Re: Manchester Syntax document ready (ACTION-205)

From: "Alan Ruttenberg" <>
Subject: Re: Manchester Syntax document ready (ACTION-205)
Date: Mon, 22 Sep 2008 22:56:08 -0400

> On Mon, Sep 22, 2008 at 7:45 PM, Peter F. Patel-Schneider
> <> wrote:
> > I don't know what you are asking for here.
> >
> > It is true that annotations interfere with the flow, and thus make
> > ontology dumps hard to read, but what else can be done?
> The issue is not the annotations but rather the display of any entity
> that does not use a human readable URI.

But how then can the Manchester syntax help?  Do you want to have a
"dump" of an entity not use its URI?  That doesn't seem to allow
reloading.  I don't see what role the Manchester syntax has to play here
at all.

> > I will change the "user-friendly" bit to talk explicitly about
> descriptions. 
> I'd rather live up to the "user-friendly". The implementation of
> Manchester syntax in Protege allows the use of a label in place of a
> localname in expressions.

Sure, and that is very nice, and a very useful feature for user tools.
But, again, what role does a syntax for OWL 2 have to play here?

> The first thing I would suggest is a syntax for comments that can be
> embedded by tools.
> "//" "#" "/* .. */" ";" are common convention, but "( .. )" fit in
> some spots. 
> With this a tool would be able to write, e.g.
> Class: obo:artifact
>     Annotations:
>        obo:IAO_0000116 ( editor note ) "There is not yet consensus this term",
>        obo:IAO_0000114 ( curation status ) obo:IAO_0000124 ( uncurated ),

> The next level of change would allow, in the case that a rdfs:label
> uniquely determines the identity of a term, a tool to use the
> rdfs:label in place of the uri ref.
> Class: obo:artifact
>     Annotations:
>        'editor note': "There is not yet consensus this term",
>        'curation status': 'uncurated',

This might be nice for display, and it is certainly useful to do in user
tools, for example when displaying an entity interactively, perhaps even
when the label is not unique.  However, to use this in dumps of ontologies
seems to be rather tricky.  What happens if the ontology is hand-edited
to remove a label used in this way, or to remove its uniqueness?  Do you
really want a syntax, even a syntax that is designed to be
user-friendly, to have to consider these sorts of things?

There is nothing to prevent tools from adding precisely these sorts of
extensions, and no interoperability concerns if these sorts of
extensions are solely used for display.

> Where the label is not unique it could be qualified by the uri
> Class: obo:artifact
>     Annotations:
>        'editor note' (obo:IAO_0000116) : "There is not yet consensus this term",
>        'curation status': 'uncurated',
> In the case that there are multiple language labels, we could leave it
> to the discretion of the tool to provide a mechanism for choosing a
> preferred language.

> -Alan


Received on Tuesday, 23 September 2008 10:30:16 UTC