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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

#151

Post by degenerate »

dstillman wrote: post #137
degenerate wrote: post #135

Earlier quoted context omitted.

Our team switched from a custom solution to Mendeley last year instead of Zotero because Mendeley lets you highlight and add notes in the PDF, which gets shared among the whole team with those markups. Zotero didn't have that. Otherwise we would have went with Zotero.

In Zotero you just do that in your PDF reader of choice. If you're using syncing, as long as the PDF reader saves annotations back to the original file, Zotero will automatically sync the updated file to other group members. The one downside of this approach is that multiple people can't modify the same PDF at the same time. The upside is that you can use whatever PDF tools you want and annotations remain accessible…

Thanks for explaining how it can be achieved in Zotero. We did try this out, but just as you mentioned, the annotated/highlighted PDF changes the file. We liked how Mendeley keeps that information in a separate DB and lets you make the markups right in the app, instead of having to do it yourself outside the application. It was simply more seamless for our non-tech people.

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

#152

Post by paultopia »

dstillman wrote: post #147
paultopia wrote: post #144

I want to love Zotero, I really do. But the last time I tried it seriously, I found that: - metadata extraction/automated adding really doesn't work right with my research workflow (a lot of google scholar searches, a lot of humanities and social science sources)---lots of inaccurate or incomplete info, lots of downloading RIS files and then manually importing and separately manually importing the PDF. - documentatio…

> metadata extraction/automated adding really doesn't work right with my research workflow I'm not sure exactly what you mean, but the primary way of adding items to Zotero is with the Zotero Connector browser extension, which lets you save high-quality metadata and PDFs with a single click from a huge variety of sources (certainly including humanities sources, since Zotero was created by historians). No other tool c…

Thank you---this is super encouraging, and a good signal to maybe go back to it.

Incidentally, one thing that would be really helpful for a documentation standpoint would be a series of articles about best practices, like which metadata sources work best.

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

#153

Post by disqard »

thatcat wrote: post #148
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 did something similar for search until I found Recoll. It has similar functions to what you describe(caching, fuzzy search) with a slick work flow that shows google scholar like context previews with an optional remote access to your library through a webui. It also searches compressed archives and generally simplifies searching many unorganized files. http://www.lesbonscomptes.com/recoll/

Thank you for the pointer to Recoll!

I'm trying it out now -- I have way too many pdfs, and I could really use the extra features (like context previews).

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

#154

Post by TsukiZombina »

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.

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

#155

Post by rufius »

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…

Neat workflow. I use a conceptually similar system though it’s proprietary (DEVONthink). Drop pdfs or websites or bookmarks in the inbox and burn through them and decide if I want to archive it in the database.

I’ve enjoyed having access to the database from my laptop as well as iPhone and iPad. It’s definitely been a workflow I’ve cobbled together. This seems to be working out better though.

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

#157

Post by mino »

harry8 wrote: post #47
zwaps wrote: post #44

I use Mendeley instead of Zotero. I really wanted to like Zotero, since I hate Elseveir like the next guy, but Zotero didn't have any of the look-up features and ability to quickly import my papers (thousands). In Mendeley, I can just throw a physical folder into a folder and it'll tag and categorize the PDFs mostly correctly. I mean it is nice that Zotero has an import browser plugin (which, btw, Mendeley does as we…

Mendeley is an Elsevier product? Might make a few academics come to a differing conclusion given Elsevier's reputation is one they've well and truly earned...

Yes. That's why I uninstalled and switched to Zotero. The import tool worked great, btw.

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

#158

Post by cpbotha »

nanna wrote: post #106
jhbadger wrote: post #100

Earlier quoted context omitted.

I guess I don't see how you can easily add citations without something like Zotero (or its closed source equivalent Endnote). At least in my use case, I go to Pubmed and click the Zotero Chrome plugin to add the reference to Zotero. What do you do, manually enter the info?

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 quite a number of papers and co-authored one textbook, all using Zotero. My workflow was Zotero for ingestion -> per-publication bibtex files for authoring)

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

#159

Post by singingfish »

jhbadger wrote: post #104
singingfish wrote: post #50

Zotero is awesome. 80% of the academic type people I've introduced it to have switched. The other 20% have Endnote stockholm syndrome.

Particularly bench biologists tend to have "The only way to write a paper is Microsoft Word and Endnote". Zotero is considered a bit eccentric and using LaTeX is practically unheard of. As a computational biologist I like Zotero and LaTeX but am often forced not to use them in collaborations.

I wrote my (social science) PhD with LaTex (eventually). Corralling it to BibTeX from Zotero was a bit of a pain, but worked fairly smoothly. What it did achieve was that it made it look like I had paid much more attention to layout and cross referencing than I actually had, which got me through with two nit-picking corrections.

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

#160

Post by davidovitch »

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 agree with what others have mentioned here: I really like your elegant workflow (thanks for sharing!!). I also like that it is generally applicable to any collection of PDFs.

However, to be fair, you can follow a somewhat similar workflow with Zotero in combination with the Firefox plugin: download pdf by adding it to the Zotero database in Firefox and Zotero takes care of the indexing. Zotero misses the fancy interactive fuzzy searching you have in your workflow thanks to fzf, but I've added it as a feature request for Zotero [1].

You don't have to organize your papers into folders (or collections in Zotero parlance since a single item can appear in multiple collections). For most academic papers the Zotero plugin will also grab the pdf's metadata as a bonus without additional costs.

[1] https://github.com/zotero/zotero/issues/1536

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