic format, describing the facts, and t…

The same people developing zotero are also developing a tool called tropy that might be partially what you're looking for: https://tropy.org/

Disclaimer: I have never used it myself, I'm just aware of it existing.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#146

Post by japanuspus »

medimikka wrote: post #35

Zotero is, if you're not in the market for a closed source silo like EndNote, the only game left in town. Mendeley went full on Evil, and Papers for Mac is Mac only, closed source, and missing dozens of functionalities that are absolutely a must have in academic writing and research. An absolute must have is BetterBibTex ( https://retorque.re/zotero-better-bibtex/ ), which adds better Citekey management and, my perso…

If the town is "online reference managers," you are probably right, but I would argue that reference managers are one of those areas where you really want something offline:

- Offline ensures that you do not suffer an externally caused downtime just before a deadline

- Offline ensures that you have a path for keeping your database throughout your research career, and to do system updates when _you_ want to.

- Offline ensures that if you leave academia, you will always have access to local copies of the academic papers you have referenced.

My favorite offline/local reference manager is `jabRef` [0] which stores all metadata directly in a bibtex-file. The GUI has an excellent pdf-integration, and everything is local and super fast.

Case in point: after a decade in industry, I am looking to get back into my academic fief. All the papers I ever read are in my Dropbox, and all I had to do to pick up where I left was download a current version jabRef and point it to my database which it read without any issues.

[0]: https://www.jabref.org/

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#147

Post by jsilence »

wosk wrote: post #13

I highly recommend going for the beta version which features a (game-changing) built-in pdf reader[1], with annotations (searchable and synced with the beta iPad app) and many more improvements. Zotero is an amazing tool and I could not imagine writing papers without it. For collaborative writing, it syncs the bibliography with overleaf[2] and google docs. The browser add-on allows to build your library with one clic…

Annotating Pdfs also works fine pre-beta with an external Pdf-Viewer that is capable of hilighting and adding comments, like for example Foxit or Pdf-Annotaor. Simply double click to open the Pdf in that viewer (has to be default app for file type), annotate, save file and back in Ztero it is possible to extract the annotations into notes with the Zotfile plugin.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#149

Post by VladimirGolovin »

markdjacobsen wrote: post #99
medimikka wrote: post #35

Zotero is, if you're not in the market for a closed source silo like EndNote, the only game left in town. Mendeley went full on Evil, and Papers for Mac is Mac only, closed source, and missing dozens of functionalities that are absolutely a must have in academic writing and research. An absolute must have is BetterBibTex ( https://retorque.re/zotero-better-bibtex/ ), which adds better Citekey management and, my perso…

Zotero and Obsidian is a killer combination. If anyone is interested, I have some videos on research tools that include a Zotero->Zotfile/MDNotes->Obsidian workflow: https://www.youtube.com/playlist?list=PLHmevVAAXtu3_beDLtsTm... .

>> Zotero and Obsidian is a killer combination.

Could you elaborate on this a bit?

I currently keep my Zettelkasten in Obsidian and my project journals in Workflowy, and I wonder if there’s a place for Zotero in my workflow.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#150

Post by jsilence »

jabl wrote: post #145
fjfaase wrote: post #137

I am doing research on a subject where almost all of the source material is in printed material, meaning that I have a lot of scans (photographs actually) that I want to reference. At first, I just extracted the facts, but then I discovered that I have to beter track the sources. What I would like is a process where I transcribe parts of the images, turn those text in some semantic format, describing the facts, and t…

The same people developing zotero are also developing a tool called tropy that might be partially what you're looking for: https://tropy.org/ Disclaimer: I have never used it myself, I'm just aware of it existing.

This is great news! Thanks for the link!
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