Docear http://www.docear.org/ is a new tool for organising academic literature and writing, a successor to the Sciplore project http://www.sciplore.org/software/sciplore_mindmapping/

I do not do any academic writing at present, and cannot say that I will be testing the software, but I found the following interesting (from the home page):

- Includes: digital library, reference manager, PDF and file manager, note taking and mind mapping.
- Docear works seamlessly with many existing tools like Mendeley, Microsoft Word, and Foxit Reader
- Docear is free and open source, based on Freeplane, funded by the German Federal Ministry of Technology and developed by scientists from around the world, among others from OvGU, and the University of California, Berkeley.

Alexander Deliyannis wrote:

Docear http://www.docear.org/ is a new tool for organising academic literature and
writing, a successor to the Sciplore project
http://www.sciplore.org/software/sciplore_mindmapping/

The video (http://www.docear.org/software/screenshots/ is quite interesting. I've downloaded it and played with it for a few minutes, but didn't completely get it. It's a beta and it seems that parts of the manual are still missing, and it wasn't all that intuitive.

I'm a bit wary of the Swiss knife type approach to writing software. While I'm impressed with efforts like Citavi or Docear that try to capture the entire writing process, I'm reluctant to give up my freedom to assemble my own system of specialist software for the various stages of the process. I guess I worry that it somehow constrains my creativity.

It's not for writing, it's for organizing research files and ebooks. The additional capabilities are there to make it better at the primary function.

There's been a major gap in this space that's been making my head hurt. This might be the solution.

Good find, Alex. Always got your ear to the pulse.

Looks pretty interesting. It would have to go a long way to beat my current setup. When I download PDF files, I drag them into Papers 2.1.17. This program does a pretty good job of dealing with the metadata of the PDF and pulling out the information that I need. You can use Papers as a reference manager like Endnote, but I generally export the PDF files into Endnote that I am working with because most of the people with whom I collaborate don't use Papers(Yet.)

For searching PDF files, I use Devonthink Pro Office. I keep the PDFs in a folder that Devonthink indexes, and I update the indexes once a day or so. Searching in Papers works pretty good, but Devonthink pulls out the exact matches, and also pulls out stuff that is similar. That's pretty handy.

I may give Docear a try, but right now my Crimping is at a relatively low level.

Jim

JB it seems that writing (paper drafting) and word processing is seen as an intrinsic part of the program. From its website:

" Where an office suite bundles several applications for office workers, Docear integrates several applications for researchers, i.e. academic search engine*, file manager, PDF reader*, mind mapping and note taking tool, reference manager, paper drafting, and word processor*."

MindMason also has writing as an intrinsic part of its program. I emailed the company several days ago to ask for its development plans beyond version 4, but have had not response.

Daly

JBfrom wrote:

It's not for writing, it's for organizing research files and ebooks. The additional
capabilities are there to make it better at the primary function.

There's been a
major gap in this space that's been making my head hurt. This might be the
solution.

Good find, Alex. Always got your ear to the pulse.

Dr Andus wrote:

I'm a bit wary of the Swiss knife type approach to writing software.
While I'm impressed with efforts like Citavi or Docear that try to capture the entire
writing process, I'm reluctant to give up my freedom to assemble my own system of
specialist software for the various stages of the process. I guess I worry that it
somehow constrains my creativity.

I'm a bit wary of the Swiss knife type approach to software in general. That said, assembling one's own system implies the interoperability of the components which is anything but ensured. So far I can think of the following de facto 'standards' for information interchange among discrete programs:

- PDFs for reference documents
- Endnote format for citation databases
- IE Favourites and Firefox Bookmarks for collections of URLs
- OPML, tab indented text, MindManager and Freemind format for outlines
- RTF, .DOC(X) and .ODT for final drafts

These leave a lot to be desired, as they don't cover staff like comments and versioning, as well as most formatting and metadata in the case of outlines. There is of course XML, but as long as there are no specific standards, one needs to be a programmer to create the necessary transformations among different implementations.

It would be great if programs could fit together like LEGO, even more like LEGO Mindstorms, but they don't. Then again, even LEGO Mindstorms are made by one single company. In fact, one could argue that a lot of interoperability already exists among several applications under Mac OS thanks to Apple's rules.

I have a dream for such seamless interoperability which can be described with the example below. I would note that there are workarounds to do such work already, but they can get substantially in the way of workflow.

- While doing research on a subject, I collect material from various sources, in HTML, PDF and multimedia form (audio, video and images). My collection tool (let's call it Evernote) can handle them all, always maintaining a link to the original source for reference.
- As I scan the material, I highlight and annotate certain excerpts. The highlighted extras and notes are maintained as virtual notecards (e.g. in Supernotecard), linking back to the original material (local copy and source URL).
- I view my collection of notecards on a virtual corkboard, where I can arrange and group them together (e.g. in Stickysorter or Visual Concepts). Patterns begin to emerge. An alternative would be to organise them in a wiki like Connected text.
- I organise the notecards within each group, e.g. with CRPA, and write an abstract for each group, representing the main underlying idea.
- I view the grouped notecards in my outlining application, e.g. Scrivener. Each group represents a chapter in the high level outline, headed by the abstract.
- I start working on each chapter. I need much more granularity, so I launch Brainstorm or Sense for the actual editing.
- As work on a chapter progresses, I review the chapter abstract and check the updated high level outline for consistency.
- At any time, I can switch back and forth between the various views, which remain in sync.

"I have a dream for such seamless interoperability which can be described with the example below. I would note that there are workarounds to do such work already, but they can get substantially in the way of workflow.
- While doing research on a subject, I collect material from various sources, in HTML, PDF and multimedia form (audio, video and images). My collection tool (let?s call it Evernote) can handle them all, always maintaining a link to the original source for reference.
- As I scan the material, I highlight and annotate certain excerpts. The highlighted extras and notes are maintained as virtual notecards (e.g. in Supernotecard), linking back to the original material (local copy and source URL).
- I view my collection of notecards on a virtual corkboard, where I can arrange and group them together (e.g. in Stickysorter or Visual Concepts). Patterns begin to emerge. An alternative would be to organise them in a wiki like Connected text.
- I organise the notecards within each group, e.g. with CRPA, and write an abstract for each group, representing the main underlying idea.
- I view the grouped notecards in my outlining application, e.g. Scrivener. Each group represents a chapter in the high level outline, headed by the abstract.
- I start working on each chapter. I need much more granularity, so I launch Brainstorm or Sense for the actual editing.
- As work on a chapter progresses, I review the chapter abstract and check the updated high level outline for consistency.
- At any time, I can switch back and forth between the various views, which remain in sync."

Good goal. I already have this.

Any research subject will fit into one of my T2 blogs. Any particular document I'm reading will create a new scratch file. The scratch file will get uploaded to the T2 and digested into the emacs tapes. Later I can consolidate all my research from the T2 to BrainStorm and sort it to develop synthetic categories (i.e. discover a pattern). During this process I will lose the connections between citations and quotes. That's fine. The originals are still there in the T2 and the Emacs tapes, so I can search either to link them back together at the end.

I write rough drafts of pages or chapters in Emacs for max composition speed, and dump them in the T2. Then when I've got enough critical mass and the blog format starts to get confusing, I switch to CT to stitch everything together.

If I need to go back a stage, e.g. do more research, the process is flawlessly recursive. Finished material naturally filters upwards, without polluting the final stages with raw unfinished crap.

And that's... Cyborganize.

JB, as I wrote, "I would note that there are workarounds to do such work already, but they can get substantially in the way of workflow."

As far as I understand, what you describe is done via copy/paste and import/export between programs, which is the same way I (and most others I imagine) do it already. But in the 21st century I want more than that.

My post was not so much for the procedure, but for the interoperability of individual tools as opposed to one Swiss-army knife program .

Oh, right... well in that case I want that too.

But will it ever happen? I don't think so. Alt-tab FTW.

You'll always have to choose between a mixture of dedicated platforms that each do one thing best, or one integrated platform that does most things poorly.

At least in Emacs selecting and copying is a keyboard-only operation. And really, it's minimal overhead even at 10k-20k words per day... and the time spent gives a useful mini-review. Spaced repetition and all that.

There are limits to the amount of material one can output in a day, and you hit those before copy-paste overhead becomes an issue.

Now, if you're trynig to preserve inline pdf comments, or any number of other non-Cyborganize workflows, then yeah overhead becomes a major problem. That's why I stick to plain text as much as possible.

In the meantime I became a fan of FreePlane and had another go with Docear (which is based on FreePlane). It's a promising application but it's not there yet. It is certainly very handy for extracting PDF comments and reading them in one page. I imported a 277-page PDF where I made 629 comments, and it was the easiest way to review the comments. Also, clicking on a comment launched the PDF and opened it on the related page, which is very handy.

However, none of the highlighted text was imported, despite the fact that Docear says "One unique feature of Docear is its capability to import PDF annotations (bookmarks, comments, and highlighted text)." When I investigated further, it seemed that highlighted text can't be imported from any of the known PDF readers yet: http://www.docear.org/support/user-manual/#compatible_pdf_readers (this is on the same page where the previous claim was made).

Plus there are particular problems with importing comments and highlighted text made by PDF X-Change Viewer, which is the app I use. So we'll have to wait and see whether Docear can overcome this hurdle.

Any other alternatives out there for reviewing large amounts of PDF comments and highlights?

Thanks all for an interesting discussion (esp re: the dream of integration; I've been searching for it and thought it was just my failings to find the perfect system that stood in the way?seems it's a problem for everyone).

At least there may be a solution to the extraction/reading of pdf annotations, if that's the correct reading of some comments here. I use Zotero as my reference manager (Open source alternative to Endnote). Very good program. You can place pdfs within it, and an add-on called Zotfile will extract highlighting, underlying and comments that you've entered on the pdf, exporting them as a plaintext file within Zotero (which could of course be pasted into any other document you wish). I've used it only a bit, and only with annotations made in Mac OS Preview, but it appears to work quite well, and does catch things like highlightings.

Happy Hunting!

justinrr wrote:

At least there may be a solution
to the extraction/reading of pdf annotations, if that's the correct reading of some
comments here. I use Zotero as my reference manager (Open source alternative to
Endnote). Very good program. You can place pdfs within it, and an add-on called
Zotfile will extract highlighting, underlying and comments that you've entered on
the pdf, exporting them as a plaintext file within Zotero (which could of course be
pasted into any other document you wish). I've used it only a bit, and only with
annotations made in Mac OS Preview, but it appears to work quite well, and does catch
things like highlightings.

Thanks Justin, I do have Zotero installed but I haven't heard of Zotfile before. I'll check it out.