If all goes well I plan to start on a PhD in the next few months. I need to sort out a reference manager.

1) As a reference manager are there strong reasons to choose Zotero over Mendeley? I love the GUI of Mendeley over all other reference managers I have tried. But I am not sure whether Mendeley being owned by a private company that deals with journal articles is a positive thing. They pretty much have access to all our research-related data we store on Mendeley! Also, I hate the fact that Zotero has one parent entry for each reference and then multiple child entries under that. It gets so complicated and cluttered. Mendeley seems nice and simple with just one entry per reference.

2) In Mendeley when syncing is carried, are the contents of Notes and Private Annotations also synced? They do not seem to sync in the multiple devices I have.

3) In Mendeley is there a plug-in that would enhance the features of Notes and Private Annotations? The former only seems to have Bold, Italics and Underline functions which is not enough and the latter not even that!

4) In Mendeley, is it possible to export the contents of Notes written in the collection of PDFs as a batch?

5) In Mendeley, is it possible to export the contents of Private Annotations as a batch? I know it is possible to do this one-by-one. Not helpful when there are heaps of PDFs though.

6) Is there anyway to have a mind-mapping tool integrated to Mendeley? In order to go from managing articles + making notes to formal writing I need a visual middle-man so I can organise my research writing and jot down ideas and have a look at how everything fits in before I actually start formal writing. Any software that would help me do this please? I tried Qiqqa and Docear - they both have the functions I need but their GUI is user-unfriendly and ugly!

Thanks very much in advance :)

1. I've only used Mendeley.

2. I think they do, but I don't really make many notes - I just highlight. I also tend to use it on one computer mainly. I mainly using for storing and searching PDFs.

3. Don't know

4. Don't know

5. Don't know

6. Don't know

1. I've found Mendeley very straightforward (only other one I tried was Endnote)
2. I haven't experienced any problems with syncing - I may double check though as maybe the notes aren't there...
4-5. Unsure
6. There isn't any mind mapping tool as far as I can tell

I'll try to answer as many of the questions as I can but from the aspect of the zotero since I've choosen it over mendeley (before that hardcore emacser, one software to rule them all)

1) Zotero out of the box doesn't offer much, what makes zotero bearable is the community and the plugins built around it. The good thing is that in zotero you own your own data and ref library. Currently, I have it setup so that all my refs sync to zotero servers (they offer only 200Mb), but only the refs, not the actual attached pdfs, notes, etc. Those are stored on my Google Drive because I have infinite space through my uni. In zotero you have by default one group named My Library and below that you can as many collections (i.e. folders) and items (i.e. references) as you want for each folder. If you need another group or to rename the default one "My Library", that is also possible but only via the zotero.org webpage after you login to your account. The changes there will be reflected on the zotero desktop.

2) Yes in zotero they are synced, I'm using it on linux desktop and macbook pro laptop, for my android phone I use ZotEZ2.

3) This is also a plague in zotero (you'll notice my comments on zotero forums), because I want latex capability in notes and only thinking that we're in the fucking 21st century and there's no decent half complete ref manager that can provide such fundamental capabilities makes me furious. (remark to myself emacs+org-mode does everything and much more)

4)In zotero its possible to do that through the usage of report exports and the equivalent plugins.

5)In zotero you can have your pdf annotated and once saved have the annotations exported automatically as notes. Once as notes you can have batch exports or reports produced.

6)There are plugins that allow to do that, I think zotnet is one but I haven't played with it.