Comments for Docear http://www.docear.org The Academic Literature Suite Fri, 29 Apr 2016 15:05:10 +0000 hourly 1 https://wordpress.org/?v=4.5.3 Comment on Docear’s new workspace and workflow concept: We need your feedback! by Horacio http://www.docear.org/2014/06/09/docears-new-workspace-and-workflow-concept-we-need-your-feedback/#comment-145338 Fri, 29 Apr 2016 15:05:10 +0000 http://www.docear.org/?p=4558#comment-145338 I’m using Docear and so far I like it a lot! As my continuous search for an efficient workflow goes, I came across with and idea/need. This is my workflow:
1. Save relevant paper/article to monitoring folder.
2. Annotate in PDF editor (in my case I use Adobe Reader)
3. Refresh Docear
So far it works perfect. However, in Docear I need to move the imported quotations/coments/etc to their corresponding theme (e.g. concept, idea, methods, etc) which corresponds to specific node. For not getting lost, what I do is to write a hashtag in each coment/note/quote in the PDF editor (e.g. #concept, #idea, #methods, etc) So when I am in docear I do a serch of the specific ‘#label’ (the hashtag is just to distinguish it from other words).
Here is the idea: it would be great that when importing/refreshing Docear creates/updates new nodes based on hashtags. Even if I have two or more hashtags in the same comment/note it will copy the same one to the created nodes, so when I go back to docear they are already sorted in their respective theme.

Is this clear? does it make sense? is it difficult to implement? do you think it would be useful for others?

regards

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Comment on Update of the Google Scholar PDF Metadata Retrieval Library by Urvashi http://www.docear.org/2014/10/13/update-of-the-google-scholar-pdf-metadata-retrieval/#comment-145276 Thu, 21 Apr 2016 02:13:38 +0000 http://www.docear.org/?p=4760#comment-145276 Downloaded the latest version. It worked fine for a while, but then started having the same issues as the previous version for retrieving articles. What to do?

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Comment on Update of the Google Scholar PDF Metadata Retrieval Library by Hidayet Tutun http://www.docear.org/2014/10/13/update-of-the-google-scholar-pdf-metadata-retrieval/#comment-145242 Mon, 11 Apr 2016 18:57:08 +0000 http://www.docear.org/?p=4760#comment-145242 Hı,
I am using new version of Docear, but, Metadata extraction is not working. you said it was included in Docear 1.2. it did not work, what should we do to work again maetadata extraction.

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Comment on Call for Donation: (Automatic) PDF Metadata Extraction and Renaming by Joeran [Docear] http://www.docear.org/2014/01/23/call-for-donation-automatic-pdf-metadata-extraction-and-renaming/#comment-145140 Thu, 31 Mar 2016 09:34:10 +0000 http://www.docear.org/?p=4089#comment-145140 there is no progress yet. however, renaming is not as easy as e.g. in jabref, because in Docear you need to rename the files and links in both bibtex files and all the mind-maps (of course, it’s also not that difficult to implement)

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Comment on How to proceed with the development of the Docear4LibreOffice add-on ? by leoperbo http://www.docear.org/2014/10/23/how-to-proceed-with-the-development-of-the-docear4libreoffice-add-on/#comment-145087 Sat, 26 Mar 2016 17:09:24 +0000 http://www.docear.org/?p=4771#comment-145087 I agree with zaxebo1, I’m using Docear for manage PDF’s annotations and reference data, then, I use the standalone JabRef application for introducing cites and generate the references list in a Libreoffice document, using the OpenOffice plugin for JabRef. If Docear team “integrates” the OpenOffice plugin in their JabRef implementation the objective will be nearly accomplished. Considering that, in words od JabRef developers, “the former plugin has become an integral part of JabRef since version 2.9 and is maintained along new releases of JabRef”, this shouldn’t be as difficult as developing “Docear4LibreOffice add-on”.

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Comment on Call for Donation: (Automatic) PDF Metadata Extraction and Renaming by Stephan http://www.docear.org/2014/01/23/call-for-donation-automatic-pdf-metadata-extraction-and-renaming/#comment-145050 Tue, 15 Mar 2016 12:56:29 +0000 http://www.docear.org/?p=4089#comment-145050 Is there any progress planned on these key features?
(I just searched through all reference managers and found docear to be highly preferable compared to mendeley and zotero, as I like to work on and with the pdf-files I already have)

I miss especially the renaming feature, which should be impressively easy to implement. JabRef had such plugin, however after plugins got disabled, it does not seem to be merged yet.
Have I missed something?

Does someone know how to replace the renaming-feature (essentially you only need the bib-files), as long as it is not implemented?

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Comment on Which one is the best reference management software? by Christopher J Poor http://www.docear.org/2013/08/27/off-topic-which-one-is-the-best-reference-management-software-tool/#comment-145033 Wed, 09 Mar 2016 10:43:31 +0000 http://www.docear.org/?p=2682#comment-145033 DocFetcher is similar to Foxtrot but is free and open source.

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Comment on Which one is the best reference management software? by Chistopher J Poor http://www.docear.org/2013/08/27/off-topic-which-one-is-the-best-reference-management-software-tool/#comment-145028 Tue, 08 Mar 2016 14:59:48 +0000 http://www.docear.org/?p=2682#comment-145028 Hi Steven,
I know about the stress and frustrations of writing a PhD. I have just started on my second one. I hope it is still going OK. I am afraid I only just came across your post on Docear’s forum.
I am also using Scrivener, although I only just started. I would be interested to hear about your experiences using it. I looked at many citation managers after deciding to ditch Endnote because of their proprietary format, high cost and charging for new releases. I settled on Zotero https://www.zotero.org/ because it is open source, free and compares favourably in many ways with most of the others. Its best feature is probably the robust ability to gather metadata from various sites: Google Scholar, Amazon, Worldcat etc. It also accepts DOIs and ISBNs for the creation of entries (you can copy and paste these from pdfs that have text layers).
Zotero works best as a Firefox plugin but also works well as a standalone app which is also compatible with Chrome and Safari. It integrates very nicely with Word and LibreOffice (even with LaTex).

If you use Zotero standalone or Zotero for Firefox you will be able to download the Mac plugin for Word from this page: https://www.zotero.org/support/word_processor_plugin_installation
Here is a youtube demo of how to cite in Word with Zotero: https://www.youtube.com/watch?v=RuRF8zxkxIo#!
One thing you might also like is the ability to drag and drop any number of pdfs from Finder into the central pane of Zotero and then right click on them to have the meta-data extracted and make a parent reference item.

If you want to you can make a “collection” in Zotero for each folder you have your pdfs in and drag them into there. I do not do this, though. I use Zotero’s collection to organize my references and their attached pdfs according to writing projects.
One thing I realized after starting to use Scrivener and dragging a couple of hundred pdfs into it is that I really should probably be doing it one at a time as I cite them and according to whether I have notes and annotations that can be added to Scrivener. This way I will be able to more easily organise the few dozen references I need rather than having an extra hundred or so I don’t.
Zotero has a great add-on to extract annotations from pdfs and it is now also integrated with Scrivener via a plugin for Zotero: http://zotplus.github.io/zotero-better-bibtex/index.html

I have also been frustrated with Spotlight not finding my files and have been using the trial version of Foxtrot http://www.foxtrot.ch/buy/index.html which works brilliantly.
I have also used Docear, but mainly for creating an outline in the mind map. Of course Scrivener is great for this also. I actually export my Zotero collection (subset) for use in Docear and can arrange the references on the mind map to get an idea of the outline. The pdfs can be inserted and Docear also extracts their annotations.
Zotero also has a good plugin to extract annotations: https://addons.mozilla.org/en-US/firefox/addon/zotfile/?src=api

As far as updating the references to more recent articles, I haven’t got any experiences with Bibliography managers that to this (apparently Docear’s suggestion help – see below, but I don’t know from my experience). What I do in this situation is search Google scholar for the article I have, look at the “cited by” link at the bottom of that entry, and then restrict the results to the latest ones (far left of Google results page).

I do have most of my pdfs that I downloaded organised in folders on my Mac. I can then find them by subject in Finder. However, lately I have been letting Zotero handle the downloads for most of them and only storing copies of especially important references in my folders. Zotero keeps the pdfs in a database which you can sync with Dropbox. You can also sync the references themselves on Zotero’s server for free (a good backup).
Zotero allows you to search very conveniently through the pdfs it stores, including the text within (as long as the pdfs have a text layer – or if you have OCRd them with something like pdfpen.)

Now to your questions:

1: I don’t know if any citation manager can pull out the references already formatted by another one in Word. I’m pretty sure this would have to be a Find and Replace labour intensive process. It would be a matter of searching for the “(“ at the beginning of a citation, copy the author’s name, and then going to “insert citation” and paste. This would then give you the citation in Zotero’s cite box. Enter and it’s inserted. Delete the old citation.

2: The cite codes you would insert in Scrivener include the author’s name. Also, the citation process brings up the author, year and title when you enter the author or any word in the title.

3: As I said, I don’t think it is necessarily desirable to try to keep the folder structure from Finder. That is one way you have the articles organized, and you can organise them differently in Zotero. Typically you would import all the pdfs you want into “My Library” and then you would organise them (actually symlinks) into “collections” according to what you are writing. You can also store “smart collections” which are saved searches that are updated as you add new items.

The second part of this question is something that I dealt with for some years while writing my first PhD thesis. My old Uni also had limited access to databases and I relied on a) Google scholar pdfs and b) The California Bay Area public library system. The San Francisco Public Library is free to join for anyone living in the area and has access to JStor. You might find similar possibilities where you are. Ask you librarian. You could also try openpdf, the Open Library, CORE connecting repositories, BASE Bielefeld Academic Search Engine; Copac National; Zetoc; Microsoft Academic Search; iSEEK – Education; ERIC – Education Resources; The Virtual Learning Resources Center; The Universal Digital Library; and Community Texts. If you have trouble finding the urls for these let me know.

4: Zotero will find and insert references into its database based on the DOI or ISBN you give it. I have found this to work well. As far as I know Zotero does not point you to similar references. As I said above, the only way I have experience with this is doing it myself on the web. However, according to this page: http://bundlr.com/clips/52de0fde35419b00150007af Docear recommender system for research papers is similar to that of Mendeley. All papers that Docear recommends are available for free in full-text, though sometimes the linked URLs are dead.
I believe that Zotero will extract the meta data correctly for your pdfs most of the time. As I said, it will do this for many pdf selected at once. This requires an internet connection and will be resource intensive. Particularly if there is another app accessing the internet from you computer (in my case it is probably Crashplan cloud backup – a good, reasonably priced service) the process may take more than several minutes for a couple of dozen files. Again, for finding files on your drive, try Foxtrot.

You could have Zotero on as many Macs as you like, also PCs and Linux (for no cost). The citations will sync with Zotero’s server and the pdfs you can sync through Dropbox.

Hope this has been of some help.

Contact me if I can provide any further info,
Chris.

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Comment on Docear 1.2 Stable: PDF Metadata Improvements & Faster Monitoring by Joeran [Docear] http://www.docear.org/2015/12/02/docear-1-2-stable-pdf-metadata-improvements-faster-monitoring/#comment-145006 Sun, 28 Feb 2016 08:58:10 +0000 http://www.docear.org/?p=5253#comment-145006 no news about docear4libreoffice 🙁

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Comment on Preview of the Docear Online Viewer by Joeran [Docear] http://www.docear.org/2013/03/21/preview-of-the-docear-online-viewer/#comment-145005 Sun, 28 Feb 2016 08:57:30 +0000 http://www.docear.org/?p=2484#comment-145005 it’s a lack of time

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