Most users of SciPlore MindMapping (including me) use JabRef to manage their references. However, I always was thinking about switching to Mendeley because they offer automatic extraction of metadata from PDFs which saves lots of time when creating your bibliography. But Mendeley is not that compatible with SciPlore MindMapping and has some other shortcomings, so I always sticked with JabRef and accepted the time consuming and annoying task of typing titles, author names etc. manually.
But now this will change: our team just created a modified version of JabRef which is able to extract metadata from PDFs. What does that mean? Well, whenever you find a PDF on the internet, you store it on your hard drive, drag&drop it to JabRef and then JabRef will automatically find the right meta data (authors, title, journal, year, page numbers, …) and create a new BibTeX entry which is linked to the PDF file.
And this is how it works:
1. Go to www.mr-dlib.org (more information about this new project is coming soon), download our version of JabRef and install it.
2. Open the software and drag&drop one or several PDFs somewhere on the table which lists your BibTeX entries.
3. A dialog will open in which you select “fetch meta data from Mr. dLib”.
4. The next steps should be self explaining :-)
If you need a PDF for testing take this one. This should definately work. If not, please contact us.
And maybe the best thing: Our modified version of JabRef also accepts drag&drop directly from SciPlore MindMapping. That means you can drag&drop a PDF from SciPlore MindMapping into JabRef, there the metadata is extracted and a BibTeX entry created and then you can access the BibTeX data directly in SciPlore MindMapping. This will dramatically improve your workflow (if you don’t know about how to use SciPlore MindMapping and JabRef for managing your academic literature and drafting papers read here or check out this video)
Some words about how all this works in detail: The meta data extraction does not take place on your computer but JabRef will transfer your PDF to our server on which it will be analyzed. Our server then returns the extracted meta data. In most cases (I would assume something around 80%) you should get at least the title. And if your PDF is an article in the field of computer science you have a good chance to get much more information. However, we are constantly improving our algorithms and database. And btw. we will not store your PDF on our servers or any information of it. Once we have analyzed it and returned the meta data to you it will be deleted from our server.
It’s frustrating:
Why do you create customized JabRef, not a plugin. It will require additional efforts from JabRef developers to decide and intergrate… By the way, have you contacted JabRef team discussing your update.
The other thing is the meta-data extracting server. You see, not all research team always have good internet connection, and what’s more important, some teams are simply not allowed to share their paper collection with 3rd parties. There is rather interesting ‘queue of requests’ on Zotero site – http://forums.zotero.org/discussion/3574/ – lots of requests and just a few answers about local server.
hello,
we are talking with the JabRef team and it looks that our changes will be integrated into the official jabref. so there is no further need for a plug in or special version.
I understand that you would prefer having the metadata being extract locally. But:
- Our tools for analysing PDFs are not platform independent and
therefore could not be easily integrated into JabRef.
- We are constantly improving our algorithms (for instance, in the
last 48 hours we made one bug fix and one other improvement). With a
webservice we just have to change our tools on the server and that’s
it. If our tools would be directly integrated into JabRef we would
have to release new versions of JabRef every few days.
- We have not developed our tools for JabRef only but for our project
Mr. dLib and the main concept of Mr. dLib is to offer metadata and
services for academic websites and tools via a webservice. So we
have little intention to release some libraries etc. for which we
would have to write detailed documentations etc. before others could
use it. Instead we will offer an easy to use webservice that can be used by JabRef and others.
Hi, it’s William Gunn from Mendeley. We’re sorry to hear that Mendeley doesn’t work well with the Sciplore MindMapping tool, but there’s no point in re-inventing the wheel. I’m just thinking now that if we worked together we could add our strength in reference extraction and you could continue to focus on what you do best. Would you like to drop me an email to discuss this further?
Hello William,
thank you for your interest in SciPlore MindMapping and our webservice. There are two problems SciPlore MindMapping has with Mendeley:
1. Mendeley is using a proprietary data format for references. I know, Mendeley can automatically create a BibTeX file but SciPlore MindMapping cannot write into this BibTeX file because it would be overwritten by Mendeley the next time.
2. Mendeley is using a proprietary data format for PDF bookmarks, so SciPlore MindMapping cannot import these bookmarks.
Because of these reasons we recommend JabRef and we do have the tools for extracting metadata anyway because of our search engine http://www.SciPlore.org. So it is no big effort to integrate it into JabRef for us.
By now you must have seen that Mendeley’s API allows you to write to it, so it still seems to me like if you wanted metadata extraction capabilities you could simply use Mendeley, which will probably result in cleaner metadata for all document types.
I have been using Sciplore Mind Mapping to manage PDF files for my Masters Degree for the past year. I have found that the reality is very few pdf files from the various online databases have metadata, not even the title. So I am not sure how useful this will be for those in non Computer Science fields. What I do is:
1. Download pdf files that I find from online databases into a directory that is monitored from my Sciplore Mind Map
2. Change the pdf filename into the title of the pdf paper (the document title)
3. Create bookmarks as needed within the pdf file
4. Download the citation information for the pdf that is usually available on the online database, and import it into Endnote for referencing.
Now what would be useful is:
1. If Sciplore Mindmap could retrieve the title field from those pdfs which do have it in metadata, and display that title in the mindmap rather than the original filename, this would save step 2 above which can be a pain with long titles.
2. If the same downloaded file that contains the citation information (for importing into Endnote) could also be drag and dropped into the relevant pdf in the MindMap, that would be sensational.
While I would consider moving from Endnote to JabRef if it could give me additional functionality over Endnote, it seems to me that Endnote is fully featured, intuative and straightforward to use (and the uni provides it for free) and so it would need to be a compelling reason.