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Document Management For Research With Annotation?
msimm writes "I'm currently looking for a document management system for personal and research-related use. Having looked at Alfresco and KnowledgeTree along with a slew of similar open source document management systems they seem to have a common set of features including version control, archiving, document permission/ownership and search/indexing. What I'd like, in order to help me manage my own continually growing collection of pdf/doc/odf/rtf/txt files, would be something that allowed me to view and annotate documents (and possibly collaborate/share notes) without requiring me to download, edit and re-upload each document. Obviously there are plenty of capable document management systems out there, so I really suspect I've simply missed something and am hoping someone can point me to a better way to index, search, collaborate and keep and share notes on the ever increasing glut of useful information I seem to use and collect."
Nothing much more to say here... I have found EndNote very useful.
if you want a low-tech approach, just install a wiki. Mediawiki is full featured while MoinMoin is easy to install and configure (no separate database needed). I haven't used any others.
Collaborate, in my opinion, implies that there is some advanced messaging going on in the background. And the persistence of that messaging (whether on a centralized server or via some P2P/Client routing protocol) is not only complex but often needs to be specific to what you want to collaborate about. Let's look at annotations. Where are they stored? How am I notified if you add an annotation to my document? How do I track my annotations? How do I share my annotations? Where is that stored? Etc. The questions raised are endless.
A coworker implemented a basic ruby service of this where I work and I have to say that he didn't find any open source alternatives before he started that fulfilled anywhere near what we needed. Ruby made it pretty easy (1 or 2 person job) with the emphasis just being javascript and DOM coding to get the interface correct. Then we just had a RESTful service for storing these and from there we'll keep adding on features like messaging/e-mail alearts/etc for the users when we get time. Yes, I'm aware that if I open sourced this you could help me out with that but I'm sorry, my employer is not on that boat (yet).
For your reference, even just document management is a sticky solution to find in open source, we've talked about it time and time again.
My work here is dung.
Does jabref suit your purpose : http://jabref.sourceforge.net/
Would Google's Wave work for you? It's real time, centralized, and browser based. I say privacy concerns aside, because the protocol is available, and people could build their own servers (such as http://code.google.com/p/pygowave-server/)...
If a man isn't willing to take some risk for his opinions, either his opinions are no good or he's no good
I've been searching for something similar for a while but can't really find anything to fit the bill.
What I'm looking for is a system that will allow you to highlight a particular quote in a PDF and attach a comment to it. When I finish my review I would like to have all my comments organized in a tabular format. The table should have the quote, page number (ideally also chapter and paragraph but this is asking too much) and my comment.
This way I can attach my comment sheet to the top of the document and inspect it quickly without even having to open the actual document. This review sheets are also "portable" because they can be shared and anyone with no infrastructure could still identify the comment and quote.
Adobe Acrobat does only half of this, you can highlight, comment but you can not control the format of export (CSV or excel would be cool)
Does anyone now a system that does this?
I use Papers. It does not do everything you want, but it is a nice management tool. It is still growing in features, and the support staff is very responsive. (They provided me, same day, a new NIB file that allowed me to use it on my small hackintoshed Dell Mini 9 screen.)
The link is here: http://mekentosj.com/papers/
Otherwise, Endnote works well. I know many who use it. There are a few others that are also out there.
Good luck with it.
Zotero may well be what you're looking for. Much better and more open source than EndNote (mentioned above).
Zotero might be worth a look. It's a Firefox plugin (open-source), mainly designed for keeping track of a collection of academic litterature. It allows you to organize the papers in folders, tag, annotate, and share the papers and annotations with others, all easily available in the FF gui. You can export lists of references to Word/OpenOffice/TeX when writing papers, they can be autoformatted to a wide range of citation styles.
It works really well (with full-text search) for storing web pages/pdfs. I don't know how well it works for .odt etc. Even if your purpose is not that of the typical university researcher it might be useful. For instance, recently I've liked using it for storing job ads, and my corresponding applications.
If you already have it installed, iTunes may be a simple solution.
http://lifehacker.com/software/pdf/geek-to-live--organize-your-pdf-library-with-itunes-240447.php
Rich And Stupid is not so bad as Working For Rich And Stupid.
About a year ago I needed a piece of software that matches your requirements. I wanted to be able to do my research from anywhere and keep track of notes and annotations in a very simple but searchable way.
Zotero is the closest thing. It's not perfect, far from it, but none of the competition came even close.
Zotero is a Firefox plugin that allows you to link or store information, be it webpages, pdf's or anything else you may see online. It's possible to group & tag your documents in various ways and there are various options for taking notes and adding annotations.
All of it is stored online so you don't need to carry anything with you. Just install the firefox plugin, enter your credentials and off you go.
Wikindx3 is a full-fledged bibliographic database that can manage *any* type of document, and permits annotations. As an added bonus, you can export the biblio info in any number of formats (including my favorite, .bib for LaTeX).
I've had good success with OpenDocMan as well, but I'm not sure if that application permits annotation (at least I've never used that feature set).
Zotero is brilliant. I could go on about how I use it every day at work and it makes everything a hell of a lot easier, but instead, just check it out.
Versioning of documents it doesn't do - but that's what Mercurial is for I guess.
Microsoft Office SharePoint includes the capabilities you mentioned (version control, archiving, document permission/ownership and search/indexing) and is on par price-wise with KnowledgeTree (though not free). They also have a hosted model, SharePoint Online.
The capabilities you list actually needing--index, search, collaborate and keep and share notes--might be better fit by Microsoft OneNote. It doesn't do version control and document permission/ownership, but it does what you described doing. At my place of business, there are two categories of people: those who love OneNote and those who haven't tried it.
For a basic, low-tech solution I'd suggest TagTeam (http://www.andrew-quinney.com/tagteam.html). It's a basic file tagging utility that makes use of filesystem metadata (PC and Mac), so any changes you make to a given file are immediately visible to others with access to the same file. It also includes a powerful searching language.
Have you tried it? It's quite powerful and free. They have a good tour video here: http://www.dspace.org/about-dspace/DSpace-Video.html
I work in a biotech startup with 12 people total. We have several thousand pdfs, mostly of scientific publications downloaded from places like pubmed, along with some .ppts and .docs and other files.
We use a endnote, a program from the behemoth in this area, thompson research, which has most of hte software in this area.
see http://thomsonreuters.com/products_services/science/science_products/a-z/procite
Based on what I have seen, there is a huge need for software that meets our needs; the thompson products are very $$ and , awfull - a classic case of crappy software with a lot of marketing.
Programs like endnote were created back in the 90s, for DOS machines, and they still look and feel like it, once you get past the pretty home page gui of the software that thompson has added on.
if anyone out there is serious about making a product to compete, give me a hollar
I use a git repository containing a bibtex file that tells me where the documents are with an annote field containing information. documents are put in the git repository. If I need to annotate them on the paper for not forgeting something about it, I use xournal. And I push everything in the git repository.
It implies that people update the repository which is in my opinion not really a problem.
You're looking for a reference management system, not a document management system. (although, they might not deal with all of the stuff that you mentioned that a document management system will)
Zotero should work for a single person, but if you're trying to do this for an office, you might want to take a look at Aigaion.
If you want to look at others to see what best fits your needs, see:
http://en.wikipedia.org/wiki/Comparison_of_reference_management_software
And , if you still can't find anything -- try asking on the Code4Lib mailing list, as you might need one of the 'integrated' library solutions.
Build it, and they will come^Hplain.
I use Bibdesk on the mac, and I like it. Specifically, I like that it organizes all my PDFs into folders and stores all the data in a Bibtex file. The only problem I have with it, is that it stores the paths and macosx aliases and so instead of getting a nice pathname, you get 1500+ characters long hash. I'd really like a way to convert those back to paths so I could migrate in the future if I need to.
I used Mendeley for about 10 minutes, but I was impressed. It looked really good. It's cross platform, and web based. The only reason why I'm not using it is because I already started with Bibdesk, and it just wasn't quite worth converting over. (Again the pathname issues.), but I'd recommend it.
Anything that doesn't support BibTeX is simply a non-starter.
So far it's one of the best I've tried and it does a pretty great job of extracting all the reference/author data. As a desktop application, for my purposes at least, it seems just about perfect with my only current quibbles (only an hour or so into use) would be 1) the way it's search handles multiple matches within a document (hint: it doesn't) 2) they way it displays matched documents (matches aren't highlighted and must be manually paged/scrolled to).
Those 2 points are kind of important issues for an indexing/search/research tool, but overall I'm still really impressed with the project and features like the folder watch (rather then manually importing new documents) definitely add value.
Of course it's pretty slick too, which is always nice.
Quack, quack.
From what I've heard http://www.agorum.com/ is what you're looking for.