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).

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is Sente abandoned?

Sente has been my favorite reference manger for the last couple of years. It has the most elegant reading interface; the annotation and quotation features are incomparable to any other PDF reader, let alone reference manger. I enjoyed every bit of the time I spend with Sente. Importing reference data, and downloading PDF files alongside, has never been as great. Unlike any other reference manager both in windows and mac environment (I have tried many of them), Sente allows downloading references from a very wide variety of sources. Its targeted browsing has been of utmost service for me. I really love how the application is designed; how it all is implemented. Sente is extremely well-crafted application; much better than Papers and Bookends in many aspects.

But, unfortunately, there is no update of any kind from Thirdstreetsoftware for the last few days. They shut down the blog, and stop replying emails. There are also some internal rummers that Sente might not bee see developments. I am truly worried if Sente is vanishing into nonexistence; all the time I spend on organizing my library; all the annotations and notes I made….I don’t know how to live without it. Very sad part of proprietary software;  the end is always ugly.

It also makes me wonder what kind of person would develop such a polished application for years; and ultimately abandon it. They have been developing it for IOS quite recently. There should be something seriously wrong!

 

 

Workflow with Sente, Devonthink, Scrivener using Hazel and Dropbox as glue: part 2

On Mirroring

In this second post, I am going to talk about a method, rather than a tool (software). I call the method “mirroring”. The method is a complementary approach for syncing. I generally like syncing files across my macs and iOS devices. The problem is: syncing is possible only when the app developers offer it. For Sente, for example, you can sync your Sente library to your Sente in IOS. But, you can not do so to other applications such as Devonthink; or Scrivener. The tags in Sente are not visible in Finder; and the notes and annotations, all are specific to the application. It is a locked application in that sense. Most reference managers are lock-down applications, unfortunately. I would be wise to avoid them; but they facilitate workflow.

 

Therefore, since I am relying on Sente and other locked applications, for my work flow, mirroring is a way around the locking weakness. What do I mirror? I mirror my projects.

My works are project based. I move from one project to another; writing small articles and developing small pieces of works for my dissertation is what I am doing, and will be doing for the next two years. I already talked about how I organize my PDF files based on projects. How do I mirror it? I mirror my project inside Sente to Finder by creating a folder. For example: if I am working on a project called “Object Shift”; i will have a tag in sente with the same name. All the PDF files that I will need to read will be tagged “Object Shift”. Look at the following picture: ppic82 When I double click the Tag, Sente hooks me to what I call the  project mood. The project mood is my favorite mood for reading in Sente. It also helps me to see the relationships and differences between the papers. ppic83

 

Now, I have all the papers I believe are important for the project. I then read and annotate them as fast as I can; and export the annotations to a Folder in Finder. The folder I create inside Dropbox is a mirrored folder; with the same name. The folder itself is inside a big folder called “Projects” which itself is inside Dropbox.  That mirrored folder (“Object Shift”) is where I keep all the notes I export from Sente  as well as the Tex file I will finally compile it to a finished paper. The “Project” folder is indexed inside Devonthink. Therefore, anything I add inside “Object Shift” is automatically available inside DT.  Now, you see I am in a good shape. My project files are in a separate folder inside Dropbox; but still in communication with the rest of my files inside Devonthink. The next step is  to develop a dozen of search algorithms (smart groups) inside DT that will hunt down all the relevant  files  to my topic. File selection and grouping in Sente is manual. Grouping inside DT is automatic. There are both pros and cons for for manual and automatic approaches of grouping files for project. I combine the two to get the best results.

 

As I have mentioned, I have “Object Shift” inside Sente, Dropbox (a folder) and Devonthink (indexed).  I also open a project under the same name inside Scrivener (I use it for some projects) and also a paper folder tagged with same name where I put all the papers relevant for the project.  That is mirroring.

It is a way of organizing myself wherever syncing is not available globally.

I mirror not only the projects and folder; but also the Statuses. The Statuses that I assign in Sente, demonstrated in the first post, are used across the board: inside Devonthink, Finder (Path Finder), Scrivener and even printed papers and books. Their application in the printed materials is actually quite interesting. I was a reading a book titled “How to Read a  Book”. In that book, the authors have a notion called x-raying the book.  X-raying a book is going through the major sections of the book, and evaluating the organization of the topics to evaluate the topics for your purpose. It is very effective method. I have developed the habit of examine the Table of Contents, the Sections and Sub-sections of the books before I read them. As soon as I finished examining the book, which takes just 2 minutes, I assign my statuses to the sections; with small notes; by attaching small stickers on them. That way, I will make sure that I l read the “Must Read” sections; and skip the “Repelling” sections (too much details or digressions) etc. As one can see from its multiple applications (on folders, projects, books and articles),  I can say that Mirroring is rather a habit; a useful habit to get things done.

You can make it your habit too.

 

Scientific research workflow, mac

I am now starting up my PhD in linguistics. I have already collected more 1500 PDF articles and books (also did my MA in linguistics). So, I am trying to build up as perfect  workflow as possible  for my future research works. The university has given me a macbook pro, so , I am no more using windows OS. Even if there doesn´t seem to exist any comparable application in Mac as MS OneNote, I am discovering quite powerful apps in mac OS too. I have already learned a lot about Devonthink, Cirus Punies Notebook, Curio, Tinderbox and the like great apps. Therefore, I will be recording my experiences with each of the apps I am trying until I come up with the final, perfect system for my work flow.   I will write a detailed review of each of the applications here in the future. But, for now , I will just put only a short summary of my experiences with them.

1. File Organizer

My first task is to properly setup files organized in a specific folder, to make them easily accessible via Spotlight (or Alfred, I prefer the latter though). For file, organization, I use two tools; Dropbox folder and Mendeley. Dropbox doesn´t require explanation. I use mendeley not only to collect references, but also rename and organize my PDFs. It is such a powerful application to do these tasks. Here I use it.

a-I set a folder in Finder, I call it “agglomeration”, to mean, a folder where I drop all newly downloaded PDFs. All the PDF I download from internet directly go there. I use a download manager  called folx to force all the pdf files to go to this folder.  You can google it.

b-I have another folder in Dropbox, call it “AllLing”. This is the folder where I keep properly organized files.

c. Then, I setup Mendeley to suck-in all the PDFs available in the  “agglomeration” folder into its library, rename and then put them all into  “AllLing” folder.

As you can see from the above screenshot, the Mendeley is organizing my PDFs into a folder, inside Dropbox. Since the files will be renamed to Author-year-title, I can search the files using any of these attributes.  I also index the folder “AllLing” into Devonthink (see next). One main reason I want to use Mendeley is the fact that it live syns Bibtex files , even if it is not as elegant as I wish it to be. Other reference managers such as Sente and Papers are great by their own, but are weaker in their integration with bibtex.

2.Database manager:

Database managers are tools to  organize files and information in a manageable manner.  I use Devonthink this purpose.  Devonthink is one of the most powerful apps I have ever seen in the  mac environment. It has an artificial intelligence which looks inside the PDF files and establish content-based relation among the PDFs. That means, if I am reading an article on “Definiteness” , the software can scan its database, find and suggest relevant articles,  articles that contain the word “definiteness” or/and other  related words in the articles for me. It is also packed with many other interesting features such as  tagging system,   notes-taking tool; organize files into different folders, smart folders, duplicate detection, replication (aliases) etc. If you are staring to use the app, the learning could be a bit steep. I definitely recommend you to watch a screen cast in  a  website (it is under a paywall unfortunately) called screencastonline. Their screencast gave me a good ground on  Devonthink. (Note: I don´t have any affiliation with any of the links I mention here). Devonthink will be an    indispensable part of  to my workflow. I have tried some of the other database apps. I think no other app as good as Devonthink for managing scientific papers. Therefore, my database agenda is closed. The challenge I am facing is to make other applications to work with Devonthink.

So, Mendeley renames and puts the files in “AllLing”; Devonthink indexes them. I then group, replicate, organize, tag the files in the Devonthink so that I could organize them for my specific projects. I am right now writing a paper about Nominalization. Hence, I search and “see also” the related papers in Devonthink, Group them in one folder; I then drag them to Sente for reading and taking notes.

3. PDF annotation and note-taking:

Macadamec has already written a great post about Sent. I recommend visiting his  post; I am not going to repeat the whole story here. I will just shortly reflect my own experience with the application and its place in my work flow.

I  am considering totally leaving Mendeley and migrating to Sente because of the fact that the application has a more elegant tools of annotating PDFs. It can directly quite, snapshot, highlight and insert all these into the Notes panel. That is brilliant. It can also rename files, just like Mendeley. The notes then could be exported to Devonthink or Scrivener using some apple scripts. brilliant!

Sente  has some fundamental flaws, unfortunately, that makes me nervous to totally migrate my data from Mendeley:

a. it fails to import PDFs from other applications,

b. the link between the note and the pdf could also be broken. Some people have experienced this problem, and I had the same issue with a few PDF annotations.  Right now, I am using it only as PDF annotation, not as a reference manager. My references and PDFs remain in Mendeley while I temporarily import the PDFs I want to read into Sente.  (just search in Alfred and drag it to Sente because the files are properly renamed by Mendeley, or go to the folder “Allling” and drag the file; but, I usually drag them from Devonthink).

c. it is also bad for Latex integration

d. Annotations are not stored in the PDF: this the problem of almost all the note-taking tools in Mac; they store the annotations in their own database. If you open a PDF from Dropbox in another PDF reader or browser, you couldn´t see the annotation done in Sente (or Mendeley or Papers) while the annotation done in Acrobat or Foxit or PDFexchange are there, everywhere you have the pdf. Storing the annotation is good for long term use, as these applications could break. But, Sente couldn´t do it, unfortunately.

4.Drafting

Here, the choice is clear. Since all the notes are exported from Sente in either OPML or RTFD format, I just import them to Scrivener.

5. Final Polishing and Publishing:

I export my draft form Scrivener in Latex format, I import the text to TexStudio, a latex editor that I use to finally polish my work. Texstudio, and also TexShop, can automatically detect and insert my references  which are stored in Jabref (in sync with Mendeley).

Finally, a shinny PDF!

End

Organize Mendeley’s Organizer using Duplicate File Detective

I have been using Mendeley Desktop for about two years now. Passing trough a lot of modifications, Mendeley Desktop has recently come out of its beta state. The best research project manager software now seems more stable and faster than ever.  Combing the potential of extracting the metadata of your PDF with the ability  organize and synchronize them with the cloud, no better application seem to exist that can satisfy all these needs.  Being a big fan of the application,  though, there are a few critical features that I am looking for implementation in its feature releases.  One of these is lack of Moving files while organizing files. If you use its file organization, it can only copy and rename  all the files in the library to a single folder. This means that, you should have a duplicate of files every time you use this feature. To alleviate this problem, I use an application called Duplicate File Detective. Of course, there are many duplicate removal applications out there. But, I prefer this application for one main reason; it can detect and delete only old versions of your files.

Here is how how to  do  it.

1. Open your Mendeley Desktop and make sure your  library as good as possible; Check the accuracy of the  metadata; check for duplicates in side Mendeley; check the dates, author, title of your files.

2.   After you make your library clean, go to Tools –>Option –>File Organizer. Check Organize my files. Click on Browse select a folder where you will store your whole library. You better select an empty ; otherwise, Mendeley will mix up your new files with the old files. You can also check Sort files into subfolders. But, I don’t recommend it. 

mendeley1

Check rename document files as the above picture, and finally Ok. This will copy all the files in your library to a folder (named AllLing in the picture). As you can see it I am also putting it in the dropbox folder. The reason is clear. Dropbox  gives more free cloud  space (2GB) than Mendeley (500MB). You can also get more free space by inviting your friends to it.

3. Since the above process copies all the files from their original folder to a new folder, you will have  two copies for each of your documents. To tackle this problem,  now you need to run Duplicate File Detective. In the DFD, select the disk where you store all your files and click Run Project.   When DFD finishes searching for duplicates, you will see all the duplicates in  a window. Go to Smart Mark (circled red in the picture below) –>mark Old files in Each Group –>Mark By File Created Date.

mendeley2

Now, give a glance on the list of files. If every thing is alright, all the old copies must be selected while the new copies stored in AllLing (in my case) remain unmarked. You can then either Move or Delete them. Now, you have cleared your clutter.

4. You can fix  a Watch Folder for Mendeley where you throw all new files that you will download from the internet. Mendeley will automatically import, extract the metadata , renamed and copy into  Organizer folder (AllLing in my case.).  After you make sure that the Mendeley has done its job, you can then manually delete the files in the Watch folder.