Reading, extracting and storing scholarly information to supercharge the writing process

Bookends has completely replaced Papers.app as my citation manager. Despite this change, my method of information gathering has changed little since I covered the topic, except for one major addition. I am now finding the majority of information through qxMD Read.My workflow for extraction of annotations differs a bit from when I was using Papers. I now use the combination of Bookends and Highlights.app to extract each of my annotations and notes as separate files. In addition, after highlighting, I’ve been extracting the entire manuscripts in 1-4 paragraph pieces.The whole purpose of extracting annotations and full text from each manuscript is to gain granular access to the information I’ve read. Through its "see also" feature, Devonthink can identify information I’m looking for. But more importantly Devonthink finds related content based on the context of my original query.After importing a manuscript into Bookends, the document becomes available on all my devices. Bookends outshines Papers in its built-in annotation tools as well as its seamless syncing between iOS and Mac.

My current preference is reading PDFs on a 12.9" iPad Pro along with an Apple Pencil. In a pinch, I’ll annotate on my iPhone. On my first pass through an article, using Bookend's built-in tools, I highlight annotations and jot notes in green. I use blue to highlight quotes I wish to use verbatim. When I’m finished annotating, I add the keyword RFP (ready for processing) to the manuscript in the Bookend database.

I have a Smart Folder set up in Bookends that finds the Keyword RFP. Uzsing this method, I can batch process multiple PDFs when I get to my Mac.When I'm ready to extract the information from the PDF into my Devonthink writing database, I export the PDF to my desktop and append the exported file’s name with FT (for fulltext).On my desktop, I open the file with Highlights. I use Copy Hypertext Link:Copy as Text from Bookends, and then open the “Edit” Tab in Highlights. Using use the text URL copied from Bookends to make a markdown link back to the Bookends Reference.When I export my annotations to Devonthink, the URL link will be appended to each file. Clicking the link within any extracted file takes me directly back to the reference in Bookends.I then turn my attention to Highlights.app. I make sure the annotations color preference is checked in Highlights.app. When checked, this preference will append the color of the highlight in each note.

Within Highlights, I use yellow to mark up the entire document over the top of my previous annotations. I highlight in 1-4 paragraph chunks. I also highlight the text of each table and figure.Once I'm done highlighting the entire paper, from within Highlights.app, I export my annotations to Devonthink from the Highlights.app menu. The annotations are saved as individual files to my Devonthink Inbox. I move the folder from the Devonthink Inbox to my desktop and then use Launchbar to move file from my desktop to my annotations folder. I put the desktop PDF in the trash, replace the RFP keyword in Bookends with DTx to remind me I've extracted the paper.

Since I’ve set up my Devonthink database to index this folder,the next time I launch Devonthink, the new information is catalogued and available for writing. The new information is also transferred to Devonthink ToGo to use while writing on my iPad.Using the Artificial Intelligence of Devonthink. I can quickly find related information. When I find an item in my database I want to include in my paper, clicking the link in the annotation takes me directly to the paper in Bookends.app.Using this method, I'm able to take full advantage of the Devonthink AI. Queries within Devonthink simultaneously find annotations, chunks of text and full manuscripts related to my search. I find this workflow invaluable when writing scholarly information.

***This workflow has been modified from here to the end-Please see Modification to Reading, Extracting And Storing Scholarly Information To Supercharge The Writing Process to see what I do instead.***

Keeping Current with Bookends and QxMD Read

In a previous entry, I covered the ways I add new literature to my scholarly manuscript collection. Technology has evolved since that entry. I’ve migrated to Bookends to keep my literature organized, and I have additional ways I find new literature I’d like to read. That’s what I’d like to cover today.In my MacWorld entry (circa 2012), I mentioned the three ways I collected new reading material:

• as a recipient of an Endnote library (when writing collaboratively)

• through personal searches on the web (and liberal use of Google’s automated search terms)

• as attachments to colleague’s emails

Since then, there are two methods I use even more commonly:

• Following individuals with similar interests and using keywords in Twitter.

• Using QxMD Read

Until recently, I was not familiar with QxMD Read. A colleague at Duke, Dr. Jordan Komisarow, brought the app to my attention. According to QxMD, Read “provides a single place to keep up with new medical & scientific research, read outstanding topic reviews and search PubMed. This iPhone & iPad app provides a simple interface that drives discovery and seamless access to the medical literature by reformatting it into a personalized digital journal.” One comment describes the app as “The Flipboard of Medical Literature.”The app was easy to set up. First I made a QxMD username and password. Then I chose my professions of interest. Finally, I chose specific journals, keywords, and collated collections.Once set up, Read began scouring the medical literature for new articles.In a single screen, I scroll through all the new publications (titles, conclusion, journal, etc.).If I find something of interest, I click on the title to find more information, including the entire abstract. While I’m scanning the abstract, Read attempts to download the full-text PDF.About half the time, Read finds a PDF and downloads it into the app. If the PDF cannot be found, I email the entry to my personalized Omnifocus Mail Drop so the paper is added to my Omnifocus Inbox.If the PDF is downloaded into Read, it is then a simple task to move the document into Bookends. The ease of importing full entries is one of the many places Bookends outshines Papers. I click Open In… and then select the Bookends icon.Bookends works its magic, finding one (or sometimes more) suggestions as matches.I choose the matching metadata and Bookends imports the PDF and metadata into its database. The paper and its metadata are immediately available on all of my devices.The process works pretty seamlessly. The only annoyance is that if you save the PDF to your library, it receives a numerical name. You must later open Bookends on your Mac and rename the PDF to your naming convention. This is a small price to pay for such power.I'm finding even more relevant information these days using QxMD Read. My challenge now is finding the time to read and process it all!