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highlightsapp

macrumors newbie
Oct 23, 2014
3
0
I am doing PhD in biophysics and I ended up developing my own app for doing literature reviews, so this is going to be somewhat of a plug. I basically wanted an app that could translate between PDF annotations (highlighting, notes and images selections) and Markdown which I use for all other types of note taking. The app basically reads a PDF and extracts the annotations. It can fetch metadata using DOIs and embed it in the PDF attributes. You can add PDF annotations and have them extracted in real-time. The comments you add in Markdown are saved back to comments in the PDF. In addition, you can have it look up references in the PDF by underlining them so you can easily go through the bibliography. Unlike how most reference managers deal with PDFs, there is no "PDF annotation lock-in" and you can export your notes to plain Markdown and HTML or directly to Evernote and DEVONthink.

The app is called Highlights (highlightsapp.net) and is available on the Mac App Store now:)
 

Cubytus

macrumors 65816
Mar 2, 2007
1,436
18
I am doing PhD in biophysics and I ended up developing my own app for doing literature reviews, so this is going to be somewhat of a plug. I basically wanted an app that could translate between PDF annotations (highlighting, notes and images selections) and Markdown which I use for all other types of note taking. The app basically reads a PDF and extracts the annotations. It can fetch metadata using DOIs and embed it in the PDF attributes. You can add PDF annotations and have them extracted in real-time. The comments you add in Markdown are saved back to comments in the PDF. In addition, you can have it look up references in the PDF by underlining them so you can easily go through the bibliography. Unlike how most reference managers deal with PDFs, there is no "PDF annotation lock-in" and you can export your notes to plain Markdown and HTML or directly to Evernote and DEVONthink.

The app is called Highlights (highlightsapp.net) and is available on the Mac App Store now:)
Sorry, doesn't work on the more compatible Snow Leopard. I'll pass.
 

skaertus

macrumors 601
Original poster
Feb 23, 2009
4,243
1,398
Brazil
Thanks so much for the comments on my blog. Unfortunately, I can't keep it up anymore, but if you'd like to write a guest post, please feel free.

Thanks for the invitation. Perhaps I can take some time to write a post or two.

To the bold? I don't know. I do have a tendency to spread across what is probably too many apps. I'm thinking about how to simplify my workflow, but when it comes to cutting out apps, I always find that I drift back to them after a while. The ones that have a stable role in my workflow are Scrivener, Bookends, EndNote, DevonThink and CPN. Everything else varies a bit :) And Word, of course, for finalising papers, but that's really only out of necessity.

In terms of formatting, I just do most of it in Word towards the end of the writing process and keep things as simple as possible up to that point. I work with unformatted EndNote references until I'm in Word.

I'm definitely not returning to Windows as my main writing app. I only work on a mac and I find MW 2011 for mac generally annoying, and use it as little as possible. But since I work in a Windows environment, as little as possible is quite regularly.

Lately, I have been using Word and Endnote to update my thesis for publishing. DevonThink is being very useful as well. Perhaps I try something different after I finish.

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I am doing PhD in biophysics and I ended up developing my own app for doing literature reviews, so this is going to be somewhat of a plug. I basically wanted an app that could translate between PDF annotations (highlighting, notes and images selections) and Markdown which I use for all other types of note taking. The app basically reads a PDF and extracts the annotations. It can fetch metadata using DOIs and embed it in the PDF attributes. You can add PDF annotations and have them extracted in real-time. The comments you add in Markdown are saved back to comments in the PDF. In addition, you can have it look up references in the PDF by underlining them so you can easily go through the bibliography. Unlike how most reference managers deal with PDFs, there is no "PDF annotation lock-in" and you can export your notes to plain Markdown and HTML or directly to Evernote and DEVONthink.

The app is called Highlights (highlightsapp.net) and is available on the Mac App Store now:)

I envy those people that write their own apps when they find out the current ones are not suitable for them...

By the way, your app looks nice.
 

Cubytus

macrumors 65816
Mar 2, 2007
1,436
18
Wow, Snow Leopard? Is that due to hardware or are you running software that requires 10.6?

Definitely your second hypothesis. I need compatible and standard unix tools that went dumbed down in subsequent versions. As well as Rosetta.
 

skaertus

macrumors 601
Original poster
Feb 23, 2009
4,243
1,398
Brazil
Which reference manager do you use, by the way? I have Endnote and Bookends, and both work nicely.

I was just testing Citavi and Biblioscape for Windows and I notice both have evolved a lot. Both have a Word plug-in that adds a sidebar in Microsoft Word, and I can search and insert citations using this sidebar.

This is the feature in Biblioscape:

word2007_ref.jpg


And this is the one in Citavi:

101_creating_a_publication_with_word-9.png


These add-ins look very handy. However, I have never seen such a feature implemented in any reference manager for Mac. The closest is perhaps the Mellel and Bookends integration, but that works differently and only because that Mellel has such support built-in.

I don't even know if it is possible to add such add-ins to Word for Mac or to Pages, for instance.

Does anybody have any insight on this?
 

jojoba

macrumors 68000
Dec 9, 2011
1,584
21
I am doing PhD in biophysics and I ended up developing my own app for doing literature reviews, so this is going to be somewhat of a plug. I basically wanted an app that could translate between PDF annotations (highlighting, notes and images selections) and Markdown which I use for all other types of note taking. The app basically reads a PDF and extracts the annotations. It can fetch metadata using DOIs and embed it in the PDF attributes. You can add PDF annotations and have them extracted in real-time. The comments you add in Markdown are saved back to comments in the PDF. In addition, you can have it look up references in the PDF by underlining them so you can easily go through the bibliography. Unlike how most reference managers deal with PDFs, there is no "PDF annotation lock-in" and you can export your notes to plain Markdown and HTML or directly to Evernote and DEVONthink.

The app is called Highlights (highlightsapp.net) and is available on the Mac App Store now:)

This looks interesting. Could you expand on how this app differs from Skim, and from apps like GoodReader and iAnnotate for iPad (apart from extracting DOI info)?

I don't even know if it is possible to add such add-ins to Word for Mac or to Pages, for instance.

Does anybody have any insight on this?

It's a while since I looked at this now, but I remember getting to the same conclusion as you - it looks really interesting, but isn't available for mac yet. I hope it will be in the future.
 

skaertus

macrumors 601
Original poster
Feb 23, 2009
4,243
1,398
Brazil
It's a while since I looked at this now, but I remember getting to the same conclusion as you - it looks really interesting, but isn't available for mac yet. I hope it will be in the future.

Yes it does.

These two pieces of software – Citavi and Biblioscape – are not available for Mac, as they are both Windows-only software.

Software which is available cross-platform – Endnote, Zotero, Mendeley, Papers – do not have this kind of functionality, as far as I am aware of. Mac-only software – Bookends, Sente, BibDesk – do not have this kind of function either.

I wonder why this kind of add-in is not available for the Mac. Is that because the specific software that contains these add-ins (Citavi and Biblioscape) are not available for the Mac? Or is it some sort of limitation of the Mac platform, that does not allow these kinds of add-in?
 

Cubytus

macrumors 65816
Mar 2, 2007
1,436
18
What is massively different in these two software? Ability to see details while typing?
 

skaertus

macrumors 601
Original poster
Feb 23, 2009
4,243
1,398
Brazil
What is massively different in these two software? Ability to see details while typing?

These sidebars only exist in these two software. They are not available in other software, nor in any software for Mac that I am aware of. These sidebars provide functionality that allows the user to search references, while this can only be done via a pop-up menu in Endnote, for instance.
 
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