4 ms·

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 an

by zwaps 8y ago

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 well), but once you have a substantial library of pdfs, it is just too time consuming to re-import it all again, type in names, years, journals etc. ugh.. Also, Mendeley can open pdfs within the app and has great features for mark-up and comments. Reviewing a paper is really nice this way. In fact, Mendeley is the program with the best mark-up features on all of Linux, in my opinon. And all this is synced across devices. I'd love to use Zotero but tbh Mendeley is just better.

lvbu 8y ago
You can just all all the pdfs by "Store copy of file" option. It allows multi sect. Then you can select all of them and do a fetch metadata together.
decasia 8y ago
Your information might be outdated -- In the latest version of Zotero, when you add a PDF to Zotero, it automatically retrieves the metadata via DOI lookup. (I don't think it would work with papers too old to have DOIs but haven't checked lately.)
- ekphrasis 8y ago
  The metadata retrieval pairs with a DOI or ISBN [1]. Articles without such handles might not work, nor will articles which are not OCR'ed (obviously) but this can be easily fixed with OCR scanning software. The metadata retrieval process is a very handy feature, especially paired with Zotero's web browser plugin. Zotero also keeps a repository of all the citation styles, which are curated and administered by the Zotero team and stored in a Github repo [2]. [1] https://www.zotero.org/blog/zotero-5-0-36/ https://www.zotero.org/blog/zotero-5-0-36/ |2] https://github.com/citation-style-language/styles https://github.com/citation-style-language/styles
harry8 8y ago
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...
- zwaps 8y ago
  I reinstalled Zotero just now, since it has a Mendeley importer now. What is the proper way to store PDFs that I annotate (say, using Okular in Linux) on Zotero with the ability to send them to other researchers and then update them? I don't mind paying money for cloud storage, but I gotta be able to work with the pdfs.
  - ekphrasis 8y ago
    You can choose to set a custom PDF reader in the General tab of preferences --> Open PDF using --> custom [1]. Then you can annotate the file and save it. If Zotero creates a copy of the file when you save your annotations, you might need to use Show file by right clicking the article in Zotero and make changes to the file in Zotero's storage. In Linux, that'll be in ~/Zotero. [1] https://forums.zotero.org/discussion/1977/changing-the-default-pdf-reader https://forums.zotero.org/discussion/1977/changing-the-defau...
    - dstillman 8y ago
      No need to use Show File. You can just open the PDF from Zotero, annotate, and save.
  - bovine3dom 8y ago
    It's a bit of a pain, but you can store `~/.local/share/okular/docdata/` in version control or your favourite cloud storage provider, and then you'll get synchronised annotations. When I say a bit of a pain, I mean it - I switched to Mendeley with great sadness because its mobile application means I can read and annotate papers on my tablet and have it synchronised perfectly with my desktop. On a semi-related note: the Mendeley mobile application makes selecting text a joy on a touchscreen with a kind of magnifying glass. I really wish it was built into Android system wide.
deleted 8y ago
[deleted]
zwaps 8y ago
yeah so I just reinstalled Zotero and imported my Mendeley library. It does that, and it can actually look up metadata from pdfs. But: It can NOT update already existing entries from such a lookup. You have to delete the pdf and re-import. Why? No reason. It's this sort of really bad usability decision that makes Zotero just not very good imo.
- tonyg 8y ago
  I'm not sure what feature exactly you're missing, but are you aware of the "Rename file from parent metadata" option you get when right clicking on a PDF in the list? Perhaps that does what you need. If not, with Zotero you have a chance of getting a missing feature added. Not so with the closed-source Mendeley. Especially now they have started doing user-hostile lock-in stuff like gratuitously encrypting users' data, making it no longer accessible to the user (see downthread). With Zotero, in principle you could hack together something using `bash` and `sqlite3` that batch-updated documents; you may not even need to look at the source code to the official app. It's ad-hoc munging like that that Mendeley has recently gone out of its way to prevent, stopping people from working effectively with their own data.
  - zwaps 8y ago
    Zotero can look up metadata if you add a PDF to your library Zotero can not update metadata for a PDF you already have in your library Hence, adding an existing library means you have to do it manually for each pdf This is bad design, because the functionality exists, but it's implemented in a way that makes everything complicated for no reason at all. Why disable the "lookup metadata" button for a pdf which is already in a library? WHYYYYY
    - tonyg 8y ago
      I see! Yes, that's not great.
- dstillman 8y ago
  It's not a usability decision — it's just one feature that hasn't yet been implemented [1]. Updating metadata is more complicated than creating a new item, because you have to deal with the existing metadata somehow. (Mendeley just overwrites the existing item, often with incorrect data, which we don't consider acceptable.) Disclosure: Zotero developer [1] https://github.com/zotero/zotero/issues/1515 https://github.com/zotero/zotero/issues/1515
icelancer 8y ago
>> I mean it is nice that Zotero has an import browser plugin (which, btw, Mendeley does as well), but once you have a substantial library of pdfs, it is just too time consuming to re-import it all again, type in names, years, journals etc. ugh.. It automatically added 90-95% of PDFs I imported, most directly from Sci-Hub with no editing from me.
tonyg 8y ago
My experience of auto-import of metadata in Mendeley is that it gets about 80% of it right. Not good enough for publication: I still had to check over each record with a fine-toothed comb when I wanted to actually use an entry to cite something. So far, Zotero's metadata lookup seems about the same quality.

by zwaps 8y ago

lvbu 8y ago

You can just all all the pdfs by "Store copy of file" option. It allows multi sect. Then you can select all of them and do a fetch metadata together.

decasia 8y ago

Your information might be outdated -- In the latest version of Zotero, when you add a PDF to Zotero, it automatically retrieves the metadata via DOI lookup. (I don't think it would work with papers too old to have DOIs but haven't checked lately.)

ekphrasis 8y ago
The metadata retrieval pairs with a DOI or ISBN [1]. Articles without such handles might not work, nor will articles which are not OCR'ed (obviously) but this can be easily fixed with OCR scanning software. The metadata retrieval process is a very handy feature, especially paired with Zotero's web browser plugin. Zotero also keeps a repository of all the citation styles, which are curated and administered by the Zotero team and stored in a Github repo [2]. [1] https://www.zotero.org/blog/zotero-5-0-36/ https://www.zotero.org/blog/zotero-5-0-36/ |2] https://github.com/citation-style-language/styles https://github.com/citation-style-language/styles

harry8 8y ago

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...

zwaps 8y ago
I reinstalled Zotero just now, since it has a Mendeley importer now. What is the proper way to store PDFs that I annotate (say, using Okular in Linux) on Zotero with the ability to send them to other researchers and then update them? I don't mind paying money for cloud storage, but I gotta be able to work with the pdfs.
- ekphrasis 8y ago
  You can choose to set a custom PDF reader in the General tab of preferences --> Open PDF using --> custom [1]. Then you can annotate the file and save it. If Zotero creates a copy of the file when you save your annotations, you might need to use Show file by right clicking the article in Zotero and make changes to the file in Zotero's storage. In Linux, that'll be in ~/Zotero. [1] https://forums.zotero.org/discussion/1977/changing-the-default-pdf-reader https://forums.zotero.org/discussion/1977/changing-the-defau...
  - dstillman 8y ago
    No need to use Show File. You can just open the PDF from Zotero, annotate, and save.
- bovine3dom 8y ago
  It's a bit of a pain, but you can store `~/.local/share/okular/docdata/` in version control or your favourite cloud storage provider, and then you'll get synchronised annotations. When I say a bit of a pain, I mean it - I switched to Mendeley with great sadness because its mobile application means I can read and annotate papers on my tablet and have it synchronised perfectly with my desktop. On a semi-related note: the Mendeley mobile application makes selecting text a joy on a touchscreen with a kind of magnifying glass. I really wish it was built into Android system wide.

deleted 8y ago

[deleted]

zwaps 8y ago

yeah so I just reinstalled Zotero and imported my Mendeley library. It does that, and it can actually look up metadata from pdfs. But: It can NOT update already existing entries from such a lookup. You have to delete the pdf and re-import. Why? No reason. It's this sort of really bad usability decision that makes Zotero just not very good imo.

tonyg 8y ago
I'm not sure what feature exactly you're missing, but are you aware of the "Rename file from parent metadata" option you get when right clicking on a PDF in the list? Perhaps that does what you need. If not, with Zotero you have a chance of getting a missing feature added. Not so with the closed-source Mendeley. Especially now they have started doing user-hostile lock-in stuff like gratuitously encrypting users' data, making it no longer accessible to the user (see downthread). With Zotero, in principle you could hack together something using `bash` and `sqlite3` that batch-updated documents; you may not even need to look at the source code to the official app. It's ad-hoc munging like that that Mendeley has recently gone out of its way to prevent, stopping people from working effectively with their own data.
- zwaps 8y ago
  Zotero can look up metadata if you add a PDF to your library Zotero can not update metadata for a PDF you already have in your library Hence, adding an existing library means you have to do it manually for each pdf This is bad design, because the functionality exists, but it's implemented in a way that makes everything complicated for no reason at all. Why disable the "lookup metadata" button for a pdf which is already in a library? WHYYYYY
  - tonyg 8y ago
    I see! Yes, that's not great.
dstillman 8y ago
It's not a usability decision — it's just one feature that hasn't yet been implemented [1]. Updating metadata is more complicated than creating a new item, because you have to deal with the existing metadata somehow. (Mendeley just overwrites the existing item, often with incorrect data, which we don't consider acceptable.) Disclosure: Zotero developer [1] https://github.com/zotero/zotero/issues/1515 https://github.com/zotero/zotero/issues/1515

icelancer 8y ago

>> I mean it is nice that Zotero has an import browser plugin (which, btw, Mendeley does as well), but once you have a substantial library of pdfs, it is just too time consuming to re-import it all again, type in names, years, journals etc. ugh.. It automatically added 90-95% of PDFs I imported, most directly from Sci-Hub with no editing from me.

tonyg 8y ago

My experience of auto-import of metadata in Mendeley is that it gets about 80% of it right. Not good enough for publication: I still had to check over each record with a fine-toothed comb when I wanted to actually use an entry to cite something. So far, Zotero's metadata lookup seems about the same quality.