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Document Management For Research With Annotation?

timothy posted more than 4 years ago | from the just-sort-by-document-size dept.

Media 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."

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If I was a retard: (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#31104002)

I would vote for Sarah Palin.

I would not believe science that doesn't agree with my insane and fraudulently presented world-view.

I would vote for the same Republicans that got us in to the economic mess that Barrack Obama is fixing.

Re:If I was a retard: (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#31104048)

Take your political bullshit posts elsewhere.

If I was a retard: (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#31104072)

I would also think that obama is really fixing things.

Criticism of Obama is racist (-1, Offtopic)

Anonymous Coward | more than 4 years ago | (#31104188)

You racist ReThuglican Jew

Re:Criticism of Obama is racist (-1, Offtopic)

amliebsch (724858) | more than 4 years ago | (#31104566)

Mr. Olberman, you should get off Slashdot and focus on your terrible ratings.

Re:Criticism of Obama is racist (-1, Offtopic)

spun (1352) | more than 4 years ago | (#31104944)

Olberman doesn't think Obama is really fixing things. Like many liberals, he think Obama simply hasn't done anything he promised he would. We wish the President were anywhere near the socialist Republicans think he is. He's a moderate, a total centrist.

Re:Criticism of Obama is racist (1)

oldspewey (1303305) | more than 4 years ago | (#31105528)

By the standards of many countries outside of the USA, Obama is not a centrist at all - he is well to the right of centrist.

Re:Criticism of Obama is racist (1)

Bodhammer (559311) | more than 4 years ago | (#31105962)

I'm not sure Cuba and Venezuela are great examples of where Obama is to the right... Thanks for playing however!

Re:Criticism of Obama is racist (0)

Anonymous Coward | more than 4 years ago | (#31108484)

He's talking about Sweden, France, hell, Britain - the Tories are left of Obama on some issues, and Labor is well to the left.

Re:Criticism of Obama is racist (0)

Anonymous Coward | more than 4 years ago | (#31106564)

That just shows how fucked up they are.

Using such stalwarts of The Left as Stalin, Hitler, Mussolini, Castro, Che Guevara, Chavez, or even Clement Attlee to show that Obama is on the right is silly.

Plus, the lack of democracy in the EU (see Constitution votes, and re-votes), the social decay of England, the nightly car burnings in Paris, the retreat from Freedom of Speech in Canada and the Netherlands, the finances of Greece, etc. etc. are not things to be emulated or to be proud of.

Just buy EndNote? (2, Informative)

Anonymous Coward | more than 4 years ago | (#31104004)

Nothing much more to say here... I have found EndNote very useful.

Re:Just buy EndNote? (1)

GrantRobertson (973370) | more than 4 years ago | (#31109910)

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 (4, Informative)

Anonymous Coward | more than 4 years ago | (#31104028)

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.

Re:mediawiki (2, Interesting)

Anonymous Coward | more than 4 years ago | (#31104400)

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 (5, Informative)

caffeinemessiah (918089) | more than 4 years ago | (#31104512)

Try Mendeley [mendeley.com] . They're still pretty new, but very promising with their desktop client for Linux/Mac/Win in addition to the web interface. They also sync perfectly with Zotero and CiteULike, which makes migration easier. You can annotate PDFs directly in the desktop, but I think only the latest beta build has support for sync'ing the annotations across multiple computers. I'm hopeful for them -- it's definitely one of the most promising Ref manager systems I've seen (oh yes, they also support Bibtex,Endnote,Refworks formats heavily)

Re:mediawiki (1)

Mab_Mass (903149) | more than 4 years ago | (#31105796)

Have you tried using them yet? Looking over their site, I see a lot of pluses, but also some limitations, such as having the docs managed remotely, limit of 10 users, 500 MB of space, etc. In practice, though, do these seem to be real limitations?

Re:Mendeley (1)

takowl (905807) | more than 4 years ago | (#31106976)

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.

Great suggestion.. (2, Informative)

msimm (580077) | more than 4 years ago | (#31108194)

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.

Quick fix (1, Funny)

nicolas.kassis (875270) | more than 4 years ago | (#31104062)

Just whip one up in rails and post a 20 minutes screencast. Done.

'Collaborate' Implies ... (4, Informative)

eldavojohn (898314) | more than 4 years ago | (#31104082)

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 [slashdot.org] about it [slashdot.org] time [slashdot.org] and time [slashdot.org] again [slashdot.org] .

WSS (0)

Anonymous Coward | more than 4 years ago | (#31104154)

..please be nice...

Re:WSS (1)

toastar (573882) | more than 4 years ago | (#31104292)

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.

Re:WSS (1, Interesting)

Anonymous Coward | more than 4 years ago | (#31108662)

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.

Re:WSS (1, Informative)

Anonymous Coward | more than 4 years ago | (#31104388)

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.

Re:WSS (1)

hex1b (46201) | more than 4 years ago | (#31104476)

I use Zotero and Mendeley http://www.mendeley.com/ [mendeley.com] .

Jabref? (2, Insightful)

Anonymous Coward | more than 4 years ago | (#31104166)

Does jabref suit your purpose : http://jabref.sourceforge.net/

Privacy concerns aside... (2, Informative)

ircmaxell (1117387) | more than 4 years ago | (#31104200)

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/ [google.com] )...

Re:Privacy concerns aside... (1, Informative)

Anonymous Coward | more than 4 years ago | (#31104724)

Bahahahahaha

Re:Privacy concerns aside... (1)

hot soldering iron (800102) | more than 4 years ago | (#31109524)

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.

It's not a DMS (2, Interesting)

Anonymous Coward | more than 4 years ago | (#31104228)

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:It's not a DMS (1, Informative)

Anonymous Coward | more than 4 years ago | (#31104526)

http://bibdesk.sourceforge.net/

For Mac, I use Papers (4, Informative)

pacergh (882705) | more than 4 years ago | (#31104234)

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.

Re:For Mac, I use Papers (1)

Dystopian Rebel (714995) | more than 4 years ago | (#31104564)

Dell Mini 9

That's a small screen for manipulating documentation. How do you OS X on the DM9?

Re:For Mac, I use Papers (1)

Dystopian Rebel (714995) | more than 4 years ago | (#31104606)

How do you like OS X on the DM9?

There, fixed that for me.

Re:For Mac, I use Papers (2, Informative)

pacergh (882705) | more than 4 years ago | (#31104890)

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 to that. I'm confident the Papers folk with have an edition for iPad.

As for actual typing, I have a bluetooth keyboard (Apple) and Mouse (Apple, old BT mighty mouse). I actually typed 2 significant (25+ page) papers on it last spring for my masters classes.

My masters dissertation, though, was typed on a 15-inch Macbook Pro. I didn't have to lug it as far, and the extra screen space was nice.

When I wrote on the Dell Mini 9, I ended up writing drafts in Apple Pages or Scrivener, and then polished them up in Word (formatting and footnotes). I had to have a good Word output file because the school's printers were attached to computers with Word. ;-)

Altogether, I do like OS X on the Mini 9. Still, I have been tempted, very tempted, to try both Moblin and Google Chrome, just to see what it's like. I'll wait until I get that iPad, though, so I won't regret losing my Apple HackBook.

Zotero (5, Informative)

yes it is (1137335) | more than 4 years ago | (#31104252)

Zotero [zotero.org] may well be what you're looking for. Much better and more open source than EndNote (mentioned above).

Re:Zotero (2, Informative)

mmsimanga (775213) | more than 4 years ago | (#31104378)

+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.

Re:Zotero (1)

loftwyr (36717) | more than 4 years ago | (#31104642)

I've been using Zotero for a year and love it. The new version (2.0) is a godsend.

Re:Zotero (0)

Anonymous Coward | more than 4 years ago | (#31105248)

Zotero is superb, and 2.0 has a sync feature too. Let's you annotate and highlight, attach files to entries etc and creates really good references and bibliographies too.

Re:Zotero (1)

gclef (96311) | more than 4 years ago | (#31105866)

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.

Re:Zotero (1)

oronet commander (1084507) | more than 4 years ago | (#31106556)

There's no need to keep your data in the cloud when using Zotero. If you wish and synch is not needed, you can keep all your data locally. If you want to synch your files (not the archived references) you also can use your WebDAV server instead of a Zotero account.

Re:Zotero (1)

gclef (96311) | more than 4 years ago | (#31107038)

Huh...interesting. I read this from their docs:

The first step to syncing your Zotero 2.0 library is to create a zotero.org account.

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?

Re:Zotero (1)

yes it is (1137335) | more than 4 years ago | (#31107198)

Nah, it's primarily a local service with some "cloud" features.

Re:Zotero (1)

yes it is (1137335) | more than 4 years ago | (#31107226)

you can use rsync to get the data sync with appropriate firefox startup scripts or whatever, all the data is just stored in a directory (user configurable but by default in the firefox profile dirs).

Re:Zotero (1)

Kaell Meynn (1209080) | more than 4 years ago | (#31109772)

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 and whatnot). I dunno what they did in ver2, but it might be doable without using Zotero.org account.

Re:Zotero (0)

Anonymous Coward | more than 4 years ago | (#31106882)

Zotero 2.0 can store data locally and/or sync over the network. Previous versions of Zotero only allowed you to store your database locally.

Re:Zotero (2, Interesting)

takowl (905807) | more than 4 years ago | (#31107504)

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.

Discuss about it. (1)

ronzed (1743320) | more than 4 years ago | (#31104256)

Hi, I currently use KnowledgeTree CE. When I want to add a note, a link or a comment to one of my document (without editing it), I add a discussion (in the Document actions portlet) to that document.

Zotero (3, Informative)

Anonymous Coward | more than 4 years ago | (#31104340)

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.

Zotero (3, Insightful)

CAPSLOCK2000 (27149) | more than 4 years ago | (#31104368)

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 (2, Informative)

pongo000 (97357) | more than 4 years ago | (#31104374)

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).

Re:Consider Wikindx3 (2, Informative)

pongo000 (97357) | more than 4 years ago | (#31104460)

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.

theres plenty (0)

Anonymous Coward | more than 4 years ago | (#31104376)

my favorite: http://www.citavi.com/en/index.html

or zotero, or jabref. there's plenty of academic reference/document manager. and even more comparisons of them.

Looked at Microsoft Office workspace? (0)

Anonymous Coward | more than 4 years ago | (#31104380)

www.officelive.com

It is free, allows upto 5GB of data. Easy collaboration by sharing individual workspaces.

Built on Sharepoint technologies, worth a look.

Cheers
HS

Zotero (2, Insightful)

tyroneking (258793) | more than 4 years ago | (#31104416)

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? (1)

JT The Geek (1121759) | more than 4 years ago | (#31104420)

Depends largely on what your annotating and why. You might want to check out mendeley http://www.mendeley.com/ [mendeley.com] which has been pretty great for just managing documents. If your more interesting in annotating and learning a lot about what and why your annotating you might want to look into the fields of mixed methods research such as EthnoNotes.com http://www.ethnonotes.com./ [www.ethnonotes.com]

Mendeley (1, Interesting)

Anonymous Coward | more than 4 years ago | (#31104448)

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.

SharePoint or OneNote (2, Informative)

KnownIssues (1612961) | more than 4 years ago | (#31104510)

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.

Re:SharePoint or OneNote (1)

CodingHero (1545185) | more than 4 years ago | (#31104702)

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 (1, Informative)

Anonymous Coward | more than 4 years ago | (#31104940)

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 page, but nothing stops subsequent edits from moving the page image while the markups remain stationary.

So, I am quite interested in finding a better solution and have been reading these replies with interest. It is strange that this category of software, which seems so natural for a computer, has lagged so far behind.

Re:SharePoint or OneNote (0)

Anonymous Coward | more than 4 years ago | (#31105668)

Couldn't agree more, i have four years of course notes from university in OneNote - it is searchable, lets you embed documents & has saved my neck revision for exams on many an occasion ;)

TagTeam (2, Informative)

Anonymous Coward | more than 4 years ago | (#31104520)

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.

Confluence (0)

Anonymous Coward | more than 4 years ago | (#31104546)

Check out Confluence [http://www.atlassian.com/software/confluence/]- wiki that allows for attachments, etc. - easy to search and use, and comments, version history

Alfresco does all that you want... (1)

mccarthymp (1743342) | more than 4 years ago | (#31104610)

Alfresco does everything you require. Why are you looking into other solutions? With Alfresco you can keep track of comments on documents or have a conversation with others regarding the document which is archived along with the document. Alfresco Share allows you to view documents with a flash front end so that you never have to download the documents into Word, Excel or Adobe Reader.

An unmet need in the biotech community (2, Interesting)

cinnamon colbert (732724) | more than 4 years ago | (#31104622)

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:An unmet need in the biotech community (1)

guznik (1743356) | more than 4 years ago | (#31105066)

You may be interested in SparkLab 360: http://www.sparklix.com/product/sparklab [sparklix.com] . Aside of document management it also provides functionality specific for biological research such as reaction calculators and experimental data analysis, and allows you to associate documents with your lab protocols and experiments. It's very "Web 2.0-ish" and cheap (free for academic use).

Re:An unmet need in the biotech community (0)

Anonymous Coward | more than 4 years ago | (#31106358)

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

This can be your answer. http://www.daeja.com

We have written our application utilizing this component

Re:An unmet need in the biotech community (1)

msimm (580077) | more than 4 years ago | (#31106718)

Ya, right now my research project revolves around ligand research. Obviously there are a lot of great oss solutions that cover the basic document management stuff, and some really useful import/index/search features. Thumbing through a large collection of PDFs would be a nightmare (fortunately even with a standard DMS this isn't necessary).

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 able to do some of the basic think we've been doing for ages with printed paper, with the advantage of better/more flexible seaching and indexing, review matches and leave notes over everything I find relevant. Something like Google Documents with a footnotes feature, but since a lot of my resources are paid articles uploading just isn't much of an option.

If you find anything that ends up being particularly useful and think about it, ping me to make sure I took a good look at it myself.

Alos, user sdw claims to be developing something [slashdot.org] that may be similar:

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.

Maybe something of interest will come from it.

Re:An unmet need in the biotech community (1)

mnmlst (599134) | more than 4 years ago | (#31109152)

BasKet - OSS. I am a PhD student and asked about this very thing of some fellow Slashdotters and they recommended BasKet, a product similar to Microsoft's OneNote. I dearly love Foxit as my PDF reader/annotator, though Okular is quite good as well when I am fiddling with my Ubuntu box. Both are free products (as in beer). As I am stuck on a Vista computer for work/research, I use OneNote, but not as fanatically as some of my associates. Incredibly, the installation of EndNote on my PC trashed my MS Word 2007, so I have had to switch over to OpenOffice's word processor with excellent results so far. Sooner or later I will get around to setting up Windows 7 which hopefully can survive EndNote. I'm really liking the MediaWiki idea and some sort of OSS solution for doing bibliographies. I haven't really had to "share" much of my work yet, but I suppose that is coming later. On a related note, I'm a big fan of lifehacker.com and autohotkey.com using the AutoCorrect file for Autohotkey to substitute a lot of tedious typing for me. I type a few letters of a word IN ANY APPLICATION and autohotkey then replaces those few letters with yet another five dollar word: quantitative, qualitative, research, management, university, student, difference, relationship, and so on are on my self-generated list. Loads of other cool stuff can be done with autohotkey as well.

Google Wave (0)

Anonymous Coward | more than 4 years ago | (#31104674)

I wonder if Google Wave would be worth looking at for this...?

basic solutions are the best (2, Informative)

godrik (1287354) | more than 4 years ago | (#31104712)

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.

Evernote (1)

Kirschey (191850) | more than 4 years ago | (#31104758)

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.

mendeley (0)

Anonymous Coward | more than 4 years ago | (#31104766)

It does everything you want. The drawback is, it is not free software.
http://mendeley.com/ [mendeley.com]

Adobe LiveCycle (0)

Anonymous Coward | more than 4 years ago | (#31104808)

Adobe has some solutions for this problem space built on top of their LiveCycle platform. The Review Comment and Approval solution is all about managing document centric collaboration

http://www.adobe.com/devnet/livecycle/solutions/review_buildingblock.html

start with the scribd demo (1)

awilden (110846) | more than 4 years ago | (#31104814)

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 PHP back end to make the situation dynamic and persistent. I was able to graft it onto wordpress+Pods without too much difficulty (though I didn't do a good enough job to release into public).

I also was able to somewhat hack a similar thing for the google PDF reader, but because their API is still closed source I chose scribd -- even though it's a bigger pain to upload to scribd, at least I know that their API is supported.

I would still love to have "on document" annotation though, similar to what Acrobat or similar would give you, and I was hoping that since Google was drawing one character at a time that I could pull this off. But again, since it was all unsupported, I walked away from it and kept the suboptimal scribd version.

From what you describe ... (4, Informative)

oneiros27 (46144) | more than 4 years ago | (#31104834)

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.

Re:From what you describe ... (0)

Anonymous Coward | more than 4 years ago | (#31105620)

Version 2 of Zotero has group functionality.

Working on it, with many new ideas (1)

sdw (6809) | more than 4 years ago | (#31104894)

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 (1)

operator_error (1363139) | more than 4 years ago | (#31105006)

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]

TeleRiddler (0)

Anonymous Coward | more than 4 years ago | (#31105016)

I know I will probably get yelled at for posting this but Windows SharePoint Services 3.0 is free for download and does everything you need. You edit documents directly within the Microsoft Office suite. If you have MS Office this might be an option for you. If you are using OpenOffice, then probably not.

      --TR

Bibdesk (1)

qvatch (576224) | more than 4 years ago | (#31105084)

On a Mac, bibdesk wins hands down. It'll store and sort, search, use external editors, etc. Open source, and uses bibtex. http://bibdesk.sourceforge.net/ [sourceforge.net]

Bibdesk and CVS or SVN for Latex on Mac (1)

m0nstr42 (914269) | more than 4 years ago | (#31105148)

If you use a Mac and are in a Latex-centric field, I find Bibdesk (http://bibdesk.sourceforge.net/) really great for managing reference pdfs and use cvs or svn if I really want to manage a document I'm working on. There's no annotation in Bibdesk but you can record notes and it generates bibtex for you.

Bibdesk and Mendeley (2, Insightful)

coaxial (28297) | more than 4 years ago | (#31105510)

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.

Papers, Skim and DEVONthink Pro on OS X (1)

iliketrash (624051) | more than 4 years ago | (#31105638)

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 (1)

spasm (79260) | more than 4 years ago | (#31105832)

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 them in the database. Finally, it allows saving of metadata to pdfs, which I think can be used to save your notes about the file to the pdf metadata. Not so useful for non-pdf documents though. Finally, it pipes direct to latex and has a good plugin for openoffice, so if you use openoffice or latex you're in business..

if you use a Mac... (0)

Anonymous Coward | more than 4 years ago | (#31106246)

Sente (my favorite. From my point of view the one with most features)
http://www.thirdstreetsoftware.com/site/introduction.html

Bookends (great one - my main compalin is the interface)
www.sonnysoftware.com/

Papers (more limited compared to the others, but with the most appealing interface)

only Mac...

Abiword and abicollab.net (1)

technosaurus (1704630) | more than 4 years ago | (#31106322)

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? (1)

pbhj (607776) | more than 4 years ago | (#31106648)

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.

SpringCM has a nice pinpoint feature. (0)

Anonymous Coward | more than 4 years ago | (#31106734)

And doesn't require you to download the document either. You can also put documents through a workflow if you need.

how about UpLib? (0)

Anonymous Coward | more than 4 years ago | (#31107338)

How about UpLib, at http://uplib.parc.com/? It's open source and designed explicitly for this purpose. It can store and index PDF, Word, Web pages, photos, email, etc., and supports extensive annotation and cross-linking capabilities. Automatically full-text indexes everything, and uses Lucene for searching. It runs fine on a laptop.

Nuxeo (0)

Anonymous Coward | more than 4 years ago | (#31108146)

Nuxeo [nuxeo.com]

Onfolio (0)

Anonymous Coward | more than 4 years ago | (#31108316)

Onfolio was/is the best software for this, hands down. But M$ bought it and killed it. I'm still using a version I installed in 2007 and have tons of research in it, and I'm nervously awaiting the day when it no longer works with my browser and I have to dump all of my data as an .xml file and figure out what the hell to do with it. So I guess I have nothing to offer except to say: FUCK YOU MICROSOFT.

Sente works and has sync (1)

chandar (713362) | more than 4 years ago | (#31108998)

I have been using Sente. It allows you to sync one library with three copies of Sente on different computers. It also allows some copies to have restricted access, so you can share your libraries with friends. It a way to annotate within a pdf or to annotate the record.

Try http://abicollab.net (1)

msevior (145103) | more than 4 years ago | (#31109338)

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 (1)

Krannert IT (1675504) | more than 4 years ago | (#31109416)

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 module (for example you could index information from an invoice and send it directly into an accounting package as a new accounts payable item to be processed which is really powerfull if combined with a good scanning package such as Kofax which can automatically recognize a document and OCR the index fields it set up for, calculate its level of confidence, and automatically release the document or prompt a user to verify what it has read based on the confidence level). The client can run as a desktop application or as a web appliction.

Annotations can be added without checking a document out. Actually editing an editble document requires checking it out. Annotations can be as simple as highlighting something or as detailed as drawings and text. With press of a button annotation appear or dissapear.

The database back end can be MS SQL (express or full blown), MySQL, Oracle, as well as others. Some add-ons require full blown MS SQL but the basic system can run on a quite a large number of platforms. The software is modular so each add-on service can be put on any supported server. The license server (the most important part of the system since nothing works without it) seems to only run on Windows 2003 Server at this point but 2008 support is supposed to be out in a couple of months. I don't think they ever plan to release it for Linux.

The Web Server (if desired) requires IIS. EMC supports SUSE as a web client so it should work ony any Linux as long as you have Firefox (I did a quick web search and did find some Linux users having trouble trying to access something using Opera and Firefox but the error indicated an old version of ApplicationXTender).

ApplicationXTender is HIPAA complient and has a full audit trail so any changes to anything are logged. I don't let my users change index fields and since only TIFF documents are currently being stored only annotations can be added by a user which does not impact the original document I really have no use for the logs but I can definately see where it could be usefull. Office documents are strored as revisions so you can always revert to an earlier version and know who did what. Additional add-ons can allow full-text indexing (requires SQL Server) and document workflow.

I only use the basic system and use another software package (Kofax) to scan and automatically index documents which is very nice. Kofax can check what it reads against a user defined list which improves accuracy for certain field (such as a clients name). It can also use a database query to fill in information to be indexed which is great for accounting records (look up a vendor ID and fill in the full name for example). I also use another package (PlanetPress) to capture print streams index the document and send them directly into the system. Currently I am only using the system for accounting records and some rather static historical files. I plan to add the workflow module but it is expensive and I have to develop my strategy for capturing mail as it comes into our office (we get tons of it for a company of our size, it takes one person about 2-3 hours to open and sort on an average day, some days it can take all day when we get certain types of monthly bills. The number of different documents that come in also make this difficult to automate. A large portion of our business is record keeping and book keeping for our clients and the payoff on the system is very evident. What used to take hours of manual labor to find and put together can now be done in a matter of seconds.

We have about 50 different "document types" for about 100 customers stored in the system (totaling about 500,000 pages with an average document containing about 5 pages, almost all TIFF images of scanned documents (tiffs are much better than PDF's for storage)). The client will start an email with attachments and convert the TIFF inages into PDF documents. I have not moved our typcial office documents into the system yet but do plan to in the future but I have a few issues with our current employees and their levels of computer literacy. I can only make so many changes on them at a time before they start to get confused and mess everything up.

In order to help keep typically MS Office documents, txt files, xml documents, and the like organized we use standard naming conventions and a faily well thought out file system stucture. I have also set up MS Search Server to allow mislabled or misplaced documents to be found rather quickly (some users just never learn, and some documents are just so specialized that 6 months later you can never remember what you would have called it or where you would have stored it).

There you have it, this is my companies document management system and it seems to work quite well. I could definately improve on it. Adding a document workflow system would make some thing so much easier, by removing to-do list maintenance from our plates and allowing better oversight of our employees work and a full text document index would also be a significant improvement but issues with OCR reliability still not make a full-text index completely reliable. Hopefully this helps.

I have tried SharePoint and hated it. Don't get me wrong, SharePoint is not that bad but I do not like the feel of it, it is not as capable as ApplicationXTender and offers less integration options. SharePoint offers some features unavailble in ApplicationXTender but they are not important to my business while the rich integration options avalable with ApplicationXTender make it much more powerfull. When it comes down to it each organization must determine what its needs are before deciding to use one of these systems. Most of our document work is not collaborative, a manager writes a document, admin proofs and mails it. We rarely work as a team on large documents, most of what we work with is essentially form letters. Our main needs were space (disk space is a lot cheaper than the equivalent square footage) and ability to find documents cheaply. Longer term part of the plan is to minimize paper usage which we have started but we are no where near what we want. If you really just want to collaborate on large documents SharePoint may be a better solution but a solid evaluation of your needs and a payback calculation is more important that a great product with tons of features you (or the users) will never use.

Pfft, the answer's obvious! (1, Funny)

Anonymous Coward | more than 4 years ago | (#31109472)

Emacs!

What to do for mobile? (1)

ezdude (885983) | more than 4 years ago | (#31109484)

So, I've been using LabMeeting and BibDesk on my Macs. But since I've got a Droid now, I'm still trying to figure out the best way to read all my papers on that device, and probably an iPad when it comes out. Since Flash is not supported, LabMeeting won't work. Obviously, BibDesk is not supported right now. In fact, I'm guessing most of the sites/programs mentioned in this discussion won't work. So? The only solution I can think of so far to store all my PDF's "in the cloud" is Google Docs or Dropbox. Dropbox might be the winner here, especially since you can get the revision history service. It's not free, but it's cheap enough to be worth it.

Yellow Marker (1)

waslap (1453217) | more than 4 years ago | (#31109796)

If potential document annotation s/w creators reads this: please build in a feature that simulates the ubiquitous yellow marker for PDF documents. Would have made my life much easier studying for the SCJP.
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