The era of "cloud reference managers"?

A place for users to ask each other questions, make suggestions, and discuss Bookends.
Post Reply
stereotactic
Posts: 4
Joined: Sun Nov 10, 2013 9:22 am

The era of "cloud reference managers"?

Post by stereotactic » Mon Jan 14, 2019 10:21 am

Over the past few days, as part of the weekend project, I decided to check out the other reference managers. Paperpile, Readcube and Mendeley. It is not a critique but it is something that I need for a long time. (I wouldn't recommend Zotero).
My primary motivation was to see how browser extension works- it integrates well with PubMed and pushing the reference, hence becomes a one click affair. I prefer to use the desktop browser over Bookends browser because I have multiple tabs opened up checking and cross referencing everything.

Paperpile and Readcubes have messed up UI as far as reading and annotating PDF's is concerned. Papaerpile depends on another external third party service that's still under development. My experience was bad. Readcubes has been there for longer but I wasn't too happy with its behavior to open up files in another tabs- one looses focus. Mendeley has a decent experience with annotations. The only good thing about Readcubes and Mendeley is "recommendations" that loads up similar articles.

Bookends beats them except for the "cloud-part". I have a massive Dropbox subscription and hence I don't care about how much storage space its going to take. Nevertheless, I do miss a browser integration via extension (not a bookmarklet) and a recommendation engine built in. If Bookends can implement this, it is GOLD.

I have no other qualms. No reference manager is perfect- I am planning to use Mendeley for the online discovery, export everything to Bookends and then attach files to the references (if any).

nh220
Posts: 10
Joined: Sat Jul 21, 2018 5:53 pm

Re: The era of "cloud reference managers"?

Post by nh220 » Tue Jan 15, 2019 8:06 am

I, too, fairly regularly "stray" from Bookends as while Bookends remains (to my mind) the single best reference management experience, some of the others mentioned are much better suited to collaborative writing and work in a cross-platform setting. But unless you really need either of those two things, I think Bookends is far and away the best option.

That said, as far as this "new breed" of managers go, I am most interested in Paperpile--especially if they can get their promised MS Word plug-in up and running (I do not write in Google Docs unless I absolutely have to). Readcube is a mess UI wise and has lots of other issues and shortcomings (lest I checked you could not insert page numbers into citations!). They have promised a new app based on the acquired (and dearly departed) Papers but have pushed this back multiple times. Mendeley is an option but there are some pretty significant debates about the ethics of their owner. And of course all of these use CLS, which I find a complete pain to edit. And none of them handle legal materiel very well.

I consider Zotero (and EndNote) less part of this new breed and more of legacy applications with some online components. I ended up using Zotero for collaborative work because it is free and allows you to sore your PDFs wherever you want (with the Zotfile extension). So, in theory--I haven't bothered looking into this yet--you could have Bookends and Zotero point to the same PDF directory synced via iCloud, OneDrive, or whatever. I actually really liked EndNote and would like to use it for cross-platform work, but they really screwed the pooch with X9, which is not usable on Mac.

All that said, I do wish Bookends handled online references a bit better. An extension a la Zotero's would be nice.

taja
Posts: 38
Joined: Sun Feb 12, 2012 10:39 pm

Re: The era of "cloud reference managers"?

Post by taja » Mon Jan 28, 2019 2:51 pm

+1 for a browser extension. There is the bookmarklet, which I occasionally find handy. And I recognise that the online search window has lots of advantages. But an extension that allowed users to use their own browsers for discovery + download with some integration with Bookends without switching between apps would be great.

iandol
Posts: 282
Joined: Fri Jan 25, 2008 2:31 pm

Re: The era of "cloud reference managers"?

Post by iandol » Tue Jan 29, 2019 12:44 am

What does an extension do that, for example, using an Alfred workflow to trigger quick-add doesn't? With such a workflow, I select any DOI/PMID/arXiv on any web page in any browser or other app, and trigger alfred-quickadd; it takes the selection and pastes it into the quick add dialog then hides bookends window returning focus to the browser, bookends adds the reference directly into the database without any extra fussing in the background (using notifications to tell you the result).

I think with some more applescript commands, we can get almost any desired behaviour — so the question is, what is the desired behaviour? :?:

taja
Posts: 38
Joined: Sun Feb 12, 2012 10:39 pm

Re: The era of "cloud reference managers"?

Post by taja » Wed Jan 30, 2019 12:26 pm

One reason is that while that workflow is great, not many Bookends users will be using Alfred, or even be particularly well-versed in Applescript. I switched to Alfred + Powerpack to use your excellent workflow, but then back to Launchbar when Jon added the floating window (of course Launchbar makes launching applescripts a cinch too). So an extension I had in mind be extremely simple. I can see that it wouldn't be the greatest use of Jon's time making it! But perhaps an intrepid user could step in....

iandol
Posts: 282
Joined: Fri Jan 25, 2008 2:31 pm

Re: The era of "cloud reference managers"?

Post by iandol » Thu Jan 31, 2019 4:19 am

taja: this applescript will give you the Quick Add functionality, just trigger it with LaunchBar:

https://github.com/iandol/bookends-tool ... pplescript

Creating a browser extension is a non-trivial endeavour and I am not yet convinced about what it would really be able to do that you can't achieve with applescript (perhaps it could auto-parse all linked refs like bookends browser can do)?

Personally, in my browser 99% of the time I want to add a ref that has a DOI/PMID/arXiv, and a browser extension is just not necessary.

----
To get back to the other major request here, yes I wish Bookends could offer some kind of collaborative cloud — it is the only thing that endnote is better than Bookends at. I also grudgingly use Zotero only for a shared collaborative database, but I hate how difficult it is to manage and edit refs. Now Bookends has already solved a major problem as iCloud sync between multiple personal devices works really well: thus if there was some way to use the iCloud API but with a different backend server (that could then be "shared" that would be a lot of the way to a solution. But knowing Apple that API backend database is locked down... :cry:

Jon
Site Admin
Posts: 8003
Joined: Tue Jul 13, 2004 6:27 pm
Location: Bethesda, MD
Contact:

Re: The era of "cloud reference managers"?

Post by Jon » Thu Jan 31, 2019 9:30 am

Have you tried creating a new Apple ID without a credit card. That could be used by members of a group to share a library.

Jon
Sonny Software

taja
Posts: 38
Joined: Sun Feb 12, 2012 10:39 pm

Re: The era of "cloud reference managers"?

Post by taja » Thu Jan 31, 2019 1:05 pm

iandol wrote:
Thu Jan 31, 2019 4:19 am
taja: this applescript will give you the Quick Add functionality, just trigger it with LaunchBar:

https://github.com/iandol/bookends-tool ... pplescript

Creating a browser extension is a non-trivial endeavour and I am not yet convinced about what it would really be able to do that you can't achieve with applescript (perhaps it could auto-parse all linked refs like bookends browser can do)?

Personally, in my browser 99% of the time I want to add a ref that has a DOI/PMID/arXiv, and a browser extension is just not necessary.

----
To get back to the other major request here, yes I wish Bookends could offer some kind of collaborative cloud — it is the only thing that endnote is better than Bookends at. I also grudgingly use Zotero only for a shared collaborative database, but I hate how difficult it is to manage and edit refs. Now Bookends has already solved a major problem as iCloud sync between multiple personal devices works really well: thus if there was some way to use the iCloud API but with a different backend server (that could then be "shared" that would be a lot of the way to a solution. But knowing Apple that API backend database is locked down... :cry:
That's really helpful, thanks!

iandol
Posts: 282
Joined: Fri Jan 25, 2008 2:31 pm

Re: The era of "cloud reference managers"?

Post by iandol » Thu Jan 31, 2019 9:17 pm

Jon wrote:
Thu Jan 31, 2019 9:30 am
Have you tried creating a new Apple ID without a credit card. That could be used by members of a group to share a library.
Do you have any documentation on how this may work? Would I then also create a new user account that would be used for sharing? To work between the rest of my iCloud files and this group ID one would switch between users? Or (though I very much doubt it) could a symlink work?

In general, this still does not do what Endnote Web does - which is like an enhanced Bookends Server that runs online. You local database syncs to the Web version, then you can share that with others even if they don't have Endnote. If they do they can then sync to you via the web service. Endnote Web offers a free basic version (50,000 refs limit), which may be another possibility for group work (export from bookends, import to Endnote Web Basic and share from there). That workflow is similar to what I have to do with Zotero currently, which is a real time sync to keep up to date. Much simpler IMO is to use shared BibTeX file (share on Dropbox or elsewhere) that both collaborators can edit. This avoids sync collisions of the main database, and means your collaborator can use a different ref manager as long as they can export BibTeX.

Building a proper Bookends Web service would be a major undertaking (getting sync working can "sink" developers, look at what happened to Things 3), and I wonder how essential it really is?

For others: if you will be sharing on a network or can configure firewall/DNS rules to share across the internet, you can setup Bookends Server so one Mac can be used to serve a group database to other users?

Jon
Site Admin
Posts: 8003
Joined: Tue Jul 13, 2004 6:27 pm
Location: Bethesda, MD
Contact:

Re: The era of "cloud reference managers"?

Post by Jon » Fri Feb 01, 2019 9:40 am

No documentation, but it's a simple notion. Create a new user account with a new Apple ID but don't add credit card information. I haven't done this myself, but I don't think you'd have to log out of your main account (in iTunes, for example) to use the new Apple ID for syncing. I'd be interested in hearing from anyone who is using this method (or attempted to).

Jon
Sonny Software

alanterra
Posts: 52
Joined: Wed Dec 20, 2017 4:55 pm

Re: The era of "cloud reference managers"?

Post by alanterra » Mon Feb 18, 2019 8:14 pm

A couple of thoughts if you go down Jon's suggested route:

Set up an administrative account on your mac with your normal iCloud login -- that way you can easily keep software up to date. You can't even download free stuff from the Apple store without a credit card.

It'd probably be a little bit of a PITA to do this if you rely on iCloud, especially if you purchased extra space. (Me, I avoid iCloud as much as possible after a meltdown that Apple created for me.)

Apple's Contacts app allows you to have multiple iCloud accounts and put various contacts in each one. And, in my opinion, the user interface for handling this leaves much to be desired. I actually use this for exactly what Jon is suggesting--I have an iCloud account set up that I use to share contacts with my wife, and another for the contacts that are exclusively mine. Coordinating which contact is where is very difficult.

drspk
Posts: 2
Joined: Thu Feb 21, 2019 7:16 am

Re: The era of "cloud reference managers"?

Post by drspk » Thu Feb 21, 2019 10:21 am

Avoid ReadCube Papers like the plague. After one crash too many on Papers the year before last, I switched to ReadCube. Yes, its metadata fetching is the best I've seen, but the app has essentially been deprecated while they work on the Readcube+Papers frankenstein app, which is long delayed. Hence, all papers uploaded to the cloud, or added via the web app *have to be downloaded file by file*.

I've just dumped them and moved to Bookends. Getting material out of Readcube is a nightmare; I've had to create four new Bookends libraries in order to get anywhere close to my previous collection. (The JSTOR/Google Scholar robot panic is a drag in Bookends, however; importing 2500 PDFs resulted in around 1000 with no metadata – and the manual addition of metadata is laborious when there isn't a DOI).

But stay away from Readcube. It is spyware and it is appallingly limited in terms of how much 'freedom' it grants you over the papers you collect. I'm glad to have discovered Bookends (and will patiently, slowly add all that metadata in the coming weeks and months – unless someone has a better suggestion?)

Jon
Site Admin
Posts: 8003
Joined: Tue Jul 13, 2004 6:27 pm
Location: Bethesda, MD
Contact:

Re: The era of "cloud reference managers"?

Post by Jon » Thu Feb 21, 2019 11:31 am

You might look into OpenURL as a way of getting metadata if you don't have a DOI. You can contact your library (if you have one) to see what access they provide. And take a look at the User Guide for a variety of free OpenURL servers.

Jon
Sonny Software

drspk
Posts: 2
Joined: Thu Feb 21, 2019 7:16 am

Re: The era of "cloud reference managers"?

Post by drspk » Thu Feb 21, 2019 12:42 pm

Thanks Jon. I’m very impressed by Bookends so far and wish I’d discovered it before entering the ReadCube quagmire.

Post Reply