I spent a couple of days researching on options how to use mindmaps to ogranize ideas related to (scientific) papers and plan research activities. It seems that Docear project http://www.docear.org is the only option currently available. Cooperation between Freeplane and Docear dates back to 2011 (https://sourceforge.net/p/freeplane/discussion/758437/thread/1e194ded/?limit=25#f28d).
Unfortunately, the main developers have to considerably decrease their activities in that project and shift to other projects to make living. This one can clearly see from GitHub commits https://github.com/Docear/Desktop/commits/master ; the last commit of the main developer dates back to August 2014. Being a researcher I find it very unfortunate that the development of Docear project stagnate. Below I would like to propose/discuss some possible solutions and alternative workflow for JabRef + Freeplane.
Docear had a big goal of doing academic literature management in general (organize, create, discover academic literature; a literature suite concept, recommendation system, etc). Docear is built on Freeplane and (a modified version of) JabRef. To my understanding the developers had to substantially modify JabRef to play nicely within Docear interface and fulfil numerous goals. As a consequence, JabRef 2.7.1. is used within Docear and it is not-trivial to update to the newer versions.
Among the many features Docear aimed at delivering, the core and the most important ones for me (and possibly for others) would be those, related to integration of Freeplane with JabRef, i.e. mind mapping and scientific literature manager. Roughly, i would say the following features are must haves:
1) a way to add a paper to the mind map with bibtex attributes (key, title, journal, year, link to the .PDF file).
2) if the node is a "paper", look at PDF and fetch all comments as child nodes.
3) export to LaTeX with \cite{abcdKye} for papers.
The first one can be achieved in the following workflow. When a user clicks Copy in Jabref, the BibTex data of the paper is copied to the buffer, e.g.
@Article{abcdKey,
Title = {Super Paper},
Author = {Jim Genius},
Journal = {Nature},
Year = {2015},
Number = {1},
Pages = {127--155},
Volume = {43},
File = {:path/to/file.pdf:PDF},
Keywords = {keyword1, keyword2},
Publisher = {SIAM}
}
I think one could Copy-Paste that info into Freeplane as a (free?) node by means of some scripts/plugins (sorry, don't know much about Java and/or GUI, I am a C++ guy) with BibTex (Title,Author,Journal attributes) stored in attributes and a link to the pdf file. That looks feasible for me.
Regarding the second, Docear was more complicated. As far as I understand, they assigned some IDs to see if a particular comment, stored in PDF metadata, has been imported yet or not. If it was not, it will be added to a given node as a parent. Additionally, they had a jump-to-page feature. None of those is a deal-breaker, IMHO.
If Docear developers could point out to a piece of Java code which did scanning of the PDF for notes, i think it could be simplified just to import all the notes found in the PDF as child nodes in Freeplane. This, of course, is not as elegant as the approach pursued in Docear, but will do the job.
As for the third one, in Docear manual it is written that there is an export filter “latex input with cites and details”. So it seems this feature is implemented already, but I could not find it within Docear. I suppose this filter could be used straight away in Freeplane.
1), 2) and 3) are absolutely independent. If I would be to rate them, i would say 1)+3) are the most important. In the current version of Docear 2) does not work much on OS-X anyway.
To sum up, the idea is not to re-do Docear, but adopt a few core ideas in a more flexible workflow (as plugins/scripts) allowing the most recent versions of JabRef and Freeplane to be used as-is,
p.s. I would be happy to be proved wrong and see that Docear is further developed, but I am not holding my breath. Above I tried to come up with some ideas which give an alternative to
Freeplane-Jabref workflow, while still providing the core functionality of Docear, as i see it.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I would very much be infavour of only point 2 : if there is a link to a pdf, then be able to fetch all annotations in the pdf and show them as subnodes. Gettgin this feature in Freeplane would just really improve it in one of my uses : scientific paper writing
I'm not a programmer myself , but a big hooray to anybody who woudl tackle this (probably as a plugin :-)
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Just to get the discussion going : I'm actually not using JabRef, but I have been following its development for quite a while. Unfortunately the integration with Libreoffice and journal specific formatting of references is just not good enough for me. So I'm using Mendeley and am relatively happy with this. However, I also use FreePlane for amnuscript as regulary link to pdf files in my information collection process for writing. And here it would just be immensely usefull to get the annotations (highlighting and comments) from the pdf files. In the docear video this seems to be really pushed : they are even synchronizing , that is when you change int he pdf, it will change in the open map automatically. Well, that's top, but already getting the annotations out of a pdf would be really helpfull, increase FreePlanes usefullness as pdf-reference information manager, while the reference-management in itself can be done by any other programm.
just my 2p
Cheers
Oliver
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I would really love to have at least the annotations feature of Docear in Freeplane. It would be very helpful and there is no other tool in the market to provide as detailed PDF annotation/outline extraction as Docear: it is not totally displayed by Docear mindmaps in the program; however when you open a Docear mindmap in a text editor, you see that Docear is even able to distinguish whether the imported text from PDF is an annotation or part of outline. Unfortunately, Docear cannot open latest versions of Freeplane mindmaps and vice versa. I wish Freeplane would have such a feature, extracting outlines and annotations from PDFs, or at least open the ones made by Docear.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
yes, I would like it very much if Docear would follow the Freeplane updates and stay in sync. But I guess this would be difficult...
Anyhow some of the pdf related functionality would be welcome.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I'm not a specialist, but it seems to me that as Doc ear has been based on Freeplane (and thus has profited of the code). is itself GNU licenced, it should be possible to get this part of their code into freeplane, no ? According to the 4th rule of GNU, "L'obligation de faire bénéficier la communauté des versions modifiées.", there should probably be an annoucement that this code is now available in Freeplane.
And development of DocEar has been stopped for quite a while now.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I spent a couple of days researching on options how to use mindmaps to ogranize ideas related to (scientific) papers and plan research activities. It seems that Docear project http://www.docear.org is the only option currently available. Cooperation between Freeplane and Docear dates back to 2011 (https://sourceforge.net/p/freeplane/discussion/758437/thread/1e194ded/?limit=25#f28d).
Unfortunately, the main developers have to considerably decrease their activities in that project and shift to other projects to make living. This one can clearly see from GitHub commits https://github.com/Docear/Desktop/commits/master ; the last commit of the main developer dates back to August 2014. Being a researcher I find it very unfortunate that the development of Docear project stagnate. Below I would like to propose/discuss some possible solutions and alternative workflow for JabRef + Freeplane.
Docear had a big goal of doing academic literature management in general (organize, create, discover academic literature; a literature suite concept, recommendation system, etc). Docear is built on Freeplane and (a modified version of) JabRef. To my understanding the developers had to substantially modify JabRef to play nicely within Docear interface and fulfil numerous goals. As a consequence, JabRef 2.7.1. is used within Docear and it is not-trivial to update to the newer versions.
Among the many features Docear aimed at delivering, the core and the most important ones for me (and possibly for others) would be those, related to integration of Freeplane with JabRef, i.e. mind mapping and scientific literature manager. Roughly, i would say the following features are must haves:
1) a way to add a paper to the mind map with bibtex attributes (key, title, journal, year, link to the .PDF file).
2) if the node is a "paper", look at PDF and fetch all comments as child nodes.
3) export to LaTeX with \cite{abcdKye} for papers.
The first one can be achieved in the following workflow. When a user clicks Copy in Jabref, the BibTex data of the paper is copied to the buffer, e.g.
@Article{abcdKey,
Title = {Super Paper},
Author = {Jim Genius},
Journal = {Nature},
Year = {2015},
Number = {1},
Pages = {127--155},
Volume = {43},
File = {:path/to/file.pdf:PDF},
Keywords = {keyword1, keyword2},
Publisher = {SIAM}
}
I think one could Copy-Paste that info into Freeplane as a (free?) node by means of some scripts/plugins (sorry, don't know much about Java and/or GUI, I am a C++ guy) with BibTex (Title,Author,Journal attributes) stored in attributes and a link to the pdf file. That looks feasible for me.
Regarding the second, Docear was more complicated. As far as I understand, they assigned some IDs to see if a particular comment, stored in PDF metadata, has been imported yet or not. If it was not, it will be added to a given node as a parent. Additionally, they had a jump-to-page feature. None of those is a deal-breaker, IMHO.
If Docear developers could point out to a piece of Java code which did scanning of the PDF for notes, i think it could be simplified just to import all the notes found in the PDF as child nodes in Freeplane. This, of course, is not as elegant as the approach pursued in Docear, but will do the job.
As for the third one, in Docear manual it is written that there is an export filter “latex input with cites and details”. So it seems this feature is implemented already, but I could not find it within Docear. I suppose this filter could be used straight away in Freeplane.
1), 2) and 3) are absolutely independent. If I would be to rate them, i would say 1)+3) are the most important. In the current version of Docear 2) does not work much on OS-X anyway.
To sum up, the idea is not to re-do Docear, but adopt a few core ideas in a more flexible workflow (as plugins/scripts) allowing the most recent versions of JabRef and Freeplane to be used as-is,
p.s. I would be happy to be proved wrong and see that Docear is further developed, but I am not holding my breath. Above I tried to come up with some ideas which give an alternative to
Freeplane-Jabref workflow, while still providing the core functionality of Docear, as i see it.
Did you find a solution?
I would very much be infavour of only point 2 : if there is a link to a pdf, then be able to fetch all annotations in the pdf and show them as subnodes. Gettgin this feature in Freeplane would just really improve it in one of my uses : scientific paper writing
I'm not a programmer myself , but a big hooray to anybody who woudl tackle this (probably as a plugin :-)
Just to get the discussion going : I'm actually not using JabRef, but I have been following its development for quite a while. Unfortunately the integration with Libreoffice and journal specific formatting of references is just not good enough for me. So I'm using Mendeley and am relatively happy with this. However, I also use FreePlane for amnuscript as regulary link to pdf files in my information collection process for writing. And here it would just be immensely usefull to get the annotations (highlighting and comments) from the pdf files. In the docear video this seems to be really pushed : they are even synchronizing , that is when you change int he pdf, it will change in the open map automatically. Well, that's top, but already getting the annotations out of a pdf would be really helpfull, increase FreePlanes usefullness as pdf-reference information manager, while the reference-management in itself can be done by any other programm.
just my 2p
Cheers
Oliver
I would really love to have at least the annotations feature of Docear in Freeplane. It would be very helpful and there is no other tool in the market to provide as detailed PDF annotation/outline extraction as Docear: it is not totally displayed by Docear mindmaps in the program; however when you open a Docear mindmap in a text editor, you see that Docear is even able to distinguish whether the imported text from PDF is an annotation or part of outline. Unfortunately, Docear cannot open latest versions of Freeplane mindmaps and vice versa. I wish Freeplane would have such a feature, extracting outlines and annotations from PDFs, or at least open the ones made by Docear.
yes, I would like it very much if Docear would follow the Freeplane updates and stay in sync. But I guess this would be difficult...
Anyhow some of the pdf related functionality would be welcome.
I'm not a specialist, but it seems to me that as Doc ear has been based on Freeplane (and thus has profited of the code). is itself GNU licenced, it should be possible to get this part of their code into freeplane, no ? According to the 4th rule of GNU, "L'obligation de faire bénéficier la communauté des versions modifiées.", there should probably be an annoucement that this code is now available in Freeplane.
And development of DocEar has been stopped for quite a while now.