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Author Topic: Basic Use
Eddy-
Morrow
Newbie
Posts: 2
Post Basic Use
on: February 1, 2013, 22:21

My innate talent to readily understand how to use Docear with my existing pdf and other document collections has hit a major roadblock. I just don't get it. Does anyone have advice on how to take a huge collection and integrate it into Docear?

How do I even begin?

Am I supposed to take all of my docs and import or cut and paste them into a new folder that is dedicated to the literature repository?

Any help would be appreciated. I've tried the basic tutorial and I feel just as lost as before I started. Docear along with Mendely look like a decent system and I'd like to give Docear a go .. but I am missing a piece of the puzzle to get back on the learning curve.
Thanks

Eddy Morrow

Graduate Student Library & Information Science
B.S. Microbiology, B.A. Clinical Laboratory Science

Thank you for your feedback. Please note that we - the Docear team - currently do not have the time to answer support questions. However, we encourage all Docear users to help each other.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Basic Use
on: February 4, 2013, 13:36

Hello Eddy,

Docear is still a very new project and we are going to improve the whole workflow and the user interface in the next weeks and months. That's why we have not created a good tutorial by now.

To get started you should define your workspace and either define the literature repository to point to the folder where you have stored your all of your literature (i.e. papers, books, ... in PDF format) or copy your PDF files into the workspace's default folder.
You can later change these information by right-clicking the workspace root node and selecting "Change library paths..." from the context menu.
Image

After that you can start reading and annotating your PDF files. For this we highly recommend you to install and use the PDF-XChange Viewer, but you can also use the Foxit Reader or Adobe Acrobat. After you have created annotations (notes, bookmarks, and if you use the PDF-XChange Viewer even highlighted text) in your PDF files, please open the "Incoming" map from the workspace panel on Docear's left side.
Please hit the refresh icon which you can see on the root node. Docear will immediately start to import all annotations you have created in your PDF files. If you change the text in your PDF files, changes will be propagated back to your mind map after updating it the next time. If you change the text of an imported annotation, the annotation in your PDF file will be updated as well.
By clicking the small red arrow above a node of an imported annotation the PDF will be opened at the location where you have created the annotation.

The Incoming map is only intended as a repository for any information you found useful, but which you have not organized yet. Please open another Library map (e.g. "Literature and Annotations"). You can easily switch between the two opened mind maps by using <Ctrl>+<TAB> as a shortcut.
You should now cut the nodes from your Incoming map and post them here. Here you can organize them as you may see fit.
If you update your Incoming map now, it will be empty because you have used all of your annotations in the other library maps. If you read new papers and annotate them, only the new (and that's why unused) annotations will be imported to the map. This helps you to keep track of your information.

After organizing your information in the Library maps, we, that is the Docear team, like to create a new mind map for every scientific paper we want to write. We create the outline of our paper directly in the mind map, with nodes on the first level representing chapters, nodes on the second level representing sections, etc.

We then add the necessary information from our library maps to the right place and add our own ideas, notes, images and even sentences directly to the map. You can collapse nodes you are currently not working with and change the whole structure of the document easily by dragging and dropping for instance your "section nodes" to another node of the outline.
After structuring your ideas inside of the mind map you have all the information you need in one place to actually write your paper.

In future versions of Docear we will greatly enhance this step. You will be able to export the mind map to a LaTeX, Microsoft Word or Libre/Open-Office document. The chapters and sections will be created automatically and your notes, images or sentences will be added to the right place inside of the document. A bibliography will be added from the information you have stored in Docear's integrated reference manager (JabRef) on the right side. But that's nothing we will be able to implement in the next weeks or months.

If you have more questions please let me know. I know that Docear is still a little bit confusing right now but we are working on it.
I hope this helps. Welcome to Docear. 🙂

Cheers,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Kyle
Newbie
Posts: 2
Post Re: Basic Use
on: February 4, 2013, 13:56

Hi

In future versions of Docear we will greatly enhance this step. You will be able to export the mind map to a LaTeX, Microsoft Word or Libre/Open-Office document. The chapters and sections will be created automatically and your notes, images or sentences will be added to the right place inside of the document. A bibliography will be added from the information you have stored in Docear's integrated reference manager (JabRef) on the right side. But that's nothing we will be able to implement in the next weeks or months.

I am so sorry to read that, because this was the main feature i was looking for. Creating mm and oraganizing ideas and references is a nice thing, but at the end i need an output. So if i understand it well i have to manualy copy everything from mm to a document. Isnt there a workaround for that for now? Because i experimenting with docear now and i see i can draft a paper with it and also i can have anotations/highlights/bookmarks exported to latex but the reference is missing.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Basic Use
on: February 4, 2013, 14:08

Hello Kyle,

I am sorry, but apart from the currently implemented LaTeX export there is no such feature yet.
For now you can only organize your ideas and information extracted from literature repository.

Maybe you can use the BibTex file from Docear's integrated reference manager?

Cheers,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

Kyle
Newbie
Posts: 2
Post Re: Basic Use
on: February 4, 2013, 15:02

Thanks for quick response.

The LaTeX export was just an example, its not so important which file format. I prefere doc, docx, odt, tex or txt. I tried almost all export methods and i noticed the odt also include path to pdf. I found the xslt DIR in docear where are the files responsible for exporting. I want to ask you if its possible to edit them so i can export at least titles of articles.

Btw i want to thank you and the docear team to create such a nice piece of software. It really opens new possibilities for effortless academic research. Keep up the good work and i hope we will soon see the full-blown export feature in the near future.

Eddy-
Morrow
Newbie
Posts: 2
Post Re: Basic Use
on: February 5, 2013, 09:45

Thanks. I'll keep plugging away at it.

On earlier attempts to figure this out I ended up with a mindmap that managed to contain all of my PDFs on one map. Maybe 400 some odd pdfs. This was way too much info crammed on the map for me to even begin culling, collating, organizing, etc. Hench the confusion and my thoughts that I am doing this wrong.

Can I use Docear to manage my PDF library? Or is it really suited for single projects not to exceed X number of documents? (This isn't my impression.) I'm certain I need to only optimize how Docear parses my PDF library.

Can I create folders within the literature repository where I can link to folders containing papers from each of my classes? Can this be done by having each "folder" in the literature repository monitor a different folder?

In my windows documents folder I have a folder named LIS and within this is a folder for each of my classes and projects. PDFs for a given class or project are filed into the specified folders.

Thanks again for your help.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Basic Use
on: February 11, 2013, 09:53

Hello guys,

@Kyle:
As far as i know you can edit them. But this is a feature of Freeplane so I don't know for sure.
If you need help with this task, it's probably a good idea to ask the Freeplane team directly. They are very nice guys and they always respond to a user's questions in their forum:
https://sourceforge.net/apps/phpbb/freeplane/viewforum.php?f=1
Btw, thanks for your encouraging freedback! 🙂

@Eddy:

Can I use Docear to manage my PDF library? Or is it really suited for single projects not to exceed X number of documents? (This isn't my impression.)

We use Docear to organize our work with more than a thousand PDF files. You can use sub folders in your literature repository as you like. They will appear as children to the root note of the Incoming map when importing the literature folder.
The idea of the incoming map is only to serve as a temporary repository for new and unorganized information. When importing annotations from your PDF files, Docear can only list annotations but does not know how you want them to be organized.

I would suggest you to create different mind maps in your Library (mind maps attached to the Library node of your workspace tree). They can be named after the different topics you are working on or in any other way you want them to be. Now you should think about the structure you want to organize your PDF files and annotations in. Please cut them from the Incoming map and insert them into your created Library maps.
Any information you don't need you should move to the "Temp" or "Trash" mind map.

After re-importing your Literature folder, your Incoming map will stay empty until you create new annotations in a PDF document inside of one of the sub folders of your literature repository.

Please also notice that you can collapse or expand any trunks in your mind maps by selecting a node and hitting the <SPACE> bar. There are icons in the top bar of Docear to collapse or expand all nodes, which makes life a lot easier when working with large mind maps. Since the root node can't collapse it's children this feature is especially useful when you have organized your ideas in your library maps.

If you have any more questions or if you need help with one of the things described above, please let me know.

Best regards,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

ZetaSeeker
Newbie
Posts: 6
Post Re: Basic Use
on: September 6, 2013, 15:32

Hello,

I realise that this is an old thread, but I would like to ask a question directly about the last post here from Stefan.

My question is, how do projects fit into the workflow above?

Specifically, I have all my pdfs in one large repository and I have a mindmap which is broken down into

Books, Papers, Theses, Application Notes.

I like the idea of having a central repository for ALL my pdfs which is easy to search, and I also like the idea of having separate project folders for all my future projects. However, it seems to me that this is the wrong way of looking at a 'project'.

Could you give an example of a workflow using projects?

Many thanks for the great work.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Basic Use
on: September 12, 2013, 12:43

Hello ZetaSeeker,

I strongly recommend you to only use one project with e.g. multiple literature repositories.
Projects are a new concept mainly designed for the Collaboration feature we are going to implement. With this feature you will be able to synchronize your projects with our server and even share your projects with colleagues. This will enable you to work with colleagues on the same mind map at the same time.
However, that's a huge project. It will take us a lot of time.

Projects can also be used if you are working on fully distinct research fields.

If you have any more questions, please let us know!

Best,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

ZetaSeeker
Newbie
Posts: 6
Post Re: Basic Use
on: September 19, 2013, 15:58

Thanks Stefan,

I didn't see you had replied, but I did set up my project in the way you have described. I like the new literature and annotations map - I keep a copy of every article there organised by format(e.g. paper, application note, thesis) and then topic. I create a new map for every project, and I periodically check the incoming node of the literature and annotations map to see if there's anything I've highlighted or commented that I have not yet pulled into my work. Since switcing to Docear I have a much better idea of what's in my library and where to find it, and I have found it easier to capture and link ideas.

Thanks for all your hard work!

Huw.

Stefan-
[Docear]
Administrator
Posts: 969
Post Re: Basic Use
on: September 23, 2013, 14:05

Hello,

and thank you very much for your nice words.
After releasing Docear 1.0 we will create some useful documentation and tutorial videos in order to let you know about all the hidden potential of Docear.

We are working hard to support every aspect of literature management a researcher might be interested in. Here are a few examples:

  • Searching for Literature and suggesting useful literature based on your field of work (that's also one of our major research topics (see: http://www.docear.org/docear/our-publications/)
  • creating and importing annotations
  • organizing imported annotations together with your own ideas
  • synchronizing your work and collaborating with your colleagues (a feature we will begin to work on soon)
  • organizing your references and paper metadata extraction
  • drafting new papers
  • and even writing your own paper (for now with the help of Docear4Word http://www.docear.org/software/add-ons/docear4word/overview/)

We have a lot of ideas how to improve the situation for any researcher out there. And we have just started. 🙂

If you have any ideas or suggestions, please let us know!

Cheers,
Stefan

Stefan Langer
Product Management & Research
Docear - The Academic Literature Suite
http://docear.org

Facebook: https://www.facebook.com/pages/Docear/137985949605902
Google+: https://plus.google.com/106965732112113749959/posts
Twitter: https://twitter.com/Docear_org

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