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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

#161

Post by Labo333 »

I tried Zotero and equivalent softwares (mendeley) a few times but never caught.

My typical workflow involves a big gdoc that I can share with my advisor. I paste the title, year, author and number of citations (to know which articles are the most influential). And, most importantly, a link to the pdf (sometimes through sci-hub).

Then I write notes under those articles, pasting screenshots of equations that I want to find easily.

When I have to write my paper, and this is the only painpoint, I have to paste the titles to google scholar and copy the bibtex code. I might write a simple bot at some point to do it for myself.

I'm taking every advice to improve this!

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

#162

Post by dr_dshiv »

westcort wrote: post #84
cycomanic wrote: post #80

Earlier quoted context omitted.

You're getting down voted because you comment seems uninformed. AFAIK Zotero is available on every OS that Firefox runs on, for example. Also you talk professional publishing, what does that exactly mean? Zotero is a reference manager, so largely aimed at academic writing (because they tend to be the ones who cité and use references the most). I would be surprised if any other setting has more stakeholders, scientifi…

Let’s say you are working on a paper with 6 coauthors for a major medical journal, hypothetically. Dr. So and so in Russia, another in Japan, a third in California, and a few others. Would you mind reviewing this draft? Oh, yeah, by the way, you need to install Zotero before you can edit the references. How do you think that is going to go? How about dealing with a graphic designer in Hungary who can’t copy the text…

This is why I just use Google docs and Google scholar... when i need to do the refs, I just alphabetize in a sheet. Frontiers has low barrier citation expectations. If I have to do ACM numbering I do it in word, as last step.

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

#163

Post by augmentedtext »

theteapot wrote: post #77

I heard an article on the radio the other day (BBC) about some researcher developing meta data standards to embed bibliography data into PDFs. Basically stash the relevant refs from your bibtex (or other) database into the PDF in a machine readable way and develop open source tools to parse that and allow navigation to online or local sources. Seems like a pretty good idea. But I can't remember who it was / what it's…

Hi, that was Vint Cerf and me, Frode Hegland. The project we talked about is called Visual-Meta. You can read about it here: https://visual-meta.info or contact me with any questions: frode@hegland.com Thanks for listening! :-)

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

#164

Post by raxxorrax »

medimikka wrote: post #55
WayToDoor wrote: post #46

Earlier quoted context omitted.

> Mendeley went full on Evil Could you explain what happened with mendeley? I've been using it for a while, and didn't notice anything different really.

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…

> the "Joe Roganization" of the pandemic

I think that was much more caused by media trying to prime people with some ridiculous stories that at least some refused to believe. A simple but honest approach is preferred to what we read in media otherwise.

We still have sci-hub at least...

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

#165

Post by black_puppydog »

diarrhea wrote: post #156
dstillman wrote: post #153

Earlier quoted context omitted.

Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference m…

I use Zotero and sync the attachments to my Nextcloud instance via WebDAV. The database is synced to the Zotero servers, because that's the only option. With a bit of care on initial setup for new machines, it works wonderfully. The real value are the PDFs, some of which are of course really hard to get by. And those are "local" in the sense of "local server", yet available to all clients. There was a forum entry tha…

I've been syncing my full-texts via syncthing for years and years now and I've never had to think about it after initial setup.

Zotero is great! :)

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

#166

Post by jrichardshaw »

dstillman wrote: post #157
jrichardshaw wrote: post #155

I've tried to use Zotero over the years, and I always stumble with it because it didn't have a good handling of arXiv id's. The arXiv is one of the primary way of finding papers in my field (cosmology), and I really want to support ingestion via them, looking up actual paper details from them (while retaining the arXiv id), and including them in bibtex exports. I check back from time to time, but I don't think that's…

Zotero has supported adding items via arXiv ID since 2018, and saving from arXiv.org since forever. There's not currently a dedicated field for arXiv IDs, but they're added to the Extra field and included in exports (and accessible however you want via Better BibTeX export). (Disclosure: Zotero dev)

Thanks, that's good to hear! I'll give it another look next time I look at switching things up.

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

#167

Post by japanuspus »

dstillman wrote: post #153
japanuspus wrote: post #146

Earlier quoted context omitted.

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…

Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference m…

Thank you for clearing this up - and apologies for not researching!

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

#168

Post by Al-Khwarizmi »

Gatsky wrote: post #103
westcort wrote: post #40

I write a lot of academic papers and never use this kind of software. EndNote creates uneditable references and slows down Word, Zotero had some limitations after which they charge a monthly fee, and none of the reference libraries are easy to share with external clients. Most other medical/technical writers I know only use these tools as a “reference library.” It might be useful for someone writing a thesis, but alm…

Interested to hear more about this, so how do you create citations and bibliographies? How do you format the bibliographies according to each journal’s style? It is true that there is no good tool for editing references collaboratively. Previous attempts at this have resulted in some poor sod having to redo all the citations.

In my field, we typically just use plain bibtex files. With a proper bibtex file and a decent journal latex template, the template should do the vast majority of the work towards formatting the bibliography the way the journal wants.

Typically there are some remaining warts (both due to suboptimal templates and to limitations of bibtex itself and its community/ecosystem like the address vs. location conundrum, those who have found it will know what I'm referring to), but often they are insignificant enough to just deal with them in the typesetting stage, and when they aren't they don't require much manual work, to me it's not even near the top in the ranking of inconveniences of publishing a scientific paper. And I'm not sure this kind of software would solve such nuances anyway.

Some years ago I tried several of this kind of referencing software, including Mendeley and a couple others (not Zotero because at that point it was Firefox-only IIRC, which was a red flag for me, I'm particular about using the browser I like) and to be honest I found them more trouble than they were worth, although seeing the general positivity here towards Zotero I think I'll give it a try now.

Of course, fields that use Word instead of Latex are a totally different world where probably nothing of my comment will apply.

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

#169

Post by faustlast »

Labo333 wrote: post #161

I tried Zotero and equivalent softwares (mendeley) a few times but never caught. My typical workflow involves a big gdoc that I can share with my advisor. I paste the title, year, author and number of citations (to know which articles are the most influential). And, most importantly, a link to the pdf (sometimes through sci-hub). Then I write notes under those articles, pasting screenshots of equations that I want to…

Workflow:

1. copy doi and extract in into zotero (automatic looks for pdf). 2. better-bibtex (zotero add-on) will automatically generate the .bib entry. 3. tex editor automatically recognize bibtex entry. 4. write all the relevant stuff with proper formatting (ready for paper). 5. git and github for sharing.

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