Au revoir Bookends, bonjour Zotero

Regard carefully please that my alternative view is that you are posting the gory details in order to give yourself permission to demean.

And rather than beating around the bush, I will be blunt: If you cannot post your entire message in the SonnySoftware forum verbatim where it rightfully belongs, primarily to allow Jon to respond as is his right but also to engage in the community of users for help as the respectable and respectful path, then your approach here could also be considered to be taking a coward’s way out of the issue.


JJW

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Oh, that’s an interesting way of putting it. So are you saying that when someone conducts themselves in a way that is suitable to demean themselves, it is my obligation to protect them from that?

In my ears, the phrase “give oneself the permission to demean” is somewhat awkward because demeaning someone is generally seen as something that you should not do, yet the phrase suggests that it might be permitted under certain circumstances. But perhaps this is precisely where our disagreement lies: you seem to think that it is never okay “to cause someone to become less respected” (and hence, giving oneself permission to do so is basically a pseudo-permission, not a legitimate justification), whereas I think that if someone conducts themselves in a way that is suitable to cause them to become less respected, then it can very well be justified to make this known. Journalists do that every day. I wouldn’t use the word “demean” in those cases, though, but “reporting”.

Also, I wouldn’t call the details I posted “gory”, as it seems to imply some kind of voyeuristic intent (and, in the present context, that they were unnecessary). Rather, if they need an adjective, I would perhaps say that they are “telling”, because they tell the reader quite a bit about how the interaction went; which was, as mentioned earlier, exactly my intention with providing them.

I have no problem whatsoever with copying and pasting my entire message to the SonnySoftware forum, if that is what you were trying to tell me all along. The reason I posted it here was because I was already engaged in a discussion about bookends here and it made sense as an update to this topic. What would have been the aim of starting a new topic on the SonnySoftware forum with this content? If I had done so, I would probably have agreed with you that it would seem like I’m

with the main purpose of complaining (given that my complain was already rejected by SonnySoftware).

Last point:

I’m not sure where those rights are derived from. If Jon cares to respond to everything that someone says about him, then he certainly has the right to respond in the place where the original claim was published (and I’d be happy to continue the conversation with him here), but I don’t see why everyone who has something to say about Bookends or SonnySoftware support to do so on the SonnySoftware forum. - Of course, if the author’s intention is to complain and get a response from SonnySoftware, then that forum would certainly the place to go, but my intention was not to complain but to report.

I don’t see what would warrant such an interpretation. The only thing I might be “afraid” of on the SonnySoftware forum could be the software on which the forum runs (phpBB), but that’s mainly because I like discourse so much (which is what this MPU runs on). I don’t even see what issue I might want to get myself out of. In my exchange with SonnySoftware, I was trying to get into an issue (and failed).

Let us leave at this to not derail the thread.


JJW

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I’ve had a moment to return to ReadCube Papers. I have an exhaustive database in it from about a decade of effort. After using it for a few hours simply to align two of my databases between it and Bookends, I noticed something significant. The friction for me to do simple things in Bookends was glaring. Here are just three examples:

  • Try sorting a list in the main panel to reveal files that have attachments or not. → NOT POSSIBLE
  • Try selecting a set of references in the main panel and exporting them as a .bib file via a context menu. → NOT POSSIBLE (you have to select files, mark them, and the use a menu option to export the hit list).
  • Try figuring out whether the paperclip icon in Bookends means there IS a valid attachment or there once WAS an attachment (but it is not here and you will have to go find it manually … (in a second window somewhere else)).

I have reached the moment of enlightenment … Grasshopper, it is time for you to go.

The one downside is that I could do what I might call “light-weight” syncing in Bookends. I would not have to carry around my reference database from more than a decade just to work on a new journal article. I am starting a list of requests on the Papers support forum to push for this as well as other features as I run across them (e.g. exposing the text edit fields to the macOS kernel so that we can run transformations or service options on them).

Goodbye Bookends, hello ReadCube Papers.

FWIW, the Papers iPad app appears also to be nicely done.


JJW

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I seem to remember having read about Papers being tied to certain publichers, but can’t find the reference now. Maybe that was before it was acquired by Readcube. Anyway: do you see any signs of possible bias towards certain publishers or databases in Papers?

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I’m not the one you asked, but I’ll chime in. You may be thinking of Mendeley — they’re owned by Elsevier.

I don’t know whether Readcube has similar ties to any publishers, but if they do, I’ve not heard about it.

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Readcube was originally created by Labtiva which is now part of Digital Science. Digital Science has been part of Macmillan Publishers Ltd which, in May 2015, merged with Springer Science+Business Media to form Springer Nature.

Papers Mekentosj was acquired by Springer in 2012 (see this short history of Papers), and was again bought by Readcube in 2016 after the merger between Springer S+B M & Macmillan Publishers.

W.r.t. a possible bias towards certain publishers or databases, I can only speak for Papers v3 (before it was bought by Readcube): Although being owned by Springer, I don’t think that there was any preference or bias towards certain publishers or databases.

To fetch metadata and auto-download publicly available PDFs, we mainly used Crossref, plus the metadata from publisher websites as well as PubMed/PubMed Central or other databases that the user had access to (like Elsevier Scopus etc). The entire metadata & file retrieval process was fairly complex where one event (e.g. a DOI being found) triggered a whole lot of further events – like getting & parsing the article webpage for that DOI, and extracting further metadata like a PMID/PMCID from it, then fetching even more metadata from PubMed, and downloading the actual PDF from PubMed Central, etc.

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In the meantime, I have gone back to using Bookends (BE) on iPadOS. I find that it is nicely designed. On the iPadOS, the trade-off compared to ReadCube Papers (RCP) are as follows:

  • BE allows me to switch between smaller local libraries
  • BE has an annotation interface comparable to DevontThink To Go (if not identical) and to Highlights
  • Annotating is more expansive in BE (more tools with better implementations)
  • RCP has a faster/more direct way to fetch links to comparable articles

I am fussing over an issue where BE does not seem to handle sharing a PDF with annotations as nicely as is done with DTTG or Highlights.

In summary, while I find working in the BE macOS version to have too much friction, I am finding less friction in BE iPadOS.

For those so inclined, the BE forum did ask about the interest for the iPadOS version work as a front end to a Zotero database.

I have always found Papers and now RCP to be most strongly focused on the PubMed fields at the expense of finding publications for the physical sciences/engineering (e.g. WebOfScience or Science Direct or IEEE).


JJW

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Could you elaborate? I’m not sure I quite understand. BE (or someone on the BE forum?) wants to use BE on iPadOS as a frontend to Zotero? :woozy_face:

See this thread Is there any interest in syncing Bookends for iOS with Zotero? - Sonny Software


JJW

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Just tried adding a book section to a book in Zotero and I’m somewhat baffled to see that each book section seems to be an entirely independent record. Is this correct, or am I missing something? If this is so, it means

  1. I have to re-enter the data for the book again and again every time I enter a new chapter (duplicating could be somewhat of a workaround, but it requires going through the entire duplicated record and deleting everything that should not be in the new record)
  2. If there is a mistake in, say, the spelling of the editor’s name (or one editor is missingm which is often the case when records are imported from a catalogue), I will need to manually correct this in every single chapter
  3. I will also need a separate copy of the book’s pdf-file for each chapter. Or is there a way of linking that pdf-file to multiple zotero records?

I can’t seem to find any evidence to the contrary but I’m so baffled by this design flaw that I’m still hoping that I’m missing something too obvious for anyone to mention it…

Can anyone enlighten me? (And if this is really how Zotero works, please tell me that bookends is the same so that I don’t have to go back and reconsider it. - What a stupid attitude. Why do you hate bookends so much? - I don’t hate it. I’m just stressed out by constantly reconsidering which apps I use.).

I’m confused. I’ve got books in Zotero but the PDF files are all in one segment so there is only a single reference in Zotero for each book. I know you can attach more than one PDF file to an entry because I have both clean and annotated versions of papers in my Zotero system and they are under one main entry but I’ve never tried that with books. I use Zotfile and it does it automatically.

I just did a quick test and you can add an attachment file by right clicking on the main Zotero entry but sicne I don’t have any books with each chapter a separate PDF I can’t test to make sure it works.

Either try that yourself or if you want can you send me a couple of chapter s of a book and I’ll see if I can get it to work in my system.

I think I may not have explained myself well: Zotero is not dividing up books into book sections. But in an edited volume, you want to be able to refer to each chapter independently, so you obviously need a zotero record for each chapter. So far so good. My point of complaint is that those chapter records are in no way associated with the record of the book. Citavi, the reference manager I previously used (and which is only available for windows, unfortunately) saves the user a lot of work by letting you enter the data for the book once and then reuse it automatically for every chapter-record that you create.

Having managed my references like this for 15 years, the way Zotero does this feels like stone age…

Maybe I’m misunderstanding, but would duplicating the first entry, and changing only the specific chapter information, effectively do what you want?

Yes, I’m not saying it’s impossible, but very inconvenient because:

But I take your responses as a confirmation that there is no other way. :frowning:

Quick update regarding bookends:

From what I can see, bookends is only slightly better at this: instead of just duplicating the book-record and then changing it to book chapter and removing all irrelevant information, bookends allows you to “Replicate as book chapter”:

When invoked, Bookends will create a new reference of Type Book Chapter that includes the relevant information placed in the correct fields (for example, an edited book’s Title is placed in the book chapter’s Book Title field).

Bookends also automatically creates a link between the parent and the child, but that’s where the comfort ends: apart from the links, these records are entirely independent, so when you correct something in the parent book, you still have to do the same correction in every child manually.

Oops. Missed the earlier post. :grimacing:

Unfortunately, Zotero will not allow me to manage PDFs as I need, and ReadCube Papers remains too self-contained to fit as easily in my eco-system.

So, I am back with Bookends. I remain frustrated with it for one reason. Its approach to certain operational functions causes undue friction.


JJW

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Why?

If you reference a book or even pieces of a book you will get the locations so why do you need to have separate citations for individual chapters?

Maybe I’m missing something but I can’t see a valid use for referencing chapters separately in a book.

If the chapters are by different authors, you might not use all of the chapters in your own work. So you’d need to be able to reference each of the chapters as an individual work and list it as such in the bibliography.

That’s a lot quicker and easier if the reference manager software can keep things straight.

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Thanks for that. I don’t think I’ve ever had a book that had chapters by different authors. I do have books with multiple authors, sometimes many multiple authors but they aren’t tied to specific chapters.