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The love-child of Adobe Reader, EndNote, and Evernote

May 2, 2010

I used to have the dirty habit of printing PDFs of medical journal articles to read and take notes on when researching for a paper. Of course, this is a huge waste of paper and I would end up looking like an idiot walking around with a giant stack of papers.  I don’t do this anymore.  I have more or less gone paperless.  I still download PDFs of journal articles when researching.  I can’t stand HTML formating of articles, especially when you have to click on a link to see a table or figure.  Hey, medical journal editors, why can’t you figure out how to insert images into your HTML?  I can do it on my blog, but the New England Journal of Medicine can’t figure it out.  The only advantage the HTML version of an article offers over the PDF is that there are (typically) direct links to source articles (but really this should be part of the PDF as well).

My preference for journal article reading isn’t the point of the post (sorry to get off on that rant).  This point of this post is to express my frustration with Adobe.  Adobe, you have created a great thing with PDFs and your widely distributed PDF reader.  But, you could do so much better.  A simple tweak and you could really be embraced by the masses (even more so than you already are).  Here is all you have to do–setup Adobe Reader so that I can essentially add a “layer” on top of the original PDF where I can highlight (multiple colors are essential here) and place “pins” anywhere in the text that allow me to add notes and be able to save all of this.  Oh, and add a button so that I can turn highlighting and notes on and off.  I mean, is this too much to ask?

I know there is software out there that does this (or something very similar).  Any suggestions for good, cheap programs to do this would be helpful.  BUT, Adobe, really, you should have this as a standard part of your free version of Adobe Reader.  God forbid a software company do something to help its users.  Instead, you’re just encouraging people to download pirated copies of your software (because it’s so ungodly expensive) or go to your competitors.

To take this another direction, if you’re a software developer, LISTEN UP.  More and more medical researchers (and probably many people in other academic fields) are reading and managing their journal libraries electronically.  BUT, there isn’t a single, good piece of software to effectively do all of this.  You have to have a PDF reader to download the articles and read them AND a citation management program to organize and collect all of your journal articles (think EndNote).  And neither of these pieces of software can do the highlighting and notetaking mentioned above.  So, here is what you need to design–a citation/bibliographic management program with an integrated PDF reader that allows you open the PDF, make notes and highlight, and save the PDF with the notes/highlighting is a separate “layer” above the PDF so they can be turned on/off.  And you need to be able to insert citations into Word documents while automatically generating a bibliography at the end of the document–EndNote actually does a fantastic job of this and however their system works shouldn’t be messed with too much.  And the last thing, no folders for organization–only tags (ala Gmail and Evernote).  Frequently, a single paper is relevant to multiple research projects, so labeling a single paper with ProjectX and ProjectY would allow me to see (and not have to remember) that specific paper relates to both projects.  Why do we even have “folders” anymore?

Essentially, what I need is the love-child of Adobe Reader, EndNote, and Evernote. And, if you want to get really fancy and fulfill all my wishes, everything needs to be stored or synched across any device (Evernote does this really well) so that when I grab my iPad* to go to a conference and have some down-time between talks I can access my background research for my next paper, highlight important points and take some notes, save all of it and bring it back up on my home computer when I get back and start writing.  (If Microsoft was smart, they would buy up EndNote and Evernote and incorporate all of this into a single integrated program with Word and sell it as an add-on to MS Office.  Microsoft, DO NOT DO THIS!  You seem to have an inexcusable knack for half-assing software.  You get about three-quarters of the way there and then add the most infuriating quirks that nobody can figure out–see OneNote for dozens of examples of this.)

As somebody who does a lot of researching and writing  who thinks paper is wasteful and impossible to organize, I would actually pay decent money for this piece of software.  And I’m guessing that if you executed this software really well, universities and research labs would pony up for high priced institutional licenses (like they do for EndNote).

Or does this magical software already exist and I’ve just missed it?

*I don’t own an iPad.  But by the time somebody gets around to creating this beast, I will hopefully have one or another similar tablet device.

2 Comments leave one →
  1. May 5, 2010 1:46 am

    I’m a scientist too (finishing PhD in Microbiology),
    the program you request exists!
    “Academic software for bibliography creation and research paper management by Mendeley.”
    the only option I’d like to see is to be able to search your notes on pdfs

  2. June 27, 2010 12:11 pm

    Have you checked out Papers (Mac iPhone iPad). It does what you asked for and I
    Have found it indespensable since it came our. It does not do reference insertion, a la Endnote so you still need that if you are going to have more 10-20 references in a paper.

    I think what is also missing is a “Pulse” for docs and scientists to keep up with the literature. There is no decent solution that also makes it fun. If you are interested in collaborating on one, let me know. All it takes to succeed is someone foolish enough to think it is easy.

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