Folder Structure to Maximize Writing with Devonthink Pro

On several occasions I have written about how I use Devonthink Pro (DTP) for scholarly writing. Although at one point I had all my information on manuscripts in a single DTP database, over the last year I have maintained separate databases; one for PDFs, another for my annotations.I accomplish this by having separate folders in Dropbox. After extracting my annotations from Highlights.app, I place the exported files in their own folder. Once a month, I export all the PDFs in my Paper’s Library to their own Dropbox folder. I use a Hazel script to throw away any duplicate PDFs in the Dropbox folder. I index (not import) the annotations folder into one DTP database, and index my PDFs into another.This setup allows a fair amount of flexibility. Not only is this setup advantageous for writing with DTP (as I will cover in my next entry), it allows easy access to my PDFs for reading with Liquidtext or listening with Voice Dream.

Mourning the loss of Integration Between Papers and Scrivener

Early indications, including personal communication with ReadCube personnel, are that Magic Citations (now called SmartCite) will no longer integrate with Scrivener. The new Papers app will only work with Microsoft Word. Bibliography formatting is not an issue for me. The biggest loss is the ability to add citations on the fly in Scrivener without interupting my writing flow.The news of this impending feature loss (along with the announcement of an annual fee) had me scrambling to invesitgate my options for citation managers. During my search, I came across this Wikipedia article, Comparison of Reference Management Software with a great table that collates the majority of software out there.My needs are the following:

  1. Ability to organize and search through metadata and pdfs
  2. Integrated citation insertion with Scrivener and Ulysses
  3. Ability to insert citations while writing on an iOS device
  4. Ability to annotate PDFs and export each comment individually appended with the article's metadata
  5. Ability to export metadata (to enable my workflows for sense-making and export of annotations)

I looked at the following:

  • Zotero
  • Bookends
  • Mendeley
  • Endnote
  • Readcube
  • No product currently fills the void left by Papers, although the consensus of users (both those seeking alternatives to Papers and those who are being forced to leave Sente) seems to be to move to Bookends. I tried the demo version of Bookends and was not impressed. I am waiting impatiently for the release of ReadCube Papers. If the majority of features are retained, I will likely bite the bullet and pay the annual fee. I plan to figure out a work-around to add citations to Scrivener / Ulysses.I'd be interested in hearing your plans / thoughts on academic citation managers.

    OmniFocus Mail Drop Trick

    Here's a quick tip for getting tasks from your email to your OmniFocus Inbox.Many times, requests for my time arrive via email. Committing and tracking this type of request used to be a multi-step process. First, I'd add the email to my OmniFocus Inbox. Then I would reply to the email acknowledging my commitment (or requesting a follow-up).I realized there was an easier way....Now, when replying to an email with a task, I merely put my OmniFocus Mail Drop email address in the bcc field. Using this method, I can respond and track the task in a single button click.

    Travel Receipt Workflow

    Here is a handy workflow to keep track of your reimbursable / billable expenses on the road.Set-up:

    I have an Evernote Notebook that is used solely for professional receipts. This notebook is named “Receipts_Work”. I’ve set up an If This Then That (IFTTT) Applet to send an email when the notebook receives a new note.When I receive a receipt on the road, I immediately scan it with Scannable then save it to my Receipts_Work Notebook. IFTTT monitors the Receipts_Work Notebook. When the new note is detected, it automatically sends an email to both my assistant and my Omnifocus Maildrop address (so the item is added to my Omnifocus Inbox).After my trip, I can go back to my Evernote, select all the receipts/notes from my trip and make a “Table of Contents” using a single button push in Evernote.This workflow simplifies management of reimbursement receipts. Hope it works as well for you as it does for me.

    Highlights.app Redux

    I was too quick to judge the program Highlights. I gave Highlights a second chance, and although not perfect, the app is slowly winning me over. Highlights has greatly sped up the extraction of information from my reading.First a little background. I use Papers for my PDF and bibliographic management. I’ve written about how I extract highlights and annotations into individual files along with their relevant references. The reason to go to this trouble is to enable Devonthink’s artificial intelligence. The Devonthink AI uses word count to find related information in other files. I use this method extensively in my writing of grants and manuscripts. With my previous method, I found by adding references to each annotation (thus similar words) I was interfering with Devonthink’s ability to find relevant information. In order to improve Devonthink’s accuracy, I stopped adding references to each individual annotation. Instead, I merely include a Papers Link back to the original file.Highlights shows the annotations you make in the app's right-hand column. A pop-up interface within Highlights allows you to make comments, underline , change colors, etc. The killer feature of Highlights is single-command extraction of each annotation / comment to its own file. This feature allows me to extract highlights (and metadata) without having to invoke my Keyboard Maestro macros. When the data is extracted into Devonthink, the individual files are in Markdown. This makes the extracted information easy to view and edit.Although I’m more enthusiastic about Highlights, there are several quirks you should understand:

    1. When Highlights explodes your annotations into individual files, it prepends the original file’s name. If you use Highlights from within Papers (e.g. selecting Highlights as your PDF reader of choice from within Papers) you will end up with a ridiculous, machine based title in your metadata. This is not Highlights fault. The use of non-intuitive file names is one of my pet peeves about Papers. The workaround is to export a copy of the PDF to your Desktop and then launch the exported file using Highlights. Using this method, the author’s name and the title of the manuscript along with the year of publication are all prepended to each markdown file.

    2. After reading and highlighting, I edit the markdown headers in Highlights (choosing the edit tab in the annotations window). I erase all but the primary author’s name and then add the Paper’s Citation and a Papers Link back to original file (copied from Paper’s Edit Menu). There is another quirk here. In Highlights Edit Mode, if you don’t leave a space between the markdown coding and the information you add, your file will be reset back to its original state, erasing your modifications.

    3. Highlights has the ability to automatically look up DOI numbers. When it works, it’s great. It takes a single click to import a reference from the bibliography into your Paper’s Database. Unfortunately, this feature is flaky, especially with longer manuscripts. I often have to revert to my Launchbar scripts to capture the bibliographic information I need.

    Once I’ve added the metadata I want to the master annotation file (and collected the references of interest), from within Highlights, I choose Export >> Devonthink. Highlights creates individual markdown files for each of the annotations. Each individual file contains the master file’s metadata. The data is copied to my Devonthink Global Inbox. I move the folder from the Devonthink Inbox to my Desktop and from there to my Annotations Folder using Launchbar.Highlights has significantly sped up the time it takes to process a manuscript. Using this method, I’m also having greater success with the “See Also” feature of Devonthink. I hope it works for you too.

    OmniFocus + Focus - Pomodoro Productivity

    Combining Omnifocus and the Pomodoro Technique is an incredible way to get things done. Years ago, I used a program called Eggsellent. Eggsellent integrated seamlessly with Omnifocus ( flagged tasks in OF were added to the Eggsellent queue). The upgrade from OF to OF2 broke the integration, and the Eggsellent developer did not update his app.In searching for a replacement, I tried Vitamin R2 and Tomatoes. I settled on Tomatoes for its simplicity and visually pleasing interface. Tomatoes did not meet my needs. The only way to get OF tasks into Tomatoes was to drag and drop (or type). This was a far cry from the workflow I enjoyed with Eggsellent.From Tim Stringer’s Learn Omnifocus website, I found a Pomodoro app called Focus. Focus is one step closer to what I’ve been looking for since the demise of Eggsellent. The Focus Interface is clean, intuitive, and attractive. Although Focus does not autopopulate flagged items from OF2, it is easy to add a task using the “Share” menu. Timers and tasks are synchronized on Mac, iOS, and Apple Watch via iCloud.Focus is still missing some of the functionality I desire in a Pomodoro app. Besides missing automatic OF2 integration, there is no ability to add tags to each item. The only way to add metadata is via a text box. Add that to the relatively steep price ($19.99 for the Mac version, $7.99 for iOS).Despite these shortcomings, Focus is my favorite modern Pomodoro app and has replaced Tomatoes as my timer of choice. Give it a try.

    LiquidText PDF Reader

    I have experimented with different PDF readers on my iPad. Over the past several months I’ve exclusively used a program called LiquidText.LiquidText has a unique, award-winning, interface that allows me to drag, drop, and manipulate text using my finger. LiquidText was named “Most Innovative iPad App of the Year” by Apple in 2015. LiquidText feels much more natural than any other PDF reader I’ve used on iOS--and I've used many. After highlighting with my finger, the exerpts / highlights / comments are extracted into their own area. The excerpts may be dragged around, linked, and repositioned at will.When reading and highlighting, I either drag text from the PDF into the notes area, or simply hit “AutoExcerpt” and the text is extracted for me. I can comment on the excerpted information.I can also view the place in the paper the highlight came from by merely touching the excerpt in the notes area.LiquidText reads and writes to a whole range of cloud services, but has limited range of export document choices.An Enterprise version is available for $9.99 that adds features like multi-document search and the ability to comment on multiple documents simultaneously. I've been using the app so much, I upgraded primarily to support the developer.There are a few features that are not (yet) available—the most critical for me is the inability to export highlights into a text file—LiquidText only exports highlights to Microsoft Word. This, unfortunately, is not compatible with my workflow for extracting highlights, but I like Liquidtext so much, I figured out a workaround using Skim—here is my entire workflow:

    • I set up a Dropbox LiquidText Folder to serve as a bridge with my desktop.
    • I open the entry in Papers on iOS.
    • From within Papers I select "open in". -this brings up action menu.
    • I open, read, and annotate in Liquidtext. This includes linking the full-text of references to each excerpt (as suggested by reader GH).
    • I export the PDF and Notes from Liquidtext to my Dropbox Folder.
    • When I get to my Mac, I open the PDF in Skim.
    • Under the File Menu in Skim, I choose “Convert Notes” making my highlights into Skim Notes.
    • I then process the annotations as discussed in this blog entry.
    • (If you want to take the time on your desktop you can also replace the Papers PDF with the LiquidText highlighted version).

    Give Liquidtext a try and please let me know what you think.

    Capturing Clinical Questions Using Drafts and Evernote

    Being a physician means a commitment to lifelong learning. In a busy clinical practice, two-thirds of clinical encounters generate at least one clinical question. In an average day the typical physician has at least 11 unanswered clinical questions. Only 40% of those questions ever get answered. Most of the questions are forgotten in the hustle and bustle of clinical care.In an attempt to improve my ability to capture (and answer) these questions, I've developed a new script for Drafts. This script uses the same concept as the technique I've mentioned to capture ideas, quotes, etc. This particular script saves information to Evernote but you could use Ulysses, DayOne, Wunderlist, or any other app you can program with an action. I chose Evernote since Evernote has the ability to find related notes anywhere in my collection. When researcing answers my question I capture those to Evernote as well-linking the question and answers in my Evernote database in perpetuity. Since Evernote is ubiquitous, the answer is available on my computer iPhone, and iPad.Here is how I approached this. First, I set up a new notebook in Evernote. I called this notebook "Clinical Questions." I then developed the following script in Drafts.Using this script it is now possible for me to quickly capture questions investigate later. I merely open Drafts and type or dictate my question, then hit the script. The question is logged to my Clinical Questions Notebook (along with date and prepended with tag ClinicalQuestionX).I’ve found myself using this script many times each day. I hope it helps you as well.Stats found on UptoDate: http://goo.gl/BDBqmH

    Drafts Script to Capture Ideas to Ulysses

    As I've mentioned in previous writing, I am a big fan of Ulysses. I now do all of my short writing in Ulysses, so I decided to transition my blog idea script from Drafts->Evernote to Drafts->Ulysses.The script prepends "BlogX" and the current date, erases the Drafts file, then places my new idea in my Ulysses Inbox.In Ulysses, I keep three blog related groups: Ideas, In Process, and Published. I no longer have to take time to move my ideas from Evernote to Ulysses. Instead, each idea is submitted to Ulysses, eliminating entirely the need for Evernote. If you use lUlysses, you can adopt this script for capturing other ideas as well. I hope you find it useful.C-4BD1E907-BF45-4BDF-A537-FD4B164DE1163.C-594A6F3A-763C-4292-8CF5-2B232346AC1CC-AD6CA981-BA55-4179-93A7-F7067F434527

    New NIH Grant Requirements - Critical Evaluation of Existing Literature

    For those of you that write NIH grants for a living, you are well aware of the changes required for new grant applications in 2016. In an effort to improve rigor and transparency as well as to increase reproducibility, The NIH now requires the grants to be written in a whole new way. A major part of these changes has to do with critical evaluation of existing literature.In light of these changes I have been formally appending my manuscripts a new way. In previous entries I’ve written how I take notes while reading, then extract these highlights and notes to their own individual files. Now, as I'm reading, I make and effort to record perceived strengths weaknesses of each study appending my comments with the text “StrengthX” or “WeaknessX.” I then extract each comment as its own text file. When writing grants or manuscripts, using Devonthink, I’m able to find similar notes to the one I’m reading. By appending StrengthX or WeaknessX, I’m able to single out my own comments instead of a seeing every instance of each word.In a future entry, I’ll talk more about the ways I’ve updated finding extracted information using Devonthink (and Tinderbox). A good portion of my writing workflow from 2015 has changed. I will write an updated writing workflow after the official release of Scrivener iOS.I'd be interested to hear how other academics are dealing with the changes at the NIH. Please leave a note in the comments below.

    Using Skitch and Papers to Capture Figures and Tables

    Few would argue that the most important point of a scholarly manuscript is made in its figures and tables. I am going to share with you how I capture figures while reading scholarly information on my Mac. This workflow uses:SkitchPapersInstall Skitch and make sure, in Skitch Preferences, to enable the “keep Skitch Helper running in background when I quit,” and “Start Skitch Helper when I log in to my computer.”Screen Shot 2016-05-28 at 9.12.13 AMAs I’m reading scholarly literature and come across a table or figure I want to save I do the following. I make the figure as big as possible on my screen. Then, from the Skitch menu in my menubar, I select the Crosshair Snapshot. I then select the figure (and sometimes the caption) trying to balance the white space surrounding the figure.Next, I go to Papers, select the reference in my Papers Library, and then from the Edit Menu:Copy As:Reference.I return to Skitch and double-click at the bottom of the figure then paste the reference text. I then balance the text. The height of the Skitch figure will expand to accomodate the new text.Screen Shot 2016-05-28 at 9.14.40 AMWhen I want to refer to or use the table or figure I view it directly in Skitch or find it in Evernote. Using this method, I can also search for words in the reference (e.g. the author’s name or the title of the manuscript) and sometimes even the words in the figure itself.If I want to use the figure in a presentation or to send it to a colleague or trainee I can export the figure from the Skitch File Menu.Using this method I’ve captured hundreds of figures. I hope this workflow helps you too.

    My OmniFocus Set-up (Part 2)

    As i've mentioned numerous times before, I'm a huge fan of OmniFocus. In my last entry on OmniFocus, I offered a peek into the way I organize my folders. If you haven't read that post, please do so now. In this entry, I’ll answer some of the questions about triaging, prioritizing, and adding time to actions.Weekly ReviewI am not strictly adherent to GTD methodology, but I do use many of the practices. My practice includes both daily and weekly reviews. My weekly review normally takes about an hour. During the hour, I review existing projects and actions, clean up remaining items in my Inbox, and set up new projects. I look at each new and existing project through two main lenses—a hard due date (e.g. tax filing-Covey Quadrant 1-CQ1), and the strategic importance of the project to my personal or professional life (Covey Quadrant 2-CQ2).As you saw in my last entry, all my projects are organized into folders by my personal and professional roles. During my weekly review I decide on the CQ1 and CQ2 projects with greatest strategic value, or with the most urgent deadlines. These are the projects that go into my “Weekly Priorities” Folder. My next most important strategic projects go into my “On-Deck” Folder. I try to have no more than three projects in each the weekly priority and the on deck folders. Those projects that are lower priority at the end of the week, but still active, go back into my personal or professional “Role” Folders.ProjectsI spend about 80% of my time working on items in my Weekly Priority and On Deck folders. I have a custom perspective that filters all my projects down to my priorities grouped by project or context.Screen Shot 2016-04-16 at 10.37.22 AMAnother perspective shows all my flagged or due items even if they are not in my Weekly Priority or On Deck Folder.Screen Shot 2016-02-14 at 1.27.05 PMAs I add new projects, or make new projects from items in my Inbox, I am cognizant of any hard EXTERNAL deadline—only items with EXTERNAL deadlines get a due date. I have a custom perspective that shows all due or flagged items regardless of whether they are in my priorities folder. This bubbles up items that are due allows me to stay on top of deadlines regardless of whether the item is strategic or not.The last part of my weekly review strays from GTD methodology—I try to roughly plot out my week, placing actions from my highest priority projects in my calendar. I try to leave free time to allow for interruptions and other inevitable delays.I’ve found time-based perspectives to be helpful in two ways…during my weekly review , when I am trying to sketch out my week, or on-the-fly when I have unexpected time (e.g. a meeting that finished early). When defining the time for actions, I try to keep each to an hour or less. If an action item looks like it will take longer than an hour, I break it down further.My weekly review is complete after I’ve sketched out my week in my calendar. Although having a plan is great, I don’t get stressed when things change. I often need to adjust my plan. This takes place in my Daily Review.Daily ReviewEach day I open OF next to my calendar and review my achievements of the day. I like to record my my major achievements (e.g. completion of a major project) in a journal app (I use Day One). Often, during my daily review, I need to adjust my plans for the upcoming day. I have a perspective actions associated only with my highest priority items. I look at this list first. Next, I look at a complementary perspective that shows me my entire list of actions, grouped by context. Anything that I have not formally placed in my calendar, but want to achieve on a particular day gets flagged in OF. When I get to the office, I use my my “Flagged or Due by Context” Perspective constantly.Screen Shot 2016-02-14 at 1.27.05 PMI hope it's helpful to see how I'm using OF.I'd love to hear what you think...and would love hear the ways you use the software in your life.Addendum:In response to Owen's request....Screen Shot 2016-07-04 at 9.07.12 AMScreen Shot 2016-07-04 at 9.06.54 AM

    Quick Idea Capture Using Drafts and Evernote

    Although I’ve already  written about the way I capture ideas using Drafts and Evernote, I thought it was worth repeating since these techniques were buried in another entry. I literally use this method multiple times a day. Using Drafts, I’ve efficiently captured hundreds of ideas, blog thoughts,and lyrics. As you’ll see below, I also use Drafts to start entries in Day One., ------------------------------------------Capturing Ideas in Evernote using DraftsEvernote extends its great power by linking to many other applications. I’ve found capturing snippets of text into Evernote is even easier than the method I described a few years ago using plaintext.I use Drafts on my iphone and iPad to capture / brain dump just about everything. Drafts is an essential program on my iPhone. Drafts allows me to capture without thinking about what app I need to open. Once the text is captured, Drafts routes the information wherever I choose. I wrote about one way I use Drafts to capture and process meeting notes. When I want to capture an idea, I merely open Drafts and type or dictate my idea into the app. When I’m done, I route the information to Evernote using the following custom action:IMG 0608The action automatically derives a title from the first line of the text and appends the date and time. Furthermore, it files the note in my “Ideas” Notebook in Evernote and tags the note with the keyword “Ideas."The note ends up in Evernote looking like this:Screenshot 2015 11 27 13 29 52When I get to Evernote, I append further information in the note as needed. I use IdeaX in the header so when I search for a list of my ideas, they are not mixed together with information I’ve gathered from other sources. If I search for a keyword(s), I not only see my ideas, but all the information I’ve gathered in Evernote—very useful.Capturing Blog Ideas, Lyric Ideas, Quotes, and other Snippets in Evernote using DraftsI use a similar scripts in Drafts to capture a whole host of other information on the go. Each class of information is filed into it’s own Notebook in Evernote. For example, here is the action I use to capture information for my blog: IMG 0609  Using Drafts for entries in Day One.Although I love Day One, I was not entering information often enough. Action URLs are a powerful feature of Drafts. Action URLs-open other applications, then perform functions. In order to increase my capture rate,  I decided to make an Action URL that transfers text  from Drafts to Day One.Here is how simple it is…..Drafts Day1 Action.jpgI have configured  Day One on my Mac and iOS devices to sync. I also enabled the #hashtag feature in Day One. Hashtags are translated into keywords in Day One.Since enabling this script, I find myself capturing both personal and professional snippets each day. Give it a try!By incorporating Evernote, I’ve greatly simplified many of my capture processes. I highly recommend giving Evernote Premium a whirl and trying out a few of these workflows on your own. You won’t be disapointed.

    My Omnifocus Set-up (Part 1)

    I am a huge fan of OmniFocus (OF). I am so dependent on the software, I’m not sure I could function without it. Although there has been much written about the use of OmniFocus, I have yet to see anyone else that uses the software quite the way I do. In this entry, I’ll introduce you to my OmniFocus set-up. In future entires I’ll demonstrate how I use this set-up to maximize the impact of my work in my personal and professional life.My set-up is an amalgamation of many different things I’ve read online. I’m sure, after seeing what I do, others will continue to build on my ideas.The struggle to keep on top of one’s commitments is not new. Before Getting Things Done and OmniFocus, the go to resource for productivity was Stephen Covey’s First Things First (amazon link). This book suggested breaking down your personal and professional lives into various roles (e.g. Researcher, Clinician, Mentor). Each week, within each role, you were to decide up to three important tasks to accomplish (based on both urgency and importance). Each task could be added to one of 4 quadrants:Covey's QuadrantsThe fact that not all urgent tasks are important, nor are all important tasks urgent was a complete revelation for me. Once I understood this, it was much easier to prioritize my personal and professional life. Per Covey, in order to maximize productivity, one is to spend the majority of their time in Quadrant 2 (Not Urgent, Important). Rather than working on projects haphazardly, Covey recommended spending the vast majority of time focused on Quadrant 2 projects. I choose to define Importance as the project’s impact on my long-term goals.I have blended Omnifocus and First Things First (and a little bit of Agile Programming—but that’s an entry for another time) to develop a system that’s truly my own. In the image below, you can see how I organize Omnifocus. I have four high-level folders: Weekly Priorities, Single Tasks, Projects, and Meta.ProjectsMy Weekly Priorities Folder contains three folders: Maintenance, Weekly Priority, and On Deck. The Maintenance Folder contains all the projects to keep my system running—reminders for my daily, weekly, and monthly reviews. The Weekly Priority Folder contains my weekly highest priority level projects (both personal and professional) I chose during my weekly review. The On Deck Folder contains other important projects—if I’m ultra productive and blast through my priority projects, I look in the On Deck Folder for next tasks to accomplish.The Single Tasks High Folder is self-explanatory.The Projects Folder contains two subfolders: Professional and Personal. Within each of these subfolders I have folders that define each of my professional and personal roles. For instance, my Professional Folder contains the following role folders: Administrator, Clinician, Communicator, Consultant, Fundraiser, Innovator/Entrepreneur, Mentor/Teacher, Researcher, Society Member. Each new professional project is placed within the folder of one of my roles.The Meta Folder Contains my Someday/Maybe project folders (things I’m interested in, but have not yet committed to doing). I also store my completed and dropped projects here.After defining a new project, I place the project into one of my personal or professional subfolders. In the Notes Field of OmniFocus, I use Text Expander scripts to label each project by Covey Quadrant. I then may use OmniFocus Perspectives to quickly locate ALL my projects of a particular quadrant.Window_and_PerspectivesUsing these methods, I am able to juggle a huge number of concurrent projects, each week prioritizing those most important to my personal and professional life. In case you’re wondering, I do most of my heavy lifting / organizing on my Mac. I primarily use OF on my iOS device as reference.In a future entry, I’ll explain how I use this set-up in my daily, weekly, monthly, and annual reviews.

    Using Hazel to Organize Grant and Manuscript Files

    It is almost the beginning of February and thus I am in the throes of writing another grant (2 actually). I thought I'd take a quick break to tell you how I keep my grant information organized using Hazel.I have a folder that has a template for all the subfolders I use during the preparation of the grant. When starting my project I make a copy of this template and name the parent folder including the funding agency, the year, and the type of grant.Folder Template 2Hazel can rename files and subfolders. I take advantage of this feature to keep the names of my files consistent.I navigate to the folder I am working on and set up new Hazel rule to rename the file and subfolders. The rule looks like this:Hazel Script 2Anytime I put a file into a subfolder, it is automatically renamed appending the name of the grant to the end of the file. This appended name is hugely helpful when I go back to search using program such Houdah Spot or Foxtrot.Folder Results 2I use the same method when I'm preparing manuscripts or working on other projects. Using Hazel I never have to think twice-every file I put into the parent folder or subfolder is appended with the name of the project.Try it out.

    Retrieval, Annotation, and Capture of Highlights (2016)

    I have a unique way of processing scholarly information, I am convinced it gives me an advantage when writing grants and manuscripts--allowing me to find specific notes and related information very quickly and efficiently without having to rely purely on memory. I’ve written a bit about this before, but the process has evolved, so I am dedicating an entry to my updated workflow. The software and utlities integral to this workflow are:

    Highlighting in Papers 3Despite lacking the outstanding features of Skim, I am back to reading/highlighting in Papers. I switched back to Papers primarily for synchronization. I do a fair amount of reading on my iPad. Any highlights I make on my Mac become immediately available on iOS. Anyhing I highlight on my iPad shows up on my Mac. Although I prefer Skim, the simplification afforded by doing everything in Papers was irresistable. Here is the manuscript we’ll be working with, highlighted in Papers.highlighting-in-papers-3Export NotesOnce I’m finished highlighting, it's time to process. Within Papers I go to File->Export->Notes and am provided with the following menu box. (1) I usually choose to save the file to my Desktop, as it needs to be easily accessible for processing. (2) I choose "Selected Papers Only" or you I export notes from my whole collection. (3) I choose Plain Text.export-notesFirst Stage of Processing the Untitled Notes File on DesktopHere is the untitled notes file saved to my desktop.first-stage-of-processing-the-untitled-notes-file-on-desktopContents of the unprocessed notes Filecontents-of-the-unprocessed-notes-fileKeyboard Maestro Script to Add Citation + Link and Save FileI have written two Keyboard Maestro scripts to help process my exported notes. The first script adds metadata to the text of the notes file we just exported, then renames the file using the unique Papers Citation. In order to use my script, in Papers, I make sure the correct paper is highlighted. Next, in the Finder, I select the exported note file. I invoke the script and it prepends the unique Papers Citation followed by a Papers Link to the top of the file.keyboard-maestro-script-to-add-citation---link-and-save-fileKeyboard Maestro Script to Add Citation + Link and Save File ContinuedThe script continues on to a save dialogue box where it replaces "Untitled" with the unique Papers Citation. I have to manually remove the curly brackets (as they are disallowed in file naming). I save the file to the Desktop.Download the script here…. You'll have to remove the .txt from the end of the file to use.keyboard-maestro-script-to-add-citation---link-and-save-file-continuedUniquely named Notes File Saved to Desktop.This note I just saved contains ALL of the exported highlights from the manuscript in a single file. As I've talked about in previous entries, I find it more efficient to access a single concept rather than having to dig through an entire papers worth of notes. I developed (along with a few others) a second KM script that copies the Metadata at the top of the note file, parses the single note file into a collection of notes files--one highlight per file, and appends the metadata to each file.Processing highlights in this way has revolutionized my grant and manuscript writing efficiency.Keyboard Maestro Script to Parse Highlights and Append metadata to each notekeyboard-maestro-script-to-parse-highlights-and-append-metadata-to-each-noteDownload the script here…. You'll have to remove the .txt from the end of the file to use.Moving the FolderI highlight the folder on my Desktop, then double click my Shift Key--this invokes a Launchbar action.Screenshot 2015-12-19 16.54.54Launchbar Moves FolderUsing Launchbar I move the text notes to the folder where I keep all the extracted highlights from all the manuscripts I'v read.Screenshot 2016-01-05 11.25.23Ulysses to finish the processAs I've mentioned previously, i use Ulysses extensively in my personal and professional life. I use Ulysses to finish the processing of my highlights, but any text editor will do. (1) Ulysses is pointed to read all the files in my Notes folder--here you see all the individual files extracted from this manuscript. (2) is the text of a single highlight, (3) is the metada added to each file by the KM script. With some notes I will add my own comments, other times, not. (4) are the references that support the statement....these are added manually by reading through the statement and copying each of the corresponding references from the original PDF. I don't go back and forth between the text file and the PDF...instead, I take advantage of Launchbar's Clipboard History.ulysses-to-finish-the-processLaunchbar Clipboard HistoryI merely highlight each reference mentioned, then in bulk I paste each of the references into the note.launchbar-clipboard-historyAppearance of NoteI showed you what this file looked like in Ulysses. Here is its appearance as a free standing text file. Depending on my mood (and time) I may or may not append refernces to each note file.appearance-of-noteCopy PDF to Indexed FolderAfter I've processed everything, the last step is to export a copy of my PDF to a location Devonthink can access.copy-pdf-to-indexed-folderUsing Devonthink to Find Concepts and Related InformationYou may aak yourself why I go to such lengths processing the information I read. The answer is Devonthink. I use the "Artificial Intelligence" of Devonthink quite extensively in my writing. As I mentioned, all the processed highlights, copies of PDFs go into a set of folders on Dropbox. I then Index (not import) the information in these folders (1) so they are "seen" by Devonthink. Why is that important? When I conduct a search (2), I can find the idea I'm looking for (3). By clicking on the "See also" function (4) in Devonthink I can see every piece of related information in my scholarly library (5), including things I have previously written. This ability has revolutionized the way I write.using-devonthink-to-find-concepts-and-related-informationConclusionIn this entry, I have shown you how I read and process scholarly my annotations from manuscripts. Although the process requires an extra ten minutes or so per manuscript, the payoff is immense.Please comment below.