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).

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

Reading inside Mendeley, better to avoid it

I have already started writing about the great research tool, Mendeley Desktop. I believe, mendeley is one of the mandatory tools every academician need to have. Many people are using it for many things. As to me, however, its main virtue is the ability to organize the actual PDF files in a brilliant manner. In this post, though, I am going to tell you why you need to avoid reading and annotating PDF files inside Mendeley itself.

If you are familiar with the fast and efficient PDF readers as Foxit and PDF-exchange, you will face too many constraints with Mendeley’s internal PDF reader, which I found to be unbearable. Of course, you can read, annotate and write notes inside mendeley. But, the main downside of Mendeley’s internal PDF reader is the fact that your annotations will be saved in separate folder. Mendeley has a system called database where it saves information about the PDF files. That database is in a different folder from the actual PDF files. Hence, if you open your Mendeley annotated PDF files in another PDF reader, you will not get the annotations. This is bad. I want my PDFs annotated wherever I open them, whenever I want.

Mendeley team has tried to alleviate the problem by adding a feature to export the annotations of the PDFs. But, I found this to be a laborious task. Should I open and export the annotations of each and every file every time I want to see my annotations in another software? no, I will not do it. So, if you are like me, the best approach is to manage your files inside Mendeley and read them using more potent PDf readers as Foxit. Your annotations and notes will be saved embedded inside the PDF files that you don’t have to worry opening them in another software.  You will enjoy your annotations to the  end of time (unless you want to remove them of course) wherever you go, which ever software you use.  So, to  open the files organized inside Mendeley with external readers, you have to right clicking the file and choose “Open file externally”. Your default reader will be fired. Voila!

Cheers

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.