interactive keys

[David Remsen]

X:ID is still in development.  In fact, we have been developed a  
version for the National Marine Fisheries division here in Woods Hole  
to use for fish identifications at sea.   This will form the basis  
for version .67.

The critique of some of the functions is warranted, however the  
functions are not required to actually use a key.  We will however,  
address at least some of the issues with the functions particularly  
"Best."   Development lags because this isn't our primary area of  
development and I'm trying to stay targeted (not easy for me).   I am  
very appreciative that Mike Dallwitz took the time to review it.

I appreciate too that he mentioned that it has many good features.    
I think X:ID works very nicely, aside from some of the non-critical  
functions.   Keys can be authored entirely via the web interface.  It  
is XML-based and keys can be styled to integrate with databased  
content.  It's open source and freely available.   We built it  
because we liked Lucid and wanted something like it we could use on  
the web as well as give away.   It meets our needs.  If you like it,  
try it.  It runs on all platforms.  If you don't there are many other  
options and that kind of diversity is healthy and refreshing to see.

David Remsen
_____________________________________________
David Remsen
uBio Project Manager
Marine Biological Laboratory
Woods Hole, MA 02543
508-289-7632


On Mar 23, 2006, at 3:35 AM, Mike Dallwitz wrote:

> Rudy Jocqué wrote:
>
>> Apparently nobody mentioned X:ID. Does someone have experience  
>> with that
>> package?
>
> This program is free, and is available at
> http://uio.mbl.edu/services/key.html. The current version is shown  
> on the
> main page as 0.66 (July 2004). I don't think it has been updated  
> since then,
> although when you click on a link to a key you get the message 'You  
> are
> looking at an old version of X:ID; in 1 second you will be  
> automatically
> re-directed to the current version'. The link to the X:ID forum,  
> which might
> have clarified this, doesn't work.
>
> The system lacks some important features, such as error tolerance and
> character reliabilities, and the 'Best characters' algorithm is  
> worse than
> useless (see below).
>
> An interesting feature is the ability to change the appearance of  
> the user
> interface by means of style sheets. However, the examples currently
> available are unsatisfactory in various ways. The style sheet that  
> emulates
> the Lucid2 interface is probably the best, except for a serious bug  
> -  the
> 'feature' description is not shown in the 'Character States Chosen'  
> pane.
> This often results in meaningless lines such as 'triangular'  
> instead of
> 'Stem shape in cross section triangular'.
>
> At the request of the authors, I made some comments on the program  
> in May
> 2005. These are reproduced below, except for some rather detailed  
> ones on
> the user interfaces. I tested only the player, not the builder.
>
> Note that these comments don't constitute a review of the program,  
> which has
> many good features. I mentioned only the faults, so that they could  
> be fixed.
>
> ---------------------------------------------------------------------- 
> -----
>
> 'Misinterpretation'
>
> The default setting should be 'Allow uncertainties and  
> misinterpretation',
> and it should be possible to change this while using a key.
>
> Bingo
>
> The Lucid 'Bingo' option is harmful in the context of  
> identification - see
> 'Principles of Interactive Keys' at
> http://delta-intkey.com/www/interactivekeys.htm under the heading
> 'Differentiating attributes'.
>
> Best
>
> The X:ID 'Best' is a extension of 'Bingo', and isn't suitable for  
> finding
> the best characters for use in an identification.
>
> The problem with 'Bingo' and the X:ID implementation of  
> 'Best' (which is
> also used in MEKA) is not just that they are unhelpful for  
> identification -
> they are actually harmful. You would do better by selecting  
> characters at
> random, provided you used the 'Prune Redundants' option (if it worked
> correctly, which it doesn't in X:ID).
>
> For example, in the 'Aquatic Plants' key, suppose that your  
> specimen is
> Alternanthera. In the 'Best' list, the first character state that is
> exhibited by Alternanthera is 'Leaf arrangement on stem  
> (phyllotaxis I):
> opposite distichous 17'. This is 142nd in the list. Thus, you have to
> examine and reject 141 character states before arriving at the  
> correct one,
> and the probability of doing this without error is almost zero. If  
> you do
> manage to do this correctly, you still have 17 taxa remaining. In  
> the new
> 'Best' list, the first character state exhibited by Alternanthera  
> (Leaf
> venation: pinnate 4) is 87th on the list, and 4 taxa remain. And so  
> on.
>
> By comparison, using the 'Best' character found by Intkey at each  
> step, and
> selecting the first state exhibited by Alternanthera, results in an
> identification after 5 characters have been used.
>
> Prune Redundants
>
> I don't see the point of this option as it is currently implemented  
> in X:ID.
> Also, it's confusing because it puts into 'Character states chosen'  
> states
> that are not necessarily exhibited by the specimen.
>
> As implemented in Lucid, the option has two effects, which I  
> describe in
> 'Principles of Interactive Keys' under the headings 'Removing  
> redundant
> characters' and 'Removing redundant character states'. The former  
> effect is
> useful, but the latter is harmful. In Intkey, redundant characters are
> automatically removed in the 'Best' calculation. I think that  
> having it
> available separately is an unnecessary complication for most users.
>
> Similar Taxa
>
> The results given by X:ID are substantially different from those  
> given by
> Lucid. I haven't investigated the reason for this.
>
> Similarities and Differences
>
> The output from this option is almost unintelligible. For  
> comparison, I've
> attached the differences between the genera of Cyperaceae, as  
> output by
> Intkey (diff_intkey.rtf) and X:ID (diff_xid.txt). [These files are not
> attached to this posting.] The X:ID output is seemingly in almost  
> random
> order (even the states of a given character are not necessarily  
> contiguous),
> and there is no indication of which taxa exhibit the states. In the  
> Intkey
> output, notice the bold parts; these indicate characters for which  
> at least
> two of the taxa have non-overlapping states.
>
> Numeric Characters
>
> I gather from the forum that X:ID can handle numeric characters, but I
> couldn't find any examples in the keys at the Web site.
>
> ---------------------------------------------------------------------- 
> -----
>
> --
> Mike Dallwitz
> Contact information: http://delta-intkey.com/contact/dallwitz.htm
> DELTA home page: http://delta-intkey.com

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