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."

It's not a DMS

[Anonymous Coward]

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?

Re:mediawiki

[Anonymous Coward]

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.

Mendeley

[Anonymous Coward]

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 everywhere.

Dspace?

[andresambrois]

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 [dspace.org]

An unmet need in the biotech community

[cinnamon colbert]

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 [thomsonreuters.com] 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

Re:Zotero

[takowl]

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 handles rather awkwardly. Any notes would be outside the file, for example, not embedded in it. Mendeley [mendeley.com] comes closer, but AFAIK it only deals with PDFs, not all the other formats.

Re:WSS

[Anonymous Coward]

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.