Looking for good note taking software for research

[v.m.]

Can you share HOW you use DevonThink for academic writing? I'm intrigued by its "intelligence", but I can't figure out how you:
(a) take notes about a PDF file (ie, the notes are somehow permanently linked to the PDF file, not just in a folder together with the PDF)
(b) organize notes - they seem determined to stay in their own alphabetical order

Thanks,
CB

CB-- actually, the blog posts linked at the beginning of the thread are mine. The way I use DTPO has changed, to a certain extent, based on the release of DT2.0, but I'm only just getting into it to see what the changes are. I finished my book and submitted it for review at a press at the beginning of June, and didn't want to change over to beta software until that was finished.

As for taking notes on PDFs, I do a couple of different things. I have long used DT's OCR when importing, sometimes in conjunction with Acrobat depending on how big the file is. My normal method would be to read the pdf in an open window in DT and drag/drop notes into new note entries. This essentially does what you feel circumspect about-- puts notes and the original together in the file structure.

All that can change with DT2.0, though, as files can be worked with in whatever application you might want to use. I think the best way to do what you want would be to use Skim as your default PDF reader from in DT2.0. (Word is, that by the final release the DT guys will include PDF annotation tools.) Skim files are now indexable and searchable by the application.

Functions I frequently use on DT--

Fuzzy search. My documents are 18th c. Spanish language manuscripts. When I transcribe, I maintain original orthography. Fuzzy search keeps me on contact with the many ways a name or a concept can be spelled in the documents, or when I make mistakes of transcription.

Words/Concordance: In looking at documents I will often look at the words, and their relative ranks to determine concept frequencies and the like. This is related, though, to the nature of my type of work.

See also. I have had see also make connections between notes/documents that I had either forgotten or not realized.

My databases for book/dissertation level projects grow to upwards of 2.5 million words in 2-3 languages. I haven't found another database program that is flexible enough and powerful enough to manage all that information other than DT. It's still snappy at packages that large.

I've just started a second book project, on Sex and Empire in the Age of Charles III of Spain. I'm going to be using DT2.0 for it, and likely Skim for pdf note-taking. I'm also going to integrate, in a form, Zotero's web interface for citation management. Zotero 2.0, once it's out of beta, is supposed to have formatted citations through its web interface which will be excellent.

 

[Scylax]

Circus Ponies Notebook?

I've only just got this so I don't know if it can do exactly what you need, but you mention one note so I really think this is worth a look. It's in the Apple online store, and it's not to expensive. Also have you checked out Story Mill? I know it wasn't made for Academia, but if you've looked at Scrivener I think you should check it out. Again, it's in the Apple online store.

 

[Michaelgtrusa]

They are all great apps. I'll need more time before i'm comfy with the apps I have before I can use DT.

 

[Michaelgtrusa]

Curio is awesome and I just bought a license for it this morning! I'm using it for brainstorming and project planning and am finding it absolutely fabulous. Just the mind-mapping alone moved my writing forward by a huge jump over the weekend and inspired several new research project ideas. The way that dates in to-do lists are automatically filled in is a life-saver, and the ability to spread ideas in many forms (text, photo, scribble, files) across a white-board is incredibly helpful for guiding my thinking and writing.

However, it doesn't do any better than the others here for organizing research notes. It doesn't keep the notes linked to the PDF if you rearrange the notes. It doesn't have a field for saving the reference info. So, it's valuable, but still not quite what we academics are looking for.

Thanks though
CB

Have you noticed that when you close Curio without having a project, that it moves a 4 kb file to the trash?

 

[cricketbird]

Settled on Scrivener

After much looking around, I decided to go with Scrivener. It's not perfect for this purpose, but it's as close as I can get with the long list of software I've now explored. As a plus, it's a very useful writing tool in addition to its note-taking abilities. I had a steep learning curve where I resisted a lot of what Scrivener had to offer, but now I'm starting to appreciate it more and more. If the developer can fix my bulk-change woes and add Zotero compatibility, it might actually be perfect for my needs.

Here's my über-detailed workflow for taking and using notes in Scrivener:

First, I drag the PDF I want to take notes from into the Binder pane, under the "Research" category.
Then I use Scrivener's split-pane view, split horizontally. I set the top pane to display the PDF I want to take notes on, and the bottom pane to "corkboard view" the same PDF document. I like to just have one row of 3 cards visible in the bottom pane, and have the top pane (the PDF) take up most of the screen. I zoom the PDF (Apple Shift +) to make the PDF as big as possible. I usually hide the binder, and often the inspector as well, to get something akin to "full screen" mode for minimum distractions.

I take notes in the bottom pane by creating a new card for each note. This is very close to good-old-fashioned note cards. I take notes entirely using the keyboard (no mouse) with the following set of keystrokes:

<RETURN> (creates a new card - but see the setting in preferences)
type title text - a few key words to remind me what the note is about
<TAB> (to jump to the body of card)
type note text
<RETURN><RETURN> (to create a new card)
etc.​

I use the fun free-ware app "Skitch" to take snapshots of figures and tables from the PDFs that I want to capture, but the Mac's built-in screenshot shortcut also works fine for this. The images show up along-side the cards.

You can also set labels, status, and keywords for each card. I replaced the built-in labels with the type of note I'm taking (methods, ideas for my own research, factoids, to do, questions) and have Scrivener set the color of each card to the label color. That way I can quickly pull out all the cards with ideas for my own research (for brainstorming in Curio), or all the different methods I want to consider, etc. I'm not currently using the status flags, but I can see how those would be handy. You can add keywords in the inspector as well, and I'm just beginning to use those.

Where Scrivener (and every other note taking application I've looked at) fall down is that there is no easy way to add reference information to large batches of notes at once (ie - you've just spent an hour taking 30 notes on a paper and want to now tag them with the paper's reference info). My somewhat laborious solution is to enter the citation info in one card's "Document Info" area, then copy and paste the citation one-by-one into each of the other cards' panes. What a pain. I sure wish the developer would come up with a way to do a batch change (or, if preferred, a batch-append feature)! You could also use Scrivener's included reference system by dragging the references into the Project References tab (be sure to note the difference between Document References (for the one card) versus Project References (your library of references) in inspector pane, but it's basically the same laborious one-by-one process and I'd rather use my own external reference manager.

When it's time to write, I take all the cards and put them in one folder (but I still know where they came from because I put a reference on each one). Then I can group, sort, etc. to my heart's content. For the writing itself, I do a vertical split of the window, with my blank document in the left-hand pane and the cards on the right-hand pane (in corkboard view) . This way I can write, referring to my cards for their info and references.

This is working out quite well for me. Hope it helps some of you. And if there are any programmers out there - here's a golden opportunity for some much-needed software.

CB

 

[vbigelow]

Still Haven't Found The Magic Program

I have tried all of the suggested programs and I still don't think we've come close to identifying one or two that really address the original concern.

 

[entatlrg]

Any new finds in the last 6 or so months?

 

[skydancer007]

Anyone used the old Papyrus software?

I used to use the Papyrus software package and it was the best I've ever used for organizing and retrieving notes. I tried to download it today, but it does not run on my INtel Mac-- it was made for the Classic environment. This is really too bad, since I haven't found anything as simple or efficient to use for research notes.

 

[ansatzjp]

..........

 

[tursiops]

another possibility

Some time has passed since the last post, but have you tried Sente? You can highlight PDF's, take notes, take snapshots of graphs, extract direct quotes and attach your notes to them, etc. In the end, you can Preview "Annotated bibliography" and voila, all notes from the document, direct quotes, snapshots, quotes with notes attached, etc appear in one document with all the reference information at the top.

In my workflow I paste the annotated bibliography I do in Sente for each article into Scrivener's research section, so I can keep all the direct quotes, graphs, quotes with notes attached, etc. that I'm going to use in my paper after a very necessary first "filtering" process (Sente separates each note/snapshot/highlight with a title and the page in the original document where it came from, a beautiful feature, I think). I simply copy and pasta the APA reference info that comes with the annotated bib for the article into the title of the Scrivener research document in question, so it stays organized within the research section also.

Because I like to be able to search each individual snippet of text according to tags, I use keyboard shortcuts to highlight and import each individual snippet that I'm using as a direct quote from Scrivener into Evernote. Because the title of the document in Scrivener is the APA reference info itself, each note copied into Evernote carries that title, and therefore the reference info itself without me having to type anything into it. All I do is add at the end the page number Sente so kindly provided for organization purposes, and then tag the hell out of it. Once you know the keyboard shortcuts is a rather quick process.

When I want the direct quotes related to (say) "fishing," "tuna" and "global warming" while I write in Scrivener a particular section, I select those tags in Evernote and voila...all the snippets from 170+ articles tagged with those terms appear. If I want to go back to the source of one of those I look at the reference and consult it and my longer notes in Scrivener, since I am writing right there. In the rare occasion in which that is not enough to clarify something I may go back to the source in Sente and re-read, but that is rare.

Lately, with the integration of Evernote and Curio I've also been using Curio to organize some of my more complex arguments in a board with direct quotes etc...

Does that help with your initial query?

 

[cricketbird]

Hi tursiops,

What you've suggested (ref manager (I use Zotero, but the functionality is similar) --> scrivener --> evernote) sounds cool, especially if you can keep the reference info attached seamlessly throughout. But as I understand it, it still doesn't solve the problem of organizing factoids into a writing order - they'll still be stuck in some sort of alphabetical order, right?. I'm intrigued, though. Can you post screenshots? I'd love to see this in action!

CB

 

[tursiops]

screenshots

You can simply add the section of your paper BEFORE the reference title on evernote, or simply (the better option I think) add it as a keyword (you search for "Introduction" would show all notes with that "keyword." Attached are my snapshots of the process...hope it helps!



Here you see Sente with a reference open as PDF, Highlighted and some of those highlights as notes on the sidebar...No comments below them here, although you can do that if you want to



Here you see the "annotated bib" window of Sente, with reference info and page # for each quote. You select all and copy to add to scrivener.



Here you see the scrivener page, with annotated reference added under reference section (title on top) and my second reading, highlighting, notes, etc. for specific project.



Here you see the clipping window from evernote on top of scrivener. I select the quote on scrivener, control-c to "copy," control-command-v to clip to evernote. It appears with "Dissertation (the project in scrivener in front of the reference). I delete that, add the page number at the end and add my keywords (easily, as evernote autocompletes according to what you already have...if they are new, you'll have to type the whole thing, obviously)



Last one...Evernote with various snippets from scrivener. You'll see the list of keywords on the side so. Additionally evernote searches ALL text if you want it too.

 

[pablocl]

Notes linked to the reference the arer from

Hello Criketbird. I just read your message about how to take notes to a document lynked and that was exactly my obsession with search over the past 3 years. I tested Sente, Papers, Skim, Bookends, Devonthink (perhaps too complex), Evernote, etc ... etc ... and countless more software. Wanted exactly what you commented, note taking software that allows lynked to a separate document ... for me that would be like a dream. Imagine the speed with which one could write an article. I am a professor at the University of Seville, deel Department of Physical Education and Sports. I wrote several emails to the designers of Papers, and tell me that they plan to do it later. Since I said that's not a day goes by without visiting their website with the illusion that they have released version that includes it. I have recently seen a video that explains how you can work together with papers and Evernote, but I study it more carefully. Have you found anything better? I leave you my email if you do not mind me at it. I thank you in advance for your help. A greeting
Pablo Camacho
pcamacholazarraga@gmail.com

 

[SlowMotn]

Solution Found

I tried all the tools in this forum and others - to no avail. But then I thought about how to use Scrivner differently. Scrivener is the tool to use to achieve the problem of: making each individual note to be organizable into a paper flow but still linked to the reference they are from.
--------------------------
1. Take Notes Like you usually would, organizing each sub-document in Scrivener, organized by source.

2. Write the bibliographic source citation info in the document notes side pane (very important step)

3. go back through your original notes and split the documents (document > split) - this will create a new document with your selected text. This new text will maintain the source document source citation from the previous document you just split. (This is the main trick.)

4. Rename the new sub-document

5. Place the new sub-document into a folder structure that creates your outline.

6. Rinse, Wash, Repeat.