Document Management For Research With Annotation? 122
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."
Just buy EndNote? (Score:2, Informative)
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So I'm supposed to pay a monthly fee so someone can lock my documents up in a cloud somewhere where I may or may not be able to get to them one day? I know there is a free version but it is just a teaser for anyone who does real research or information hoarding.
mediawiki (Score:4, Informative)
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.
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This implies a painfully manual process of copy-pasting quotes, references, etc. While a wiki system would be a good repository a front end system is needed to open the documents, select the text and attach a comment to it.
Re:mediawiki (Score:5, Informative)
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Re:Mendeley (Score:1)
Mendeley is designed primarily as a local application: you store files on your own desktop, it just takes care of indexing them. Online syncing is an added bonus, from that point of view. They're not in the business of giving out huge amounts of free fileserver space.
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Great suggestion.. (Score:3, Informative)
Those 2 points are kind of important issues for an
Quick fix (Score:2, Funny)
'Collaborate' Implies ... (Score:5, Informative)
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 [slashdot.org] about it [slashdot.org] time [slashdot.org] and time [slashdot.org] again [slashdot.org].
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God the OP's requirements read like an advertisement for sharepoint, I just can't come to suggest it. I think the OSS person in me says wtick with a wiki.
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God the OP's requirements read like an advertisement for sharepoint
Maybe, just maybe that is because Sharepoint is one of the few well known products which does exactly what the author (and I presume many others) want? I've used Sharepoint, and while it definitely has its weak points, it does offer a collaborative system that sounds exactly up the author's alley.
Personally, I would start with the wiki approach, but Sharepoint does not deserve an immediate dismissal.
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I use WSS as it's free, but sadly not open source. My documents are not locked in though so I'm not tooo concerned. It's worth a look/assessment at the least.
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Jabref? (Score:2, Insightful)
Does jabref suit your purpose : http://jabref.sourceforge.net/
Privacy concerns aside... (Score:3, Informative)
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Bahahahahaha
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You left out the version control system, access controls, expandability, and design for collaboration. It already embeds documents in the Waves, including video and audio (lab recordings). The only problem is getting decent documentation on setting up your own server. It's still so new, and under heavy development, that the documentation is lagging. Big Time.
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It's not a DMS (Score:2, Interesting)
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 in
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http://bibdesk.sourceforge.net/
For Mac, I use Papers (Score:4, Informative)
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/ [mekentosj.com]
Otherwise, Endnote works well. I know many who use it. There are a few others that are also out there.
Good luck with it.
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Dell Mini 9
That's a small screen for manipulating documentation. How do you OS X on the DM9?
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How do you like OS X on the DM9?
There, fixed that for me.
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I like it a lot. It makes me sad that Apple is forcing me to install another OS sooner rather than later. Right now I have OS X Tiger, but won't update it further.
As for docs, I mainly use it for viewing purposes. That's why I got it: a way to carry all my PDFs in a form factor larger than an iPhone. (I had an iPhone, but found it a pain to read and manage my collection on it. 4-hour reading sessions on the small text of the iPhone screen is not ideal.)
With the iPad coming, I'll probably work to switch
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I like it a lot. It makes me sad that Apple is forcing me to install another OS sooner rather than later. Right now I have OS X Tiger, but won't update it further.
Is this because the Mini can't run Leopard?
With the iPad coming, I'll probably work to switch to that. I'm confident the Papers folk with have an edition for iPad.
I had been excited about the iPad before it was announced, but the product disappointed me, personally. I think a netbook is a better all-round companion device.
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Ack, I'm not keeping track of my OS X versions. I have Leopard on it, but not Snow Leopard. Also, I can't update Leopard. Apple's new Kernel no longer supports Atom processors. There are probably hacks, but I'm too lazy.
As for the iPad versus Netbooks, I don't know where I fall. I want to see a camera, and then I'd gladly give up my Hakcintoshed Netbook.
And I was underwhelmed by the iPad, but I think it will serve a good purpose. If for no other reason than getting Papers on a larger, easier read scre
Zotero (Score:5, Informative)
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+1 Make sure to go to the actual Zotero.org site and install the beta, version 2. It has a whole more features than the version available from the Firefox addons site.
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I've been using Zotero for a year and love it. The new version (2.0) is a godsend.
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Is there something like Zotero that *isn't* a cloud service? I'm really getting tired of the whole "give us all your data" services floating around. I'd love to use something like Zotero, if and only if I can control the server that the data lives on.
The market seems hypnotized by the "cloud" BS, which makes me sad.
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Huh...interesting. I read this from their docs:
and took that to mean that it's primarily a cloud service with some outside storage allowed. Basically it looks like they're making a distinction between "data sync" and "file sync." The data sync is the interesting part, since it's the really hard part of all this...is there some other way to do the data sync they're talking about without a Zotero account?
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I use Zotero (but version 1). I just put my zotero data directory inside my Dropbox folder. Then when I change computers I reload firefox and it is all synced. I do not have a Zotero account. This however wont work for multiple users at once. If version 2 has something where it will reload the data files for you before performing any change to the data, then this might work (although you would have to deal with the ensuing race conditions with multiple users, and may have to use locks and semaphores an
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Is there something like Zotero that *isn't* a cloud service?
Well, you could always use it without the sync feature: giving them your data is very much optional. For most users, their institution is likely only aware of Endnote, and won't set up a server for them, so Zotero's hosting the server themselves makes sense.
I'm not sure that it really meets the OP's needs, though. It fits how I work brilliantly--it's designed for indexing web pages, like a highly structured bookmark manager. But the OP specifically talks about a collection of local files, which Zotero handl
Discuss about it. (Score:1)
Zotero (Score:3, Informative)
Zotero [zotero.org] 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.
iTunes... believe it or don't (Score:3, Informative)
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 [lifehacker.com]
Zotero (Score:4, Insightful)
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.
Consider Wikindx3 (Score:3, Informative)
Wikindx3 [sourceforge.net] 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 [opendocman.com] as well, but I'm not sure if that application permits annotation (at least I've never used that feature set).
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OWL [sourceforge.net] is a nice setup in that it will automatically index all your PDF/RTF/whatever files. Its UI is a bit clunky, and documentation is sparse, but if you have the patience, it might be worth your time.
I use all three of these apps (see parent also) in various capacities. Which, as you have discovered, indicates that there really doesn't seem to be a "killer" F/OSS app out there that handles everything for a full-fledged document management system.
Zotero (Score:3, Insightful)
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.
What are the annotations used for? (Score:1)
Mendeley (Score:1, Interesting)
http://www.mendeley.com/
Desktop client that syncs with online account. Keeps track of all kinds of documents. I use it for research (at university). For me, it works great for keeping track of journal articles, you can add them by title, DOI, arXiv, and it will look up all the details automatically. Entries can be linked to files, PDFs, etc. You can also just add PDFs and it will usually pull out the metadata (can also monitor folders for new documents to track).
And of course, it syncs, so it's with you eve
SharePoint or OneNote (Score:3, Informative)
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.
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Actually from what I understand, Windows SharePoint Services is free and provides a lot of functionality on its own. I'm sure it would cost a lot to get set up and running though.
Re:OneNote vs pdf's (Score:1, Informative)
I use OneNote. Generally, I really like the concept behind the program. However, it has one fatal flaw for a academic environment: its poor ability to handle pdf's. Given that OneNote is a Microsoft program, I have little hope this flaw will ever be fixed.
Currently, I insert pdf's into OneNote as print outs. This makes OneNote deal with each page as a separate image. While the images can be viewed, it is impossible to attach notes or highlights to an image. Markups can be placed over the image of the
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TagTeam (Score:2, Informative)
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.
Dspace? (Score:2, Interesting)
Alfresco does all that you want... (Score:1)
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An unmet need in the biotech community (Score:3, Interesting)
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I'll be installing and reviewing a lot of software over the next few days, but there seem to be some great suggestions here.
At the end of the day I'd like to be abl
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PageCenterX can store and organise your PDFs including full-text search, indexing and page-level annotation which can be kept private or shared at a user or group level. Advanced import allows rule-based decollation and routing of documents if required.
http://www.lrs.com/eom/PDF/fly-Product-Flyers/fly-PageCenterX-english.pdf
Full Disclosure: I am employed by LRS
basic solutions are the best (Score:3, Informative)
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.
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I'm interested in your method as I use something similar but I'm a bit confused. I assume you use Xournal for your handwritten annotation ( perhaps on a TabletPC) but then do you replicate that annotation on the relevant bibtex field?
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I use xournal to keep "personal explanation" or ideas on the document. I write a sumup of what is important in the bibtex file. Typically, what I would write in a "related works" section of an article. I also use a keyword field in my bibtex that I write mannualy as well. It allows me to search my whole bibtex file using bibtool.
Evernote (Score:1)
Try Evernote. It lets you markup everything and make notes on images, documents and everything else. It is multiplatform too.
http://www.evernote.com/
Good luck.
start with the scribd demo (Score:1)
I was researching the same thing the other day. I came across a scribd demo where they are associating comments with individual pages and bookmarks with the entire document. So when you click on a bookmark, the viewer takes you to the relevant page. Each time you scroll to a new page, it displays the relevant comment for the page.
Of course their demo has hardcoded bookmarks and comments, but their data structures are clear, the code is readable, and it takes little imagination on how to provide a dynamic
From what you describe ... (Score:5, Informative)
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 [wikipedia.org]
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.
Working on it, with many new ideas (Score:1)
This is exactly the area I've been feeling pain for years, and recently have been working to address. My key innovations are around interface / visualization methods, automation, and collaboration. Please email me at sdw@lig.net if you have a wish / idea list, pointers to interesting related ideas / technology, or want to be a beta tester.
firefox scrapbook extension (Score:2)
Someone else mentioned Zotero, which looks really good and I'm meaning to try it, once I've cleared out over due projects.
What I have used for quite some time, with great results, is the Firefox extension called Scrapbook. Just select the HTML you want to keep from a web page, and you're nearly done. https://addons.mozilla.org/en-US/firefox/addon/427 [mozilla.org]
Bibdesk (Score:1)
Bibdesk and CVS or SVN for Latex on Mac (Score:2)
Bibdesk and Mendeley (Score:2, Insightful)
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,
Papers, Skim and DEVONthink Pro on OS X (Score:1)
On OS X, check out Papers (already mentioned in response to OP), Skim (free) for awesomely marking up and notating PDFs, and DEVONthink Pro (optionally, the DEVONthink Pro Office version for OCR and added functionality). I don't think these will provide you with all the functionality you mentioned (version control, however. But Skim and Papers play nicely together.
Jabref (Score:2)
Jabref? http://jabref.sourceforge.net/ [sourceforge.net] It's open source & cross platform (java). I use it to manage about 1500 articles and related academic texts in a mix of pdf, odt, and doc. You can add notes about files. It can operate as a standalone or can be connected to a shared mysql database (to allow sharing of the files, their cites, and any notes you add). The one thing it can't do directly is annotate the original documents, but you could presumably annotate them using something else before replacing
Abiword and abicollab.net (Score:1)
Abiword can sufficiently handle most all of the documents you want to manage (pdf support is better but could still use improvement) and you can mark them up and collaborate via abicollab.net. The best part about abiword is that is portable to a large number of platforms including handheld devices (maemo), portableapps.com (for win32 on usb), mac and most *-nix as a package
http://abicollab.net/ [abicollab.net]
http://abisource.com/ [abisource.com]
okular? (Score:2)
Just because nobody seems to have mentioned. Okular the default kde4 document viewer allows you to annotate any doc it opens, stick post-its on things and add marker highlighting. Presumably this also links in with the document search system which includes tagging via the dolphin file manager. The bit it doesn't appear to do is collaboration but it certainly seems that they're taking it that direction if indeed it isn't just a feature I've not found. Don't really know much about it.
Sente works and has sync (Score:1)
Try http://abicollab.net (Score:2)
Try http://abicollab.net./ [abicollab.net.]
Clicking "open" on the doc automatically loads the doc into abiword, which you can annotate as you like. Clicking "save" in abiword sends it back to http://abocollab.net./ [abocollab.net.]
You can easily share and collaborate in real-time. You can tag your docs, share then amongst groups of people etc.
I guess it's not quite what you're after but it's collaboration features might make it work better than you expect.
EMC ApplicationXTender (Score:1)
EMC has a great product but it may be overkill. ApplicationXTender, in its most basic form, can do everything you are looking for. It is not cheap but it can handle any document type (although the built in viewer works only for PDF, TIFF, and MS Office documents to my knowledge). ApplicationXTender can also intgrate with any ODMA compatible application to allow new documents to be indexed and stored within the document management system. It can integrate with many other applications using an Integration mo
Pfft, the answer's obvious! (Score:1, Funny)
Emacs!
What to do for mobile? (Score:1)
Yellow Marker (Score:1)
docmeeting by madepublic (Score:1)
A Prof Using Drupal (Score:1)
Agorum (Score:2, Informative)
Re:Agorum - for those whose German is rusty... (Score:2)
From what I've heard http://www.agorum.com/ [agorum.com] is what you're looking for.
Do they have a page in English? I couldn't see one.
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OQUMA - Quality/Environmental document management (Score:1)
We provide a business specific service to support Quality Management or Environmental Management.
Also, we have an open methodology (under Creative Commons), published in our Wiki [oquma.net]. So you can just grab the documents, change, and upload them to create a management system with version control, archiving, document permission/owne
Document Management For Research With Annotation? (Score:1)
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When you use condescending statements like, 'Thanks for playing however!' you should really make sure all your ducks are in a row, or you end up looking the fool. Seriously, have you ever traveled outside the US? Read anything about other countries? We are, quite simply, the most right wing country in the entire world.
Other countries have actual socialists. They make our rabid left wingers look like Reagan worshiping free market ideologues. Other country's centrists are our far leftists. No other country ha
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