7 ms·

Zotero has improved a lot, while Mendeley has repeatedly regressed. Mendeley used to be quite a good program, but recently you can not export annotated PDFs me

by zwaps 8y ago

Zotero has improved a lot, while Mendeley has repeatedly regressed. Mendeley used to be quite a good program, but recently you can not export annotated PDFs meaningfully. For example, sending a folder of annotated PDFs to a co-author during a literature review is impossible. This is obviously the case since Elsevier does not want you to trade research papers, whether you have lawfull access or not. The updates that took away features were silent. What happened to me some time ago was these updates occured during a high-stress phase with a short deadline until conference submissions (if you are a researcher, you know what I mean). I had used Mendeley for years to annotate and categorize literature. I was now in need to send my categorized PDFs to a central repository for my co-authors to evaluate and add to. After some update, without me noticing it, it was no longer possible to export folders of PDFs or PDFs in general! I had everything in Mendeley, weeks of work. I was completely f'ed - deadline approaching. I had to re-aquire all PDFs and go through all annotations by hand. ELSEVIER IS SIMPLY ANTI SCIENCE. Collaboration is a key in science. Sharing results, research and literature is crucial. Mendeley makes this impossible. It does NOT allow you to fully access your own work! So in conclusion, USE ZOTERO. It's good now, better than before. You can use a PDF reader with annotations to open and save the PDF and Zotero will keep those annotations. You can export Bibliographies, including notes AND files. You can not do that with Mendeley. So again, as a researcher, I emplore you to drop Mendeley completely, as I have done. Thank you.

walrus01 8y ago
Elsevier is to science as Oracle is to database software licensing.
- mdip 8y ago
  Thank you for this. As someone who does not make a habit of hanging around academia, I have very little experience with Elsevier short of what I read here. However, as someone who worked in a large IT organization for a huge company and wrote software for license compliance tracking, I completely understand. Grab me a pitch fork, I'll march.
AnaniasAnanas 8y ago
> I had used Mendeley for years to annotate and categorize literature. I was now in need to send my categorized PDFs to a central repository for my co-authors to evaluate and add to. After some update, without me noticing it, it was no longer possible to export folders of PDFs or PDFs in general! This is exactly why you should not depend on proprietary software for anything even remotely important. This is not the first nor will it be the last time that something like that happens. Letting a company (or an individual) dictate how and if I can access my work is unacceptable to me. Thankfully Zotero is FOSS, I will be staying with BibTeX though.
- andrepd 8y ago
  The adage is certainly true: "with proprietary software, the user doesn't control the program, the program controls the users".
lou1306 8y ago
Personal experience: I made the switch soon after starting my PhD and never looked back. Also, their Connector plugin for Firefox is a life saver. 90% of the time I only have to lookup the title of a paper on DBLP, then export it as BibTeX and pronto, the reference is now in my library with most of the relevant metadata. Much better than Mendeley's quite opinionated plugin (which also won't work unless you log into Elsevier's servers)
- zwaps 8y ago
  I never used the Mendeley plugin, but I imagine it must be pretty horrible to store PDFs from all the convoluted sources and proxy setups or library file-servers that universities use. It probably only works well if you logged into your Elsevier(tm) account. In any case, the Zotero plugin works great and just saves Metadata and PDFs, as it should. For the usual preprint or paper providers, it works perfectly. So even here, using Mendeley is just bad.
zwaps 8y ago
Also, you may remember me being hesitant to switch to Zotero because in the past it lacked the ability to meaningfully edit saved citations and files, in particular, it would not detect from PDFs for files that you had already downloaded. It worked only well with the plugin, getting the file "fresh" from the publisher. Mendeley's advantage was that you could just drag and drop a pdf in and it would add meta-data. I am happy to report that Zotero does this as well now. And it works quite well, sometimes better then Mendeley. So if that was your reason, like it was for me before I was hit with the "no export disaster", go ahead and switch. Let Mendeley die the lonely death it deserves.
boyband6666 8y ago
Zotero has improved a lot, though sadly it still has a way to go on the user experience of Mendeley. My main gripes are - The way that it still doesn't play nice with cloud services (syncing the directory and its just a matter of time until you get database corruption. It takes a lot of wonky setting up to get it to kind of work, which just shouldn't be the case - The lack of developers and thus slow pace of improvement. I'm a researcher not a programmer - which I think describes most people using it. That means unfortunately we are reliant on one or two volunteers to improve the product. The pace of improvement is slow, and theres also no way to meaningfully advance it - be that through offering bounties for someone to implement certain features, just inputing lists of bugs/feature requests (the list is already v long, and doesn't move much), or anything else. It's a really good bit of software (and I don't want to sound ungrateful), I just know it still has a lot of quirks. This means it can't always do what you want, and it isn't an easy obvious choice for new researchers - Mendeley is certainly more familiar and easier to use.
- zwaps 8y ago
  It is a good idea to get some Zotero cloud storage. The sync works perfectly for me. Since any serious library will be over the Mendeley free limit, I think it's a fair comparision. Of course Zoteros development is less funded and less agile. Given that, I think they have worked on many shortcomings. The interface is now good, the group-based sharing works, PDFs are read and meta-data is added well. The import plugin is better than that of Mendeley. Mendeley has an advantage in that it has a great PDF viewer and editor. But since you can not do anything with these PDFs and annotations, like export them or send them anywhere, it's now pretty much useless. Switching is not easy, but in the long run I don't think you'd be faced with much issues going from Mendeley to Zotero. It was certainly worth it for me. As it stands, you can still import from Mendeley to Zotero, so I'd at least do that now, until Elsevier finds a way to shut this down completely.
- Libbum 8y ago
  What cloud service are you attempting to connect to? I'm using my universities' box.com account - which generally has pretty appalling support (on linux at least). Zotero has managed this flawlessly.
bocklund 8y ago
> but recently you can not export annotated PDFs meaningfully FWIW, I think they brought back exporting annotated PDFs in the most recent version, 1.19.3 At least maybe there is hope for exporting your work to Zotero.
greeneggs 8y ago
How easy is it to leave Zotero? (Either to move to a different paper manager, e.g., Mendeley, or to leave the paper manager ecosystem entirely.) Can Zotero respect my filesystem organization (à la Lightroom)? I have thousands of papers organized, and don't want to move them all in (too much work, what if I don't like it?), but I also don't want to have two copies of some subset of the papers, which might not be in sync.
- j88439h84 8y ago
  Yeah it can do that, with the use of some plugins.
  - boyband6666 8y ago
    Easy to leave? They are good about that. Respect the filesystem? Erm, again we're in the world of the murky where it probably is possible with Zotfile, but out of the box, it wants to rearrange them in to folders like 'MN8YD'. I've made my peace with that, but if you are very touchy about it, try it with a copy first and see how you get on.
- burtonator 8y ago
  Can't comment on Zotero but in Polar we have a similar issue where we need to move over the PDFs. We're going to start using hard links so at least if it's on the same drive you can have the same copy just in two different places.
natechols 8y ago
> ELSEVIER IS SIMPLY ANTI SCIENCE. +1. I worked in publicly-funded research labs for 15 years and there is no single organization I despise as much as Elsevier - only Springer-NPG comes close. If the company went bankrupt tomorrow it would be a great day for science.
burtonator 8y ago
I've been looking at this too. I have a new app I've been working on which is similar to both Zotero and Mendeley. https://getpolarized.io/ https://getpolarized.io/ It looks like they're "encrypting" by saying that there is some sort of GDPR requirement when in reality it's more plausible that they're trying to lock in users.

by zwaps 8y ago

walrus01 8y ago

Elsevier is to science as Oracle is to database software licensing.

mdip 8y ago
Thank you for this. As someone who does not make a habit of hanging around academia, I have very little experience with Elsevier short of what I read here. However, as someone who worked in a large IT organization for a huge company and wrote software for license compliance tracking, I completely understand. Grab me a pitch fork, I'll march.

AnaniasAnanas 8y ago

> I had used Mendeley for years to annotate and categorize literature. I was now in need to send my categorized PDFs to a central repository for my co-authors to evaluate and add to. After some update, without me noticing it, it was no longer possible to export folders of PDFs or PDFs in general! This is exactly why you should not depend on proprietary software for anything even remotely important. This is not the first nor will it be the last time that something like that happens. Letting a company (or an individual) dictate how and if I can access my work is unacceptable to me. Thankfully Zotero is FOSS, I will be staying with BibTeX though.

andrepd 8y ago
The adage is certainly true: "with proprietary software, the user doesn't control the program, the program controls the users".

lou1306 8y ago

Personal experience: I made the switch soon after starting my PhD and never looked back. Also, their Connector plugin for Firefox is a life saver. 90% of the time I only have to lookup the title of a paper on DBLP, then export it as BibTeX and pronto, the reference is now in my library with most of the relevant metadata. Much better than Mendeley's quite opinionated plugin (which also won't work unless you log into Elsevier's servers)

zwaps 8y ago
I never used the Mendeley plugin, but I imagine it must be pretty horrible to store PDFs from all the convoluted sources and proxy setups or library file-servers that universities use. It probably only works well if you logged into your Elsevier(tm) account. In any case, the Zotero plugin works great and just saves Metadata and PDFs, as it should. For the usual preprint or paper providers, it works perfectly. So even here, using Mendeley is just bad.

zwaps 8y ago

Also, you may remember me being hesitant to switch to Zotero because in the past it lacked the ability to meaningfully edit saved citations and files, in particular, it would not detect from PDFs for files that you had already downloaded. It worked only well with the plugin, getting the file "fresh" from the publisher. Mendeley's advantage was that you could just drag and drop a pdf in and it would add meta-data. I am happy to report that Zotero does this as well now. And it works quite well, sometimes better then Mendeley. So if that was your reason, like it was for me before I was hit with the "no export disaster", go ahead and switch. Let Mendeley die the lonely death it deserves.

boyband6666 8y ago

Zotero has improved a lot, though sadly it still has a way to go on the user experience of Mendeley. My main gripes are - The way that it still doesn't play nice with cloud services (syncing the directory and its just a matter of time until you get database corruption. It takes a lot of wonky setting up to get it to kind of work, which just shouldn't be the case - The lack of developers and thus slow pace of improvement. I'm a researcher not a programmer - which I think describes most people using it. That means unfortunately we are reliant on one or two volunteers to improve the product. The pace of improvement is slow, and theres also no way to meaningfully advance it - be that through offering bounties for someone to implement certain features, just inputing lists of bugs/feature requests (the list is already v long, and doesn't move much), or anything else. It's a really good bit of software (and I don't want to sound ungrateful), I just know it still has a lot of quirks. This means it can't always do what you want, and it isn't an easy obvious choice for new researchers - Mendeley is certainly more familiar and easier to use.

zwaps 8y ago
It is a good idea to get some Zotero cloud storage. The sync works perfectly for me. Since any serious library will be over the Mendeley free limit, I think it's a fair comparision. Of course Zoteros development is less funded and less agile. Given that, I think they have worked on many shortcomings. The interface is now good, the group-based sharing works, PDFs are read and meta-data is added well. The import plugin is better than that of Mendeley. Mendeley has an advantage in that it has a great PDF viewer and editor. But since you can not do anything with these PDFs and annotations, like export them or send them anywhere, it's now pretty much useless. Switching is not easy, but in the long run I don't think you'd be faced with much issues going from Mendeley to Zotero. It was certainly worth it for me. As it stands, you can still import from Mendeley to Zotero, so I'd at least do that now, until Elsevier finds a way to shut this down completely.
Libbum 8y ago
What cloud service are you attempting to connect to? I'm using my universities' box.com account - which generally has pretty appalling support (on linux at least). Zotero has managed this flawlessly.

bocklund 8y ago

> but recently you can not export annotated PDFs meaningfully FWIW, I think they brought back exporting annotated PDFs in the most recent version, 1.19.3 At least maybe there is hope for exporting your work to Zotero.

greeneggs 8y ago

How easy is it to leave Zotero? (Either to move to a different paper manager, e.g., Mendeley, or to leave the paper manager ecosystem entirely.) Can Zotero respect my filesystem organization (à la Lightroom)? I have thousands of papers organized, and don't want to move them all in (too much work, what if I don't like it?), but I also don't want to have two copies of some subset of the papers, which might not be in sync.

j88439h84 8y ago
Yeah it can do that, with the use of some plugins.
- boyband6666 8y ago
  Easy to leave? They are good about that. Respect the filesystem? Erm, again we're in the world of the murky where it probably is possible with Zotfile, but out of the box, it wants to rearrange them in to folders like 'MN8YD'. I've made my peace with that, but if you are very touchy about it, try it with a copy first and see how you get on.
burtonator 8y ago
Can't comment on Zotero but in Polar we have a similar issue where we need to move over the PDFs. We're going to start using hard links so at least if it's on the same drive you can have the same copy just in two different places.

natechols 8y ago

> ELSEVIER IS SIMPLY ANTI SCIENCE. +1. I worked in publicly-funded research labs for 15 years and there is no single organization I despise as much as Elsevier - only Springer-NPG comes close. If the company went bankrupt tomorrow it would be a great day for science.

burtonator 8y ago

I've been looking at this too. I have a new app I've been working on which is similar to both Zotero and Mendeley. https://getpolarized.io/ https://getpolarized.io/ It looks like they're "encrypting" by saying that there is some sort of GDPR requirement when in reality it's more plausible that they're trying to lock in users.