Gosh how timely!!!
I am just doing a knock-down, drag-out evaluation between Papers3 and Bookends. I can state categorically these findings so far:
Certain functions that Papers3 once had as best in class are now no longer reliable. Find similar does not work. Matching does not work. I suspect (and have heard in passing somehow) that Papers/Readcube has lost/dropped their rights to access certain Web portal databases that gave them the data they needed to do these two functions.
Papers3 does far better than Bookends at allowing you to set up group searching methods on internet searches. Consider ((au: somename) OR (au: someothername)) AND ((all: some term) NOT (all: someterm)). You can do this in Papers3. You cannot do this in Bookends.
Papers3 has a far better approach to searching multiple resources on the internet. In Bookends, you must run each resource one at a time. First PubMed. Then Google Scholar. Then … Then … Then … In Papers3, they are all run at once.
Papers3 allows you to merge duplicates (sometimes poorly though) while Bookends make you think “What the heck am I doing … I don’t want to REMOVE duplicates, I want to compare/combine/merge them”? And when you are going to “remove” them in Bookends, you have again to do the process in a tedious one-at-a-time, move to a hit list first approach.
I am still struggling with what I consider to be a complex or cumbersome or counter-intuitive layout of the menus and preferences and terminologies in Bookends. For example, I would be looking for a menu or preferences simply saying (Set) Search Engines, not looking for a menu File : Import Filter Manager (which, since “import” is also a verb, could be taken to mean “import the filter manager as a file”).
Neither Bookends nor Papers3 are well-enough equipped to set up group searches on content that is already in your database. You CAN run complex REGEX searches in Bookends, but only on the meta-content to an article. This is useless when you have an article from 1966 that did not import well and therefore only has the title “A New Finding in Physics” that is supposed to be handled by the search on the same grouping list that I gave above. At least Papers3 also searches the document with some levels of simple groupings on internal searches. But its internal search panel only allows you to think sequentially with ALL or ANY, not in groupings with booleans.
The iPad version of Papers3 just a viewer for your entire database. The iPad version of Bookends is nicely done to split the database to “bite size chunks” as needed.
I am heading to a point where I am almost convinced that I will
Use Papers3 to do complex searches over multiple external databases. Bookends is a recalcitrant mule by comparison to the Papers3 rarin’-to-go race horse for this need.
Use Devonthink to search my Papers3 database (as an INDEX resource) for collections of ideas in various ways. Neither Papers3 nor Bookends offers the strength of grouped-term-level search capabilities that I need to get this done without spending more time constructing hack-around-folder hierarchies than actually just constructing group expressions and getting the results.
Extract my findings from Devonthink and export them back to a “Share” Bookends library to allow me to review them on my iPad. This stage of my workflow is still a dream/hope to be tested.
Right now, I am culling my Papers3 database for duplicate files. My cursory review of my Devonthink index on the Papers3 database shows that I need to do a lot of pruning. I need a good Duplicate Cleaner (and will go searching here … @quorm had a reliable recommendation that I lost in an upgrade of my SSD a few months back).
Update: BeyondCompare in this thread.
As for Readcube/Papers … I tried it briefly. The UI is nicely done but the Web app is all that exists and that has far fewer of the core features that I absolutely need from Papers3. I would stay with Bookends over the newest Web-only version of Readcube/Papers.
As for Paperpile … I do not like Web-based apps to manage my citation resources.
Summary: I am probably going to stay with Papers3 until it truly just dies (has anyone tested it under Catalina???). I will not upgrade to Readcube Papers until it is a desktop app and only then when I am convinced that it has not dropped the features I need to do complex searches on external databases.
One other side note. I am convinced that the medical field must be the ones who need these tools compared with science/engineering folks. Why for example do either Papers3 or Bookends not have an entire section in their user’s manual devoted to how to run IEEE searches as they already do with how to run PubMed searches? Maybe the sci/eng folks pay for EndNote instead???