Modification to Reading, Extracting And Storing Scholarly Information To Supercharge The Writing Process

In Reading, Extracting And Storing Scholarly Information To Supercharge The Writing Process, I wrote about how I extracted both highlights and full-text of entire manuscripts in order to give me granular access to information. Although I’ve continued my extraction of highlights, the extraction of full text (by highlighting the entire document) proved much too time consuming. Instead, I’ve been experimenting with an alternative that is much quicker (as suggested by Andrew in the comments of the entry)—saving the entire manuscript as single-page PDF documents. Here is what I’ve been doing.

After highlighting a manuscript in Highlights.app, I extract my highlights (along with color tags) to Devonthink Pro using the built in export function. By default, Highlights.app saves my extracted highlights files to the DTP Inbox. I move the folder from the DTP Inbox to my Desktop. Within the moved folder I make two new sub-folders: 1. HighlightsX and 2. PDFx. I then move the extracted markdown files to the HighlightsX sub-folder.Within Bookends, I export the annotated pdf to my desktop. There, I open the file with Adobe Acrobat (any app able to add headers and split documents will work).

In the left most header I put the Bookends citation (Bookends: Edit: Copy Citation), in the center I put the DOI number, in the right header, I put the Bookends link (Bookends: Edit: Copy Hypertext Link: Copy as Text). These headings are added to each page of the PDF. I then split the manuscript into multiple single-page documents. I save the split PDF documents to the PDFx sub-folder.

I then move the parent folder my Dropbox Writing folder and Index the folder using DTP. Within DTP I make sure both the main folder and the subfolders will have their tags included (option click on a folder in DTP and make sure “Exclude from Tagging” is unchecked)

.Although this method is faster—there are trade offs. The “Find Also” feature of DTP depends on the words in a document. A document with too many words dilutes the accuracy of the semantic search. A page of text has far more words than an extracted paragraph and thus is slightly less accurate in finding granular information. The other trade-off comes in the amount of text that must be read when searching. It is faster to scan a paragraph versus a whole page of text in a PDF. Regardless, the savings in time using this method far exceeds the trade-offs in accuracy.Let me know what you think.

Highlighting PDFs from Within Scrivener

Here is a quick trick to use with Scrivener.I’ve been working on some short executive summaries. For longer projects I tend to keep my research in Devonthink. For these shorter reports, I’ve been importing all the supporting information into Scrivener. On several occasions, I’ve wanted to highlight PDFs within Scrivener.It’s very easy to do. In Scrivener, just click on the button indicated in the picture to launch the imported PDF in your default reader.Holding the button down lets you select a different PDF Reader (and lets you choose to make it your default application). Any highlighting changes are saved back to the PDF in Scrivener. I've used this trick numerous times over the past few weeks. I hope you find it useful too.

Voice Dream-Listening to Scholarly Information (PDFs) on the Go

Keeping up with current medical literature is a constant struggle. The amount of information in healthcare doubles every 5-7 years. To keep up, I try to take advantage of time that would be lost (for instance, while driving in my car). I typically use my commute time (a 20 minute drive each way) to listen to audio books, but occasionally I’ll “read” a scholarly manuscript using a PDF-to-voice conversion program.My favorite app for converting PDFs to sound is Voice Dream. I initially found this app while looking for a way to listen to web content (before the feature was built into apps like Pocket and Instapaper). I was pleasantly surprised when I found Voice Dream could also translate PDFs.I prefer Voice Dream to other readers because of its customizability. I’ve customized the voice speed, pitch, and volume. The readback speed takes some trial and error in order to find the proper speed to keep your attention and allow understanding.Voice Dream loads PDFs from Dropbox, Box, or Google Drive. I have a designated folder on Dropbox specifically for manuscripts I’d like to listen to. The interface for Voice Dream is intuitive. As the voice reads the text, the program highlights its current position in the text.Using this method, I recover almost 40 minutes of time that would otherwise be lost. Let me know what you think.