Re: [Obo-format] OBO BNF by Ian Horrocks

[Christine G. <Chr...@un...>]

Hi Chris

> it is likely the obof1.3 will have a formal semantics defined
> directly in FOL and will have some support for n-ary relations,

sorry I may have missed some emails on that list,
is it possible to have a short explanation about this?

thanks

Christine
----- Original Message -----
From: "Chris Mungall" <cj...@fr...>
To: <st...@in...>
Cc: "Dilvan Moreira" <di...@gm...>; <obo...@li...>
Sent: Thursday, February 08, 2007 12:50 AM
Subject: Re: [Obo-format] OBO BNF by Ian Horrocks


>
> On Feb 7, 2007, at 3:24 PM, st...@in... wrote:
>
> > I agree with Dilvan, a spreadsheet or a Wiki could capture the
> > discussion better. I'd hope that the semantic mapping would not
> > require us to revisit the annotation (synonym/dbxref etc) mapping
> > we have agreed on - they ought to be pretty much orthogonal. (i
> > realise OWL 1.1 would provide additional annotation possibilities
> > which would be worth exploring)
>
> It's way too early to discuss the mapping of Obof1.3 to OWL (1.0 or
> 1.1) since the roadmap for the former is coalescing. Details will be
> posted when they are ready. As well as tidying up some minor details,
> it is likely the obof1.3 will have a formal semantics defined
> directly in FOL and will have some support for n-ary relations,
> particularly time-indexed instance level relations. Most of this will
> remain completely invisible to the average user.
>
> We can still discuss obof1.2 to OWL 1.1 as details of the latter
> become clear. But we should draw a line between this and our current
> stable mapping for obof1.2<->owl1.0
>
> > There two obvious 'scoping' questions:
> > - how much progress can be made in mapping to OWL without pulling-
> > apart GO terms e.g. represent Carbohydrate and actsOn in order to
> > represent 'CarbohydrateMetabolism'. This has been tried, of course,
> > is anyone continuing this work?
>
> I think this is orthogonal to the OboInOwl discussion - there is the
> obo-crossproduct list for this; see also the link I previously posted:
> http://www.berkeleybop.org/ontologies/#logical_definitions
>
> This work has nothing to do with OWL per-se
>
> > - as OBO 1.2+ mirrors OWL, and we have OWL plugins and parsers for
> > the major editors, is there not a case for just using OWL? -
> > apologies if this is old ground rather than new....
>
> It is old ground, and the answer is emphatically, no :-)
>
> > Stuart
> >
> >
> > Quoting Dilvan Moreira <di...@gm...>:
> >
> >>
> >>   Hi,
> >>
> >>   This thread has been quite interesting to follow. But it seems
> >> that the
> >> subject changed from OBO BNF to mapping OBO 1.3 to OWL 1.1. I went
> >> to Ian
> >> web site, and there is a mapping from OBO 1.2 to OWL 1.1. But it
> >> would be
> >> great to have some form of tentative mapping from OBO 1.3 to OWL
> >> 1.1. We
> >> could use Google Spreadsheets to make it public and use the
> >> current mapping
> >> as a start point (the advantage is that everybody can edit it). It
> >> certainly
> >> would be very useful to understand the changes and new goals of
> >> both formats
> >> (OBO 1.3 and OWL 1.1). It can also be used to guide a future
> >> release of the
> >> current mapping, so we won't introduce future incompatibilities.
> >>
> >>   Chris and Ian, would you like to jump start such a spreadsheet?
> >>
> >> --
> >> Dilvan de Abreu Moreira, Ph.D.     di...@st...
> >> SMI-Stanford Phone: 650-725 6236     http://java.icmc.usp.br
> >> Warning: I use a spam filter, some emails sent to me CAN be lost!
> >>
> >>
> >
>
>
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