[topicmapmail] k42 and superclass-subclass and class-instancerelationships

[Magdalena Litwin]

----- Original Message -----
From: "Thomas B. Passin" <tpassin@comcast.net>
To: <topicmapmail@infoloom.com>
Sent: Friday, March 21, 2003 1:57 AM
Subject: Re: [topicmapmail] k42 and superclass-subclass and
class-instancerelationships


> How you model something will depend in part on what you want to do with
it.
> My immediate inclination is to make the value of the EC number to be an
> occurrence of an enzyme.  The type of the occurrence would be a topic
> labeled, probably, "EC Number".
>

Hello,

I will thing about modeling "EC numbers" as occurrences but my problem was
not how to model this particular part of may database but how to build
superclass-sublclass and class-instance relationships in teh Empolis k42
application.

Let's try another example :-). There are six types of enzyme. Each of them
has got a lot of subtypes and each of this subtypes has got sub-subtypes
etc.

Enzymes
    -> oxidoreductases
    -> transferases
    -> hydrolases
    -> lyases
        * carbon-carbon lyases
            # carboxy-lyases
                - pyruvate decarboxylase
                - oxalate decarboxylase
                ...
                - sulfopyruvate decarboxylase
            # aldehyde-lyases
            ...
            # other carbon-carbon lyases
        * carbon-oxygen lyases
        * carbon-nitrogen lyases
        ...
        * other lyases
    -> isomerases
    -> ligases

I though its enough to mark such kinds of associations:
            *enzyme* is a superclass of *lyases*
            *lyases* is a superclass of *carbon-carbon lyases*
            *carbon-carbon lyases* is a suerclass of *carboxy-lyases*
            *carboxy-lyases* is a superclass of *pyruvate decarboxylase*

But it seems that the Empolis k42 application does not regard
superclass-subclass             relationships as tranzitive. According to
that a *pyruvate decarboxylase* is not an *enzyme*.
How can I model this hierarchy in the k42 application?

Regards,
Magdalena Litwin