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Searching and traversing? (Read 1731 times)
Mike77
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Searching and traversing?
Apr 13th, 2016, 11:10am
 
I am considering using Tinderbox for information management in our biology research lab. Can anyone describe for me, how can searching be done in this system, and in particular, can I follow/traverse links from a node to other nodes it's connected to?  I want to use this as a "lab brain" for storing a web of connected pieces of knowledge but it's essential that the user can easily get to connected pieces of info from any one node. Is this something that Tinderbox is good at? Looking for opinions relevant to our use case. Thanks!
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Mark Anderson
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Re: Searching and traversing?
Reply #1 - Apr 13th, 2016, 11:59am
 
Within a single map (sibling notes from an outline perspective) all links can be shown and when a note is selected all non linked items on the map are dimmed and connected items thus highlighted. Selection of the 'next' item is then manual.

Within a note's text ($Text), clicking a link to another note moves the text pane context to the link note. The left pane will select that note if (a) the new focus is in scope of the current view.

There is also the 'roadmap' which is initially viewed as a pop-over but can be 'torn-off' as stand-alone dialog.  This shows separate listings of the current note's inbound and outbound links (and the link type, etc.). Double-clicking an item in either listing allows the current (text pane focus) to move to that item.

Tinderbox can definitely store interrelations of items and, in my experience, is wonderful at allowing for emergent structure.  IOW, instead of starting with a blank forms you have to populate, you can add things as needed. This involves a small amount of set-up/configuration; once done that is usually not repeated. Also, whilst like anything new some set-up tasks may appear familiar, they are easily learned (others may differ on that, but I'll let them offer a counter view if they have one).

My hunch is the biggest adoption challenge is whether the vital parts of the task match (unstated?) assumptions about how things should look/work. Tinderbox itself has no problem tracking linkages and plays well with everything-buckets like DEVONThink.
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AsafKeller
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Re: Searching and traversing?
Reply #2 - Apr 14th, 2016, 11:08am
 
I have been using TB for several years for a similar purpose: A knowledge base of specific neuroscience topics. I find it invaluable, and I highly recommend it.

I still, however, hope for a map view in which navigation, and, in particular, viewing notes located in different containers, is more robust. TheBrain.com provides inspiration, as previously discussed here http://bit.ly/23HYD93.
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Mike77
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Re: Searching and traversing?
Reply #3 - Apr 15th, 2016, 7:52pm
 
>  I have been using TB for several years for a similar purpose: A knowledge base of specific neuroscience topics. I find it invaluable, and I highly recommend it.

  excellent!! Have you found any limitations as the database grows?  Do you attach large files/data to nodes? I need sort of a hybrid mind mapper and information manager (like Evernote or DevonThink) to keep our ideas and their attendant data files organized. Can you describe your use?
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Mark Bernstein
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Re: Searching and traversing?
Reply #4 - Apr 16th, 2016, 6:55am
 
When discussing performance at scale ("limitations as the database grows") it helps a lot to know what scale is contemplated.

If you have n items, opening and saving Tinderbox documents is (naturally) O(n). In practice, this is seldom much of an issue in Tinderbox 6.  

Spatial hypertext is usually thought to be most suitable for projects with hundreds or thousands of notes.  If you need hundreds of thousands of notes, a database is your only practical option. If you only need a dozen notes, Tinderbox might be overkill.
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jfontana
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Re: Searching and traversing?
Reply #5 - Apr 16th, 2016, 7:38am
 
One thing I find strangely missing, given the central role of hypertextuality in TB and other products from Eastgate is the ability of introducing anchors within notes. I know notes are meant to be short but sometimes they just grow long and one would like to be able to link to a particular section within a note from some other note.

This might not be relevant for automatic information extraction via agents (which is one of the strengths in TB) but it would certainly make information management more useful for users trying to gather relevant information from their notes.

JM

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David Bertenshaw
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Re: Searching and traversing?
Reply #6 - Apr 16th, 2016, 8:05am
 
I may be misunderstanding what you want, but you can highlight a selection of text in any note and create  a new note from it either as a sibling or child. (It's on the Note > Footnote menu.)

You can also select text and link it to an existing note (highlight the text, click Shift-opt-L and enter the desired target in the dialog box). In either case, press cmd-opt in the text and the anchor will be highlighted.

What you can't do, as far as I know, (and it would be really helpful if you could), is highlight a note (i.e. not text within, but the note itself in a map or outline) and use a shortcut key to create a new linked note.
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jfontana
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Re: Searching and traversing?
Reply #7 - Apr 16th, 2016, 8:57am
 
Hi David,

I didn't explain myself clearly. I was aware of the Shift-opt-L option but this doesn't do what I describe as "introducing anchors". What I mean is something which is very basic in HTML: linking within a page (http://www.echoecho.com/htmllinks08.htm).

So, I want to be able to link to a specific section of a not from within some other note. So, I'm writing text in a note and then I remember I have some relevant information inside another note. I write: "See an alternative view here."

If I do  Shift-opt-L I know I can link to the relevant note but I would like the link to take me to a specific fragment of the note. If the note is short, I can live with the present system but if the note is a little long, finding the relevant information can be difficult sometimes. It would be nice to have some back button to go back to the note containing the initial link  Wink. Anyway, this is what you can achieve with anchors.

I was aware that now it is possible to create footnotes but I had not used this feature as I don't use Tinderbox to create documents that I intend to publish. I've checked the functionality, though, and I see that it can be used to do something which is almost as good as what I wanted to do with the anchor: if you create a "footnote" with the relevant section, the footnote becomes a note which then you can link to. Cool. I did not think of that. Not exactly what I wanted but it will make things a lot better.

Thanks!
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Mark Anderson
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Re: Searching and traversing?
Reply #8 - Apr 16th, 2016, 11:06am
 
As it happens Tinderbox does, well - did, support lnbound links to note anchors. I think it was dropped as no one used them. In part I think this was due no one making use of the feature.

I'd suggest you contact Eastgate and explain your needs for their return.

As regards HTML export, exporting in-$Text anchors and linking to them has never been supported.
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David Bertenshaw
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Re: Searching and traversing?
Reply #9 - Apr 16th, 2016, 11:22am
 
Glad it helped

Quote:
I've checked the functionality, though, and I see that it can be used to do something which is almost as good as what I wanted to do with the anchor: if you create a "footnote" with the relevant section, the footnote becomes a note which then you can link to.


You don't even have to do anything to create the link -- TBX automatically creates an inbound and outbound note.

1. Select the text and click cmd-opt-cal-F for a new sibling note (shift-cmd-F for a new child note).

2. You'll be taken to the text field on the new note, which is automatically titled with the selected text. Add any clarifying text.  This new note has an inbound 'note' link from the original, and a outbound 'note+' link back to it.

3. Once you finished editing the new note, type cmd-return and you'll be taken back automatically to the text of the original note.

The text doesn't scroll back to your original location, unfortunately (I think retaining the edit location has been request by some people for a future version), but the apart from that it's a smooth process.

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« Last Edit: Apr 16th, 2016, 12:16pm by David Bertenshaw »  
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jfontana
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Re: Searching and traversing?
Reply #10 - Apr 16th, 2016, 1:16pm
 
OK. Thanks Mark and David. I'm surprised they decided to suppress such a basic HTML functionality if it was already there. Unless it created a problem, I think it would have been better to leave it alone in case some user decided to leverage it.

If I'm the only one that has a need for it (which I find a bit surprising), though, I'm not going to make other people waste their time.

It's not the easiest way to do it, but I'll use the footnote functionality as a way to get around this limitation. Knowing that you can go back to the original note using cmd-Enter helps in case you need a bit more context.
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Mark Anderson
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Re: Searching and traversing?
Reply #11 - Apr 16th, 2016, 2:49pm
 
I don't think it's lack of consideration. Tinderbox, being an open ended tool has a lot of little used feature. Each has to be maintained through lots of OS releases and hardware improvements. Little-used features are thus a cost. Pre v6, Tinderbox used the old Mac multi-window form of UI, keeping track of the scroll state of each text window proved problematic.

Implicit - it me - in your question is that the link target is also clear in the displayed note  That means more than just scrolling to a line in the $Text. Is the target (anchor) highlighted somehow? Should it be start of (displayed) text? The latter requires a different render from just laying in the $Text from the start.

Don't assume the developer won't listen, until you've asked. This is a user-to-user forum, not formal tech support. Asking for a feature here is not asking a question of the development. I'd email support. I think you'll find them more receptive than you perhaps presume.
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AsafKeller
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Re: Searching and traversing?
Reply #12 - Apr 17th, 2016, 2:55pm
 
Quote:
Have you found any limitations as the database grows?  Do you attach large files/data to nodes? I need sort of a hybrid mind mapper and information manager (like Evernote or DevonThink) to keep our ideas and their attendant data files organized. Can you describe your use?


I have about a dozen topic-specific files, the largest has about 1,500 notes.
No, I do not attach files or data; the notes are text only.
Some of the notes are exported to html; you can get an idea of their use by visiting: http://bit.ly/1lfRYCt (yes, that database needs some TLC...) (And thanks to Jack Baty for the blog template!)
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« Last Edit: Apr 17th, 2016, 2:58pm by AsafKeller »  
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