Bibliography & Referencing Software

This fall I have once more tried to figure out the best way for me to manage my papers and make referencing as easy as possible. Long answer short: I am not happy with the outcome.

In the past six years I have repeatedly looked into different bibliography and referencing services and software and they never seem to do what I want them to do. This might very well be my fault and that I have uncommon or too specific needs and wishes, but I feel like other people are struggling with this too and that the current software available could significantly improve. For those people and for myself for future reference, I have here structured my thoughts and findings on the topic.

I talked to a number of colleagues and friends that all do academic research and realized that almost everyone was approaching the problem in a completely different way. Some of them didn’t even see any point in using referencing software. I therefore want to start with a list of things that we all have in common.

  • We find papers of interest to us and our research. This is probably the point with the most diversity from reading printed journals, using software such as Feedly to subscribe to feeds of new articles, google scholar alerts, google scholar searches, newsletters, university library searches, to having them personally emailed to you by other people and many more options.
  • We read papers, and some of us like to highlight, annotate, bookmark etc. I have a huge preference to do this on my tablet, others prefer doing it on a computer or printing them out.
  • We save papers. This is where it gets complicated, because “saving” a paper can mean different things and people seem to use it for these two options separately or also combined.
    • Saving the paper content. This could be keeping a hard copy, saving a pdf in a folder on your computer, saving the pdf in an app on your computer or tablet, or even just remembering it in your mind to name a few common options. I think many people (me included but definitely not everyone) prefer to save papers in a way that is consistent with how we like to read papers and that also allows us to keep any highlighting, annotations, etc.
    • Saving the paper metadata. Information needed to cite the paper, but also the abstract and information such as the authors institution, number of citations etc. It is common to use software such as Mendeley, Zotero, Endnote, Papers, Paperpile for this. Some people also just maintain a BibTex file or other lists that they manually add entries to as needed.
  • We organize papers. Some people actually don’t do this, but others go crazy about it. It can be about categorizing papers, assigning labels, notes, ratings, cleaning up metadata information and much more. Creating reading lists for teaching classes is also a common way to organize papers.
  • We retrieve papers. Again, sometimes we want to retrieve paper content (e.g. re-read) and sometimes we want paper metadata (e.g. to cite a paper). In the process of doing one of them (e.g. “I want to cite the paper that made statement X”) it might become necessary to also do the other one (e.g. “It was written by author Y in year 2000, but there are 3 publications of that author in that year” => “I have to look up the content of these three papers to find the one I need”).  For retrieving paper content and metadata, we can only reasonably retrieve any of those in the way that we saved them.
  • We cite papers. How we cite papers depends on how we write our own papers. The most common ways are probably LaTeX and Word. To allow for a seamless easy citing experience we often need to create a BibTex file or have a Word plugin to access the saved paper metadata.

A list of wishes and preferences (ranked by importance) that I realized I had. They basically describe my dream come true workflow with papers and referencing.

  • I want one service / software that handles everything. Or if there are several different ones, they should cooperate / be integrated with each other such that it feels like only dealing with one. Mendeley is probably pretty close to this, but their tablet app is really bad. Paperpile might also be a good choice if you don’t want to use it on your tablet (it also currently only works in Chrome).
  • I realized that I really appreciate having a grid view of the first page of the pdf together with the title of the paper. I guess I am a visual type and this helps me a lot in finding a specific paper and keeping an overview.
  • I want to be able to read, highlight, comment, annotate, search in, make doodles, bookmark, etc. in individual papers as pdf files on my tablet (happens to be an ipad). There are numerous apps for this that are great (I love Goodnotes, but Notability is also pretty good), but they usually don’t allow for saving metadata. The only apps that I found that combine saving the pdf and metadata are Mendeley (which is bad), Papers 3 (which is ok), and PaperShip (seems to be ok too, works with Mendeley and Zotero).
  • Metadata about the paper should be imported as automated as possible and with a lot of detail (e.g abstracts) I think that is a huge problem across all different platforms.  This is not necessarily their fault, because the accuracy and detail of the imported data depends on the source.
  • Cleaning the library should be easy (e.g clean up duplicate authors or journals) Currently annoying everywhere, but I guess there are subtle differences that I don’t know.
  • I want to know the number of citations (I use the google scholar number of citations often as an indicator for the “importance” of a paper) I don’t know if that exists anywhere.
  • I want to assign labels / keywords and group papers and be able to filter by combined criteria. Papers can’t do this. Mendeley and Paperpile seem to be able to do this. Not sure what else.

My solution so far was to handle the paper content and the paper metadata in separate applications. I have been using Goodnotes to read, annotate, and save pdfs of papers, and Mendeley to save and clean metadata and create BibTex files. However, this is prone to cause obvious problems due to inconsistent libraries. I have some papers in Goodnotes, but not in Mendeley and the other way around. Looking up the paper in the other repository once I have located it in one of them is not straightforward. This has repeatedly led to disruptions and serious annoyances in my workflow, which is why I recently started an attempt to transition to Papers 3. It seemed promising in that it has an app that I can use on my tablet somewhat like I have been using Goodnotes, but with the added functionality that it can also store metadata and sync with the desktop application on my computer which I can use for everything that I used Mendeley for in the past. But…

Papers 3 is relatively buggy. The in-app google scholar search to match a pdf with metadata from google scholar recently stopped working, they fixed it in the tablet app, but it is still not working on my desktop. Cleaning up duplicate authors didn’t seem to work for a while, now it does. I couldn’t figure out a way to filter by multiple labels. Probably because it is not possible. And finally, their documentation is a joke.

Besides that is also the fact that the functionality of the tablet app is not as amazing as Goodnotes is and I am giving up on some functionality there as well as some Mendeley functionalities that I really appreciated such as getting emails with recommended papers based on my library and filtering for combined key words.


Please excuse the probably numerous typos in this text. This is mostly written for my own reference.

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