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I am looking for a desktop application that can be used to efficiently manage hierarchical data structures, much like a filesystem tree hierarchy but that saves my hierarchy in a file. MSFT Excel is not great because it is really like a database table and I want to be able to click on a node and then add a child node to it and display it accordingly.

Ideally, each node name would be text but you could put anything in the body (e.g. media attachments etc.)

Does anybody know of an application like that?

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1  
you do not tell us which operating system you are using. –  Martin Jan 10 '13 at 20:41
    
you should also tell us what kind of information you want to manage (text, numbers, formatted text, ...). It would be helpful to tell more about the features you'd need. –  Martin Jan 10 '13 at 20:45
    
@Martin -- ideally, each node name would be text but you could put anything in the body (e.g. media attachments etc.) –  amphibient Jan 10 '13 at 21:24
    
hm, I'd say DevonThink Pro does what you want. –  Martin Jan 10 '13 at 21:53
    
If you want something "like a file system" why not use a file system? Is there a special reason why you want a single file? What about a directory structure in a mountable container file? –  0x6d64 Jan 14 '13 at 12:04

5 Answers 5

Zim meets your requirements of - hierarchy based editor - link/attachement of file - display image/table/mathematical formula - follow basic wiki syntaxe (header, bold, ...)

each node is saved as basic text file (and folder when necessary). it is also open sourced and cross platform...

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Please expand you answer by adding more details why you think the software will be an answer for the original question. Also, if you are affiliated with it, you have to disclose this. –  bytebuster Jan 15 '13 at 9:29
    
I'm not affiliated. Just a user who did take too much time to find this software when I had almost the same requirements. –  jojo l'abricot Jan 16 '13 at 10:29

I am using Keynote NF (Open Source Tabbed notebook with RichText editor and multi-level notes)

KeyNote NF is a flexible, multi-featured tabbed notebook, based on Windows standard RichEdit control. Its always accessible with a single keypress, even if you work in another application.

The basic idea in KeyNote NF is that you can include many separate notes within a single file. This means that you do not need to open several files - for most purposes it is enough to create only one file and hold all your notes inside it. With the addition of the tree-type notes, you now have a three-dimensional notebook: many notes within one file and a multi-level, nested pages within a single note. Keynotes interface and behavior are extremely configurable.

With powerful text formatting capabilities, easily navigable interface and additional features such as styles, macros, plugins, and templates, KeyNote is has become the favorite note keeper, diary, outliner, knowledge base and information manager for thousands of users (including myself)

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DevonThink Pro does what you want, IMHO.

It creates a database (not one single file, but you do not have to care about the file structure inside the database) and you can create a hierarchical structure of directories in this database.
Each directory can contain subdirectories and/or files (afaik you can save every possible file in there).

more features:

  • you can create text "nodes" on the fly
  • each file in the database has a name (title) in text format
  • you can assign tags to the objects in the database
  • you can create hyperlinks
  • you can save web pages in the db
  • the software can also handle several databases in parallel, so you can split or join existing databases
  • you can create "virtual" folders (collecting a subset of items from the database, based on complex search criteria)

it's a very powerful software and I'm using it for some years now for my research work and for storing text snippets, images, etc.

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What about mind mapping?

There is a lot of mindmapping software out there, commercial and free...

Freeplane is free and a very powerful tool, that can

  • create hierarchical tree structures only with keyboard commands,
  • can use html code in nodes,
  • can add attributes to nodes,
  • can be extended with groovy scripts and much more.
  • can easily link to external files or other mindmaps, however embedding files afaik does only work for images and the image is saved in a separate file (managed by freeplane)
  • And it is platform independent, so available for Windows, MacOS and Linux

http://freeplane.sourceforge.net/

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You could also use an outliner software.

I'm not sure which ones exist for MS Windows.
For MacOS X there is e. g. OmniOutliner.

And there is also the excellent Emacs org-mode, which can be used to create tree-like outlines in plain text files with lots of useful features (from TODO lists, to time-tracking or hyperlinks between entries...)

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