Mirroring ‘Oxford Scholarship Online’ on your mac using Bookends

 

Oxford publications started up a sort of revolution on how printed books are accessed online.

Most other publishers put the exact same book, in a single PDF or Epub format, online for sale. Oxford makes an important change that seems to start a revolution on how we consume books online. In Oxford’s system, each of the chapters of the books stand by themselves as published articles. Each of the chapters of the collection gets their own DOI that they can be read, downloaded or referred independently of the main book.

Look at this video how it works.

Now, we are in a position to have the cake and eat it at the same time. The old conflicts on whether to keep books broke into their chapters and sections (as such a system facilitates searching and discovery on each of the chapters), or, keep it together to be able to see the work as a whole immediately disappears. We have both the whole and the individuals at the same time.

So, I have been wondering on how to mirror that system in Bookends. I experimented on how each of these independent chapters could be managed. Bookends has a mechanism to manage Chapters separately; while still linked to the main book.  Bookends is such a well-thought application: each of the chapters are able to live by themselves just exactly like they are presented in Oxford Scholarship Online. I am so impressed. I haven’t seen any other offline reference manager that is able to manage chapters like Bookends (Oxford).

The more I use each of the features, the more appreciate how well-designed Bookends is.

For me, I used to split PDF books into specific page ranges (page 1-50; 51-100 etc) just to keep the large pdf books easier for my searching tools like Foxtrot. I have already explained the system before.

Now, with Oxford Scholarship online and Bookends, I don’t need to split. I simply download each of the chapters and attach them as chapters into a single reference entry in Bookends. The pdf files of each of the chapters are attached to their corresponding entries. It is much better system because I won’t have duplication of information. I only hope that all other publishers offer books in the same way to the Oxford Scholarship online.

 

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Where Bookends rocks

Before, I wrote a few complains (https://dellu.wordpress.com/2016/03/28/where-bookends-sucks/) I have on Bookends as replacement for Sente. It has been almost 9 months since that post.

Now, I am updating my experience with the Bookends.

The good news: the latest version of Bookends (12.7.7) has solved one of the major complains I had on the application. That is: it can now extract references from a plethora of sources that the source of extraction is no more a problem.

In addition, I learned in the course of the previous months that the right method of finding references of PDF books is to use the ISBN associated with the books. Once you write the ISBN of the book in the ISBN field, Bookends happily can download all the reference data from Amazon using its Autofill feature. The Autofill feature is a super-feature. One day,  I put about 400 PDF articles collected over the years into Bookends watch folder; all of them have their DOIs printed in the first pages of the articles. It was just magic to see all the PDF files find their references filled automatically in a couple of minutes.

I also leaned that Bookends is much potent application than Sente when it comes to managing references. The tools embedded into it are unbelievably rich. It has organizational tools like: smart folders which support REGEX,  static folders,  labelling (color coding). It has a fully configurable Format Manager which enables the end user to import or export; rename the references in endless ways. The Format Manager in Bookends is the greatest feature I have ever seen in any reference manager. It is a dream come true. It is a liberating feature. I cannot say enough about it.

Bookends has other tools under Global Change. Finder replace that works across the whole library; batch changing of reference types, batch inserting data..and, other many types of manipulation tools.

Attachment handling and file renaming is superb in Bookends. The best part is: files are managed very transparently. You can explicitly put your files in a Dropbox folder without any hassle: while still they are attached to their references.

The Duplicate Finder tool embedded into Bookends is the best in the class. Jabref is great for finding duplicates. But it cannot reach the complexity and elegance of the duplicate finder in Bookends. You will never miss a duplicate with it.

If you are into Latex, it is also one of the most Bib friendly non-bib reference manager. It can assign unique Bibtex keys: and, the Format Manager can be manipulated to export in any of the Bibtex formats (Bibtex or BibLatex). You can also manipulate your format to export distinct (unique) bibtex fields. You don’t even need to export the reference to get your bibliography to work with Latex. You can make Bookends to work with your Latex file directly.

Bookends has  AppleScript dictionary. That again opens a world for who are into the scripting.

Integration with other super applications: I have never seen any reference manager as flexible as Bookends (I admit, Zotero could be even more flexible: I just don’t like that app; never tried it seriously.). For me, the fact that Bookends works well with Devonthink and Tinderbox is the best part of the story. Bookends is hand in glove with both Devonthink and Tinderbox. You can export and import in both directions; you can even directly sync them using some scripts (all the three are scriptable). Combining the three power tools is the nirvana for the knowledge worker. The world has never been greater.

The only feature I am still missing from Sente is the reading and annotating capabilities of Sente. The reading experience in Bookends is nowhere closer to Sente. Otherwise, as I am more using Bookends more, I am getting more surprises how a reference manager could be so rich and so capable. In an ideal world, BE would incorporate the annotation tools of Sente.

Mendeley vs Citavi vs Qiqq (also Sente and Bookends)

I haven’t used my Windows machine for a while now. I was then curious how the reference managers progressed in these periods. I was specially curious about Mendeley because I struggled with that application for some time then.

So, here is my observation: Mendeley stayed the same for the last couple of years. There is no real development; nor any change of any relevant sort since I knew the application. All the icons, the settings, the menus; the features: I see no changes. It is as clumsy as used to be; in many areas. One of the properties that Mendeley sucks at is how reference is downloaded from the internet. It attempts to use Google scholar; combining with its metadata extraction too. What it does is: it attempts to detect some DOI or other identifier to the PDF in the first few pages; and then, use that information to download reference information from Google scholars. For me, the result is a total debacle. It has always been a debacle. Mendeley can detect the papers only less than 5% of the times; as my PDFs don’t typically have metadata information; nor are they always published articles. Many of them are books; or drafts of books, and earlier versions of published articles I received from friends.

My favorite feature of Mendeley, which had been, still is: the BibTex sync feature. I have to admit, I have been tempted to live with Mendeley because of that feature. But, heck, if you have wicked reference data, what is the point of syncing it to Bib file. You will have incomplete citations ultimately. You will be embarrassed in front of colleagues when you realize that your references are incomplete after you sent out the paper. Because of the importance of the feature, I will focus on this feature in comparing the reference managers.

Citavis is not very far better than Mendeley when it comes to reference extraction from the internet. It can even be worse. I was able to download references from the internet only if the book has ISBN numbers or the article has DOI number. Otherwise, manual insertion is the only way I am left with. Look at this tutorial to learn how the process is clumsy in this application: https://youtu.be/MyaW9q_464w?list=PLkLfx87WKrTZTfifTvttqgKwzyQSTDYY5

In Citativ, when you read a PDF file, you can highlight or quote a certain text: comment on it; or give a short title to the comment and the quote. I totally love the idea of giving a short title to the quotation I make from a PDF reading. This feature is also available in Sente. The idea is: you quote a certain sentence or paragraph from the PDF; then, give a title which summarizes the core point of the quote and tag it if you want to. These quotes serve as a short summary of the article. The titles are your reminds of the core points of the quote. It is like summarizing the summary. Very neat approach to reading articles. The neat part in Sente is each of these short quotes could be exported as a separate note file. That means, if you have 20 quotations from the article, you will have 20 short notes: titled appropriately in a folder in finder. The problem with Citavi is each of the quotations are not exportable to separate notes. They can be exported as single file only. That means, it is not any better than reading and annotating a PDF in Acrobat Reader or other PDF readers (PDF exchange; or Foxit in windows: PDF expert in Mac)  and exporting a summary.

Qiqq is very different. Its way of extracting references from Google scholars is comparable to Sente. You click the PDF; click BibTex sniffer: you will be given Google scholars to pick the references. If Qiqq failed to detect the title of the PDF correctly, you can manually select the title. Qiqq immediately populates the scholar search with the selected text.

I have given the following book for all the three reference mangers: It was only Qiqq which correctly imported the full reference information.

gq4omd

I think the reference downloaded in Qiqq is much better than Sente. Sente has an advantage of downloading from multiple sources like WorldCat; Stanford, British libraries…very good results in some sources, weaker results in others. I used to get the most complete reference data from Stanford library website. But Sente sometimes fails to download the Publisher Field from many sources. Bookends can pick from Google Scholar, Justor and two other sources. But the process  of downloading a reference data (called Autocomplete in Bookends; targeted browsing in Sente; BibTex sniffing in Qiqq) is most elegant in Qiqq and Sente.

 

The other interesting feature of Qiqq is the brainstorming feature: absolutely brilliant tools to play with your references. It can also be used to track the positions one author took over time, how his/her ideas change in the long run. it can also be used to study the history of ideas: where a certain phrase appeared first; then, how other authors reflected that phrase in their publications. Look at these tutorials to see how the Brainstorming works in Qiqq:

 

My ratting of these reference manager’s capability of downloading references from the internet:

  1. Mendeley = 4/10
  2. Zotero= 3/10
  3. Citavi = 2/10
  4. Bookends = 7/10
  5. Sente = 9/10
  6. Qiqq = 8/10

Why is Sente higher in this ranking?

Because it offers much better choice than Qiqq on the sources. Qiqq does it elegantly on Google scholar; but, it cannot download from other sources which potentially offer more complete reference data.

Conclusion: if I ever have to move to Windows, I will definitely use Qiqq (in combination with OneNote or ConnectedText).

Where Bookends sucks

I am now checking out other alternatives as the fate of Sente is looking dismal. The best alternative for the users of Sente looks like Bookends. I think there is some kind of communication between the developers of the two applications. One of the reasons that we suspected the abandonment of Sente came from the developments on the Bookends side. we have seen, the developers of Bookends have been preparing to grab the former users of Sente.In their latest updates, since June 2015, they have been modifying their application to import Sente references. But, still, there are a lot of glitches to move references from Sente.

But, personally, I am more worried about the capabilities of Bookends as a reference manager than the migration. The migration is a work of few days. But, if the application has some fundamental weakness, that will be a pain for a long time; that I am afraid the pain of migrating my references might not worth the effort.

First the strengths:

  1. Bookends seems faster than Sente; at least at the startup.
  2. It works well with a number of other applications such as Devonthink, Tinderbox and Scrivener.
  3. And, most importantly, it has some cool tools called **Global Change**  which seem very useful. These tools helps to make a change to a number of references in one sweep. Sente also has this system; implemented differently.I think the Bookends has an upper hand here. One of the worst footprints of Mendeley from the Windows that remained in my reference for ages was: the Titles of the references were placed in the place of the Journal. I don’t why Mendeley does that. But, the Titles were exported as Journal. I was not able to change that for a number of years within  Sente. Bookends does it in a sweep, just a couple of seconds to fix about 1500 references. Yes, that is great programming.

 

and the issues:

I think bookend is quite good reference manger. But, it has some really deep issues:

  1. The PDF reader is ugly; and not even comparable to the reader in SEnte. Sente gives the best PDF reading experience ever; not even the dedicated PDF readers like PDF Expert, iAnnotate, Acrobat Reader can reach it. Bookends has a mediocre PDF reader.
  2. Not well organized: the tools and features are jumbled here and there. It is really not clear which of the menus do what. At the first look, the app generally looks unattractive. But, honestly, I am less worried about that. I just think some people might not appreciate it. Personally, I just want my job done. I am not going to wear this app for  my birthday party.
  3. But, the real issue, and the true depth of shit of Bookends is on the reference detection and downloading part. The whole focus of the Bookends seems on the MedPub. Generally, most reference managers can detect references from the major databases (search engines) like PubMed and Google Scholar. But, Sente has been efficient in doing it from a broad array of sources: that I cannot list all here. The most important of them, for me have been: Worldcat and  Stanford University Library. Sente made the process perfect by its feature called Targeted Browsing. The two sources offer the cleanest references while Google Scholar gives out the most incomplete metadata. So, when I was trying Bookends, I was hoping that Bookends would do the same.

Assume that I received a PDF book from a friend. I want to download the metadata. In Sente, I would drop the PDF to the library, Sente displays its Citation Lookup  dialogue box in which I will select the Title of the book and choose WorldCat.

joudw

The top 5 sources are the most important. The title of the book, “Italian Syntax…” is going to be automatically pasted in the WordCat. Now, look at the WordCat website.  gku8e

That Red Circle makes the insertion of reference so elegant. Clicking the red button populates the reference information. Worldcat gives a complete reference data; i rarely find a mistake. Note that these 5 sources can be expanded, if required. I used to have a large number of other sources including Stanford University.

Bookends has a similar feature. But, the implementation is inefficient because it is restricted to a few If I want to do the same in Bookends, the process is clunky and inefficient. The sources are not expandable that, if they don’t work for you, you will be stuck. The fact that I cannot grab references from the WorldCat database is really disconcerting to me because that is the number one source for me. All the references for books come from it. It gives the most complete metadata.

 

First, Bookends asks you to attach the PDF. You will get the citation window after  the PDF is attached. That is way step away. After you attach the PDF you will have the following window:

txpz41

This is where I am frustrated. The part I marked with the big red rectangle is supposed to display the Title of  the book. But, it doesn’t. Therefore, if you have to put the title, you are supposed to do it manually. You have remember the title, or copy it before hand. That is strangely sluggish. Second, the sources at the right lower corner  are really useless to me.

Except Google Scholar, the rest are useless, really. I cannot modify or add a new engine either. So, I am stuck. The offer is Take it or leave it. You will be happy if you are a medicine student; fucked otherwise. Google Scholar is quite ok for articles. But, it is one of the most incomplete sources.

Bookends has another method of downloading references using an internal browser. But, I think that one is even worse. I put the title of an article; out of the total of 20 articles in google scholar, which Sente detected all of them, Bookends was able to detect just two.

All in all, I think Bookends is not really polished at downloading metadata.

The difference between Sente and Bookends might seem minimal here, from outside. But, for some one who will use the process thousands of times, even the tinies further step is one more pain. While I like many of the features of the application, I find it hard to adopt the app as my main reference manager  because of  this problem. So, I am contemplating either to stay with Sente to the last breath of the app, or check out other alternatives, Papers 3 probably.

 

2017-02-05: update

  • Now, Bookends has included further sources of data extraction. Now, I am now using Bookends as my main reference manager. Even if it has some weaknesses on the reading side, it turn out to be one of the most complete reference manager out there. I have noted my observations here.