Monday, February 26, 2018

How to organize your scientific PDF library?

During my training I downloaded and collected tons of journal articles for future reference. Most of these articles were in a pdf form and I had assigned these to variously named folders for easy retrieval. Most of us probably have some version of such “digital library” on over laptops/desktops. And, I am confident in saying that when the time comes to find THAT specific paper – we struggle. Digital organization is not our forte!

I scoured the internet for ways to improve my digital library arrangement, watched videos read blogs and even made a new folder in my library about managing a digital collection of papers!! Eventually I started using Mendeley for reference management and file organization. While the reference management part was good, I was still not happy with the file library organization function.

Knowing that I was not the only one with this difficulty, I posed my question to ASN Communities, hoping to tap into the collective wisdom of the ASN. And sure enough, I received some excellent answers that I will summarize next.

Dr Edgar Lerma, a Chicago Nephrologist has an innovative and user-friendly way of organizing references. He created a twitter hashtag #Nephpearls to link tweets with reference articles/material. He organizes papers by firing off a tweet with the hashtag #Nephpearls AND the subject of the paper, with an online link to the pdf (if free) or PubMed (if gated). To make it even more enticing he usually has a figure or a table from the paper attached to the tweet. In this way, papers are archived online for everyone who wants to retrieve it. As an example say - you are looking for Cardiorenal syndrome, all you have to do is to type in the hashtag AND topic (#Nephpearls Cardiorenal), in the search bar in twitter and this will result in several relevant tweets with figures, tables, clinical trials, excellent reviews, textbooks and even comics, all related to cardiorenal syndrome. Everyone can share in this library using the same method as Edgar. He adds these nephrology pearls (Nephpearls) regularly. Brilliant!

Another very well-organized way also was the method described by Dr. Roger Rodby from Rush University. Dr. Rodby uses a Google drive to organize and share (with his Fellows) his greater than 6000 articles. He keeps the Master PDF “Literature” Folder on his personal computer which syncs only one way to the Google drive (his computer’s Literature folder to the Google Drive’s Literature folder). By doing that he prevents anyone other than him from adding or deleting any articles to the PDF database. And also in doing so he can assure that the filing system and naming system stays intact. Dr. Rodby classifies subject headings into 39 somewhat arbitrary Nephrology topic folders:

Then he uses a unique way for article nomenclature within each topic subfolder (which is something I found very unique and clever), thus keeping an organized list of entire disease condition topics. There is a fine line between “lumping and splitting” how an article gets titled in this organizational scheme. The key to it is a short name followed by an abbreviation of the Journal Source and the year it was published. Below is a but a small snapshot of his >1400 articles in the “GN” folder”:

Rarely a day goes by that he doesn't add an article or two.

In the same vein, Dr. Nikhil Shah a nephrologist at the University of Alberta, began using Google Drive for creating and sharing a literature library with his co-fellows and staff during his fellowship years. In addition to the Dr Rodby’s list of folders (see above), he incorporated presentations from staff and other fellows to this library. These presentations are Core Nephrology teaching presentations and Nephrology Grand Rounds presentations at the University of Alberta. This Google Drive is shared within the Nephrology group locally and provides an enduring collection of teaching material to all fellows and faculty.

Another important well-organized source of high-yield landmark trials in nephrology is the online site ( created by Dr. Jordan Weinstein. It is organized in nine major categories (see picture below). It also includes a separate section for #VisualAbstract.

I used Rodby's way to organize my digital library, and screen #Nephpearls and ukidney for topics I am looking for.

So, what is your method to this madness?? Share with us your organization methods and I will include them here as well.

Mohamed Elrggal 
Alexandria, Egypt
NSMC Intern, Class of 2018


mohamed essam said...

Organizational scheme great but not perfect. For example, where do you file the hypokalemic met alkalosis? Overlap of genetic, hypoK, Met alk, HTN, each of which have own sections. Sometimes I duplicate and put in multiple sections (Comment by Dr. Rodby on Twitter)

mohamed essam said...

I have created separate library for each subject( one library for SSNS, one for SRNS etc ) in Endnote software. I keep on adding new content to it and update it (comment by Airavata on Twitter)

Anonymous said...


Nephro in 5 said...

Many thanks Dr. Mohamed for your nice blog, is there any link for google drive of Dr. Roger Rodby and Dr. Nikhil Shah.

VA said...

Another addition to the Rodby approach is to rename the file by adding a message. For example a paper of FSGS in my library is titled 'Tacro regimen 6 month target 5-10, 6 month target 3-6 if some response. Tacrolimus Therapy in Adults With Steroid- and Cyclophosphamide-Resistant Nephrotic Syndrome and Normal or Mildly Reduced GFR.pdf' or 'Iv solumedrol 60mg iv daily for 10 days followed by oral Tacrolimus for 9 months. Tacrolimus Monotherapy after Intravenous
Methylprednisolone in Adults with Minimal Change Nephrotic Syndrome' Google drive allows renaming the files (without special characters).