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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

#181

Post by westcort »

dr_dshiv wrote: post #162
westcort wrote: post #84

Earlier quoted context omitted.

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.

This is the way. Numbering should happen right before submission.

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

#182

Post by westcort »

austinjp wrote: post #117
westcort wrote: post #84

Earlier quoted context omitted.

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…

For what it's worth, I've seen the same sort of interoperability issues with all similar software. Author A wants "the latest copy of the Endnote file" but nobody's using Endnote; Author B insists on emailing PDFs as attachments and uses their email as their personal literature database; Author C has set up a Dropbox full of PDFs but nobody uses it; Author D has created a shared Google spreadsheet with links to each…

Yes, I think that makes a lot of sense. Maybe the issues I am referring to are more to do with the general frustrations of putting together a paper with multiple authors and less to do with specific software.

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

#183

Post by westcort »

Gatsky wrote: post #136
westcort wrote: post #113

Earlier quoted context omitted.

A RegEx-based parsing system in JavaScript helps with the reference formatting. EndNote makes references uneditable (unless you also have a copy of EndNote) and often cannot adjust to a particular journal's idiosyncrasies...but I can do that easily with home-built software. Zotero may be great, and I cannot really make an assessment one way or the other. All I know is that hardly anyone in my industry uses it. It's r…

I see, so you wrote your own solution which you have to maintain and extend for each different citation style… pros and cons to that obviously. Why is it so important that a citation system works in 2003 and in 2021? Papers once published become historical artefacts essentially.

I am thinking of one particular journal that had a problem with historical reference libraries under RefMan that all broke after the EndNote migration. A library of thousands of purchased articles, including pivotal trials that are commonly referenced, essentially became inaccessible after RefMan was purchased by EndNote. I believe EndNote also remotely inactivated the software and engaged in some other chicanery. That experience turned me off of reference manager software. Maybe Zotero has gotten it right this time! I don't know. I just know that few things last in tech and least of all libraries of data housed in software that may or may not be updated or supported by future systems.

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

#184

Post by westcort »

cycomanic wrote: post #80
westcort wrote: post #71

Earlier quoted context omitted.

Fair enough, but not every client is going to want to use the same operating systems, processors, be allowed to install third party software, etc. This might work in a strictly academic setting with few stakeholders, but in professional publishing, interoperability makes these systems unpopular. Downvoting that won’t change reality. I guess there is not much interest in feedback or possible routes to improvement.

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…

Maybe it actually is something I should try and it sounds like there have been some major improvements over the past few years. I dislike EndNote, but that doesn't mean the same issues exist with Zotero, so maybe I will give it a try. I should also define my terms better. When I talk about professionals publishing, I am referring more to corporate publishing houses, agencies, and pharma and chemical industry publishing. Academic publishing is probably the most professional type of publishing of all, so I should clarify that.

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

#185

Post by fluidcruft »

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 can do anything EndNote can do

My biggest frustration with Zotero is that it has no real support for standards documents.

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

#186

Post by lijogdfljk »

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…

On the technical side, anyone know how their browser extension to save webpages.. works?

I'm writing a personal reader / reference tool. More of a knowledge base than a formal reference tool, but i want similar functionality, and so i've been researching ways to locally archive web pages to cite in notes. To save effort, i was trying to reuse existing methods in Reader-like libraries. The best i found so far, i think, is Telegram's library of "Instant View" parsers. A community managed set of scrape instructions basically, XPath and whatnot, that i could write an implementation for and - in theory - support everything Telegram does.

This is a fair bit of work though. I debated instead simply saving the whole webpage, but that may require saving the JS and i really don't want to execute JS as part of the citation.

Anything i might be missing here? Instant View is the only community managed format for scraping i've seen, i'm surprised this isn't more commonly outsourced to communities for Reader modes and whatnot

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

#187

Post by dredmorbius »

jptech wrote: post #54
jabl wrote: post #20

I used to use Mendeley, but after the evil empire bought them out and added anti-features like preventing export of the DB (or something like that, I don't remember exactly what it was anymore), I switched to Zotero. I was on the verge of exiting academic research at the time, so I don't have as much experience of Zotero, but it seems very solid. Strongly recommended! (Occasionally I wonder about how Zotero developme…

I have been and still am a Zotero user. But I found it unfortunate that back in grad school many of my peers still used Mendeley. The school library even had workshops/classes in which they taught how to use the software. I found it ironic that despite paying loads of money to Elsevier for the journal subscriptions, they were advertising their software too!

In all likelihood, Elsevier were subsidising or oturight funding those classes.

TANSTAFL. Especially in consumer technology "training", which is really sales-pipeline-building, and hooking addicts for life.

You might find FOIAing the library or univesity interesting, for contractual relationships.

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

#188

Post by mattkrause »

medimikka wrote: post #143
mattkrause wrote: post #109

Earlier quoted context omitted.

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 th…

Our workflow is decidedly uncool and old-fashioned.

Scripts produce figures as PDF files. We aim to have the script produce more-or-less final figures, but sometimes the last 5-10% is easier to do manually.

We don't bother putting them into the manuscript text while editing, and the captions are usually on a separate page, as most of our target journals seem to require. The manuscript gets written in Word + Endnote, with ad-hoc figure reference like See Figure XXX_DOSE_RESPONSE_XXX that get find-replaced at the very end.

This is definitely a local optima (if that!), but works pretty well for us especially since it's a pretty diverse group: some computationally-minded folks might be happier with LaTex, but we've also got 85 year old prof, DoD folks, etc who want track changes and familiarity.

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

#189

Post by xtracto »

cycomanic wrote: post #66
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…

I use zotero and I really want to like it, but it's not that good. The tagging functionality seems like an afterthought, the bibtex support is only reasonable with betterbibtex and even with it I have issues. For example journal abbreviations don't work consistently, every start up I get told that the betterbibtex styles have changed and I need to restart zotero... File management is also only bearable with zutilo, a…

Aaah JabRef, that was my choice 15+ years ago when I was doing my PhD. I think today a combination of portable JabRef and GoogleDrive/DropBox or similar would do the trick.

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

#190

Post by jiggunjer »

kuhewa wrote: post #122
jiggunjer wrote: post #69

Earlier quoted context omitted.

Having used Zotero, Mendeley and Endnote I ended up on Endnote. I like their metadata scraping, their Word plugin and that many journals offer a pre-configured reference template. But yes as a DBMS it lacks alot in the filter/grouping features and date fields don't convert format intelligently.

First manuscript in my PhD I just hand-typed the bibliography. But when you get to a few hundred in a document and over 1000 relevant to your work that you want to keep track of, ah and when you need to resubmit manuscripts with a different reference format, and once I made the jump to actually using it and figuring out a few of the quirks, I now quite like Endnote since my institution has a site licence.

Yes. Professionals don't hand-edit references in the writing document. Update the template and click refresh. That said, I also use Endnote because it's free for me.
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