[brachiator]

Does anyone know of good note-taking apps that function as databases? I'm going to be starting the first academic-type research I've done since my 3x5 notecard days, and I'd like to be able to type up quotes and notes and bibliographical information and then search them out by keyword, etc.

I am taking a look at NoteWorthy, which does this using the old notecard metaphor, but I wonder if there isn't another solution. Or maybe I should learn to run MySQL?

thanks! Mike

[squilla]

There are several apps that might do, depending on how fancy you want to get. Try iData for a basic app that does most things pretty well. Try Supercard for something programmable with lots of possibilities. SuperCard is a HyperCard replacement.

[midwinter]

Honest-to-god, a basic text editor is what you want.

[brettcamp]

I used to use Hypercard for this, and if apple had given us an OSX version, I'd STILL be using it. (In fact, I will until the project I started in hypercard is done. Then, no more Classic!) I auditioned a few replacements, including iOrganize, Parsnips, and MacJournal, all of which had their strong points. Boswell also looks quite promising. But I finally settled on DEVONnote (there's a richer version called DevonThink but I didn't really need the extra features), which is quite powerful and pretty cheap. Also has a helpful user community and is very Mac-oriented.

Here are some more (not all are relational) that I looked at briefly but rejected because of cost or some other unsuitability for my needs, but you should check them all out and see what works for you.

Miss Lonelynotes (don't let the dreadful name keep you away)
Hog Bay Notebook
Circus Ponies Notebook
Notetaker
Ulysses
iOrganizeX
iPasteboard
MyMind
OmniOutliner
Noteworthy Virtual Notecards
Boswell
CopyWrite

Let us know what you decide.

[Shades of Gray]

If you want a detailed evaluation of the process of note-taking, outlining, and database intergration, take a look at what Ted Goranson (the grandfather of this area) has written in a series of articles over the past 18 months:

Outliners, NoteTakers, and More

[threestain]

voodoopad works quite well like this - I use it to write up all my medical notes

[brachiator]

Thanks so much everyone! This info is just what I needed.

My concerns here are two: certainly, to be able to search out the whole kaboodle by keywords, but also to be able to conveniently "flip" through all or a group of the notes without searching. Now, off to chew through the suggestions for the one that fits me...

Incidentally, and in response to midwinter's comment, I went through the Tiger preview on the Apple site last night, for the first time. Spotlight is pretty cool, and I wonder if I mightn't even just be able to create a bunch of basic text-editor files as "note cards" that would then be accessible via Spotlight in whatever way I wanted...

Thanks again! Mike

[besson3c]

My suggestion:

Install a Wiki (such as Mediawiki - the Wikipedia is based on this).

You can run it locally if you don't always have internet access.

[Mithras]

Originally posted by besson3c:
My suggestion:
Install a Wiki (such as Mediawiki - the Wikipedia is based on this).

This is a very nice idea. WikisAreWonderful.

[lavar78]

Originally posted by Mithras:
This is a very nice idea. WikisAreWonderful.

VoodooPad is a good choice if you want a Wiki.

[BHD]

There is no ideal application as yet. VoodooPad, unfortunately, completely misses one of the key points of Wikis, which is not just about linking, but also about easy authoring of semantic content. Its XML export support is sort of a joke in that context.

Wikis are great for note-taking, and there are a bunch of free ones in all sorts of languages (the Ruby-based Instiki is nice and simple to install). Unfortunately, none of them are yet well-suited to bibliographic data. The open source bibliographic application RefDB has good underpinnings and an extended note feature that is designed precisely for this use, but it does not yet have a good web front-end to make it accessible.

Whatever you do, I suggest finding a solution (or group of them) that are really good on open data export; preferably clean and semantically rich XML, or at least XHTML..

[midwinter]

Originally posted by BHD:
There is no ideal application as yet. VoodooPad, unfortunately, completely misses one of the key points of Wikis, which is not just about linking, but also about easy authoring of semantic content. Its XML export support is sort of a joke in that context.

Wikis are great for note-taking, and there are a bunch of free ones in all sorts of languages (the Ruby-based Instiki is nice and simple to install). Unfortunately, none of them are yet well-suited to bibliographic data. The open source bibliographic application RefDB has good underpinnings and an extended note feature that is designed precisely for this use, but it does not yet have a good web front-end to make it accessible.

Whatever you do, I suggest finding a solution (or group of them) that are really good on open data export; preferably clean and semantically rich XML, or at least XHTML..

Bingo. I use VoodooPad from time to time. MacJournal from time to time. DevonNote from time to time. They all have their own problems, most of which revolve around exporting data and syncing data among multiple computers.

As I said earlier, a plain word process or text editor is what I keep going back to. Usually, I even print out note cards of everything I type up, but in the end, being able to search for information is what it's all about, and "Search" in a word processor covers that.

[BHD]

Originally posted by midwinter:
As I said earlier, a plain word process or text editor is what I keep going back to. Usually, I even print out note cards of everything I type up, but in the end, being able to search for information is what it's all about, and "Search" in a word processor covers that.

Well ... that depends on your needs. In my case, I have around 1,500 bibliographic records, many of them with extensive annotations. In that context, flat files aren't realistic at all.

My preferred solution these days involves storing a bunch of linked XML files in an the free eXist XML DB. That provides a lot of power (for example, you can take HTML docs, convert them to XHTML, attach class attributes to chunks of content, and then query them), though it still needs a nice web front-end, particularly for content authoring.

[midwinter]

Originally posted by BHD:
Well ... that depends on your needs. In my case, I have around 1,500 bibliographic records, many of them with extensive annotations. In that context, flat files aren't realistic at all.

My preferred solution these days involves storing a bunch of linked XML files in an the free eXist XML DB. That provides a lot of power (for example, you can take HTML docs, convert them to XHTML, attach class attributes to chunks of content, and then query them), though it still needs a nice web front-end, particularly for content authoring.

I'm pretty sure I know what you're talking about (I'm a professional researcher and academic). I'm just saying that every attempt I've ever made to use some kind of database-driven software/application just for my notes has been an abject failure.

With that said, You might want to look at some of the bibliographic software out there, though, as well as DevonNote. Hell, I even gave Moveable Type a spin at this a while back.

[brachiator]

midwinter and BHD, yes, these are precisely my concerns. It's not just notes, as such, but also bibliographic material and quotations. In my legal research I do it pretty much with an ever-growing Word file, but that has its drawbacks, and the new project would be multi-disciplinary. I guess that I'll have to take some time to play around with some of the options. I'd just hate to get locked into one proprietary format, and I understand that is why so many have suggested something exportable to XML.

Ideally, I suppose, I'd like to be able to include images and PDFs in the database. That's why the idea of Spotlight sounds cool... I don't want to have to spend a lot of time coding or maintaining the DB.

[Millennium]

If you need to cross-reference your notes, then there's nothing better than a wiki. Most of them have good search engines too. Personally I use OmniOutliner, but it doesn't have the cross-referencing capabilities that you want.

I've got MoinMoin installed on my machine; it's not my usual note-taking style, but it works quite well. Installing MoinMoin isn't for the fainthearted, though; the instructions are good but it still delves into the world of Scary Terminal Hacks.

What would really be neat would be to combine an outliner like OmniOutliner with wiki-style cross-references. Is there an app which does this?

[BHD]

Originally posted by Millennium:
I've got MoinMoin installed on my machine; it's not my usual note-taking style, but it works quite well. Installing MoinMoin isn't for the fainthearted, though; the instructions are good but it still delves into the world of Scary Terminal Hacks.

This is among the reasons I was suggesting looking at Instiki . It's really easy to install (aside from needing Ruby 1.8 or later installed), and has good export support.

[Shades of Gray]

Originally posted by Millennium:
What would really be neat would be to combine an outliner like OmniOutliner with wiki-style cross-references. Is there an app which does this?

Many years ago Palimpsest from an Australian company seemed moving in this direction. However, they stopped development on it about four years ago, when OS X was still under development.

[BHD]

Originally posted by brachiator:
midwinter and BHD, yes, these are precisely my concerns. It's not just notes, as such, but also bibliographic material and quotations. In my legal research I do it pretty much with an ever-growing Word file, but that has its drawbacks ...

Yes, like potential lost data. I would never trust any important data to Word and the .doc format.

I guess that I'll have to take some time to play around with some of the options. I'd just hate to get locked into one proprietary format, and I understand that is why so many have suggested something exportable to XML.

Right.

Ideally, I suppose, I'd like to be able to include images and PDFs in the database. That's why the idea of Spotlight sounds cool... I don't want to have to spend a lot of time coding or maintaining the DB.

A lot of wikis support images, and pdf files can just be links. I suggest your first thing to play with is a wiki. Apps like OmniOutliner 3, NoteTaker 2003, Notebook, or DevonThink are also�as already mentioned�worth exploring.

[Millennium]

Originally posted by Shades of Gray:
Many years ago Palimpsest from an Australian company seemed moving in this direction. However, they stopped development on it about four years ago, when OS X was still under development.

Ah yes, WestCiv. They currently make Style Master and Layout Master, though current trends are disturbing: they seem to be shifting towards Windows-only development.

[brettcamp]

DEVONnote and -think both support Wiki links as well as static cross links to other files within the Devon database or any other file. Now I'm trying to figure out how Wiki can help me with researching and writing. Seems a potentially powerful tool.

[brachiator]

[QUOTE]Originally posted by BHD:
This is among the reasons I was suggesting looking at Instiki . It's really easy to install (aside from needing Ruby 1.8 or later installed), and has good export support. [/QUOTE

I think that I will start by playing with a wiki. Mediawiki was also mentioned -- any comments on the relative ease of use among Mediawiki, Instiki, and the rest?

thanks!

[Love Calm Quiet]

It might take a sophisticated combination of db files, but I wonder if FileMaker Pro couldn't be used to build an app. I'm surprised I haven't heard of an attempt as yet.

[Millennium]

Originally posted by brachiator:
I think that I will start by playing with a wiki. Mediawiki was also mentioned -- any comments on the relative ease of use among Mediawiki, Instiki, and the rest?

Installing MediaWiki isn't for the fainthearted. I've done it before, and it requires a fair amount of Terminal hacking. You'll also need to get the MySQL database, which throws another layer of complexity on top of things (Instiki and MoinMoin don't use relational databases). Fink is your friend when it comes to getting MySQL, but you'll still have to get it set up properly.

Instiki would be the easiest to install, were it not for one thing: you need Ruby 1.8 to go along with it. Panther only comes with Ruby 1.6.8, so you'll need to get the latest version of Ruby first. I think you might be able to do this through fink, but I'm not certain.

MoinMoin probably has the best documented of the three when it comes to installs, and it has no additional requirements. That doesn't mean it's necessarily easy, though; if you want it to always run at startup then you'll need to install it into your version of Apache. This is well-documented, but delves pretty severely into Terminal stuff.

Of the three wikis I mention, MoinMoin is also the only one you can install without requiring the Developer tools at some point in the process, because everything you need already comes with Panther. So if you don't have the Developer tools installed, MoinMoin is really your only choice in this area.

As for using these once they're installed, a wiki is a wiki, more or less. There aren't really any substantial ease-of-use differences between the three. If you've never used wikis before then there's a slight learning curve.

[squilla]

Originally posted by brachiator:

I think that I will start by playing with a wiki. Mediawiki was also mentioned -- any comments on the relative ease of use among Mediawiki, Instiki, and the rest?

thanks!

ProjectForum might be of interest if you want a wiki. It installs like any other application-- no fuss with databases, apache, etc. It's meant to support group projects, but it will easily support one-- and I think there's a limited free version which might suit.

[TheAlbinoBowler]

Originally posted by Millennium:
What would really be neat would be to combine an outliner like OmniOutliner with wiki-style cross-references. Is there an app which does this?

Hog Bay Notebook is a great outliner (it can have outlines of outlines) that supports wiki links within its notes and lots of other pretty unique features.

[Shades of Gray]

Originally posted by Love Calm Quiet:
It might take a sophisticated combination of db files, but I wonder if FileMaker Pro couldn't be used to build an app. I'm surprised I haven't heard of an attempt as yet.

Me too. I have FMP 7.0 and would love to develop something there. My database development skills are just above zero. And time is in short supply. But a FMP solution would be most welcome!

[BHD]

Originally posted by Shades of Gray:
Me too. I have FMP 7.0 and would love to develop something there. My database development skills are just above zero. And time is in short supply. But a FMP solution would be most welcome!

With all of the excellent free software databases out there (Postgres, MySQL, SQLite, etc.), and nice web development languages like PHP, Ruby, Python, etc., why bother with FM?

[Big Mac]

Well, BHD, I assume it's because the free tools have steep learning curves and require at least a modest appetite for programming.

[Shades of Gray]

And since I have FMP already (I got a very good deal on upgrading from FMP 2.1), why not use it?

[headbirth]

There's also jotz and my favorite ScrapIt Pro (http://www.johnvholder.com/sipxdesc.html)

[brachiator]

Hi gang, any new insights on this, or new apps? Thanks!

[Rainy Day]

Well, with CoreData in Tiger, you could practically build your own without doing any programming. Take a look at the videos on this page to see what i mean.

[swamibooba]

If you're working on research, with a lot of documents that need sifting through, DEVONthink is the best option in OS X. It takes some work to get up and running, and for it to really work a database needs a lot of documents. But what DEVONthink lacks in quick setup it makes up for in very powerful searches. Since it looks for the semantic relationships of words, it's easy to find near-hits which are usually more interesting.

I'm a hard core information junkie, and I have virtual piles and piles of scanned documents, web pages, as well as all of my writings and notes. And I can find something I collected a year ago pretty quickly without having to know many details about the document. It's also very useful to open a document and us its "See Also" pane which shows other documents which are similar.

There's several different versions of DEVONthink. I use the Pro version because it lets me manage very large files and I don't have to worry about file restrictions, and so I can have multiple databases. If you can live without those (and a few other things) the Personal version is just fine. Also, if all you need are smallish text files like your note cards, then DEVONnote would be just fine.

I can't recommend DEVONthink enough for document management. It blows away any system I've ever used.

(BTW, Steven Berlin Johnson has a great article on how he uses DEVONthink for research.)

[kman42]

I'll jump in. Yojimbo made a big fuss when it came out, but I haven't tried it.

For bibliographic data, especially in biomedical fields you can't beat Bookends. It is one of the best apps around and it gets better with every FREQUENT version.

I used to use Devonthink, but it was overkill and SLOW. Now I attach all my PDFs to my references in Bookends. I am still considering an application like Yojimbo to keep the other scraps of data I have piling up, but for now I just throw it all in a folder and let Spotlight do the work.

I get the idea that you are doing a different type of research so these might not be right up your alley, but definitely check out Bookends if you need bibliographic software.

kman

[brachiator]

Thanks, Rainy, Swami and Kman! I will look at DevonThink. Building an app with Core Data is a bit beyond me just now (in time as well as skill).

What I have just started doing is using a wiki. I tried to install Instiki without much success and am now trying MoinX, which is available as a binary.

I took a look at Bookends, but could not quite figure out how to use it to make "note cards" of quotations &c that would be linked up to the bibliographic entry card...

I'll keep you posted! Thanks again. I'm off to read the Steven Berlin Johnson article now... :-)

[threestain]

could try stickybrain as well - with that and voodoopad I'm somehow in control half the time.

well maybe...

[Gee4orce]

HogBay (now Mori) would be my choice : but they're in the process of re-writing the whole app and it has the feeling of being semi-complete.

OmniOutliner is my default note-taker, but obvously it's geared up to outlines.

you could even just rely on folders and text files in the finder - or maybe HTML pages if you wanted a nicer interface when reading.

[peeb]

Have you tried WikiNotes? It's free, basic, and quite fun.