[Om] Newbie troubles...

Christoph LANGE ch.lange at jacobs-university.de
Thu Mar 25 21:29:59 CET 2010

Hi Herli,

  let me reply to both of your mails here, including the mail that you posted
to om3 at openmath.org.  As I said, the OMDoc mailing list
(http://lists.jacobs-university.de/mailman/listinfo/project-omdoc) will be the
most appropriate place for discussing the details, so let us know when you got
subscribed there.

So you already have an OWL ontology for physics and want to _add_ information
about mathematical formulae and inferences?  Or do you want to start from
scratch and are looking for the right ontology language?

> My dissertation project is about representing Physical Science concepts. As
> first step i wrote an OWL ontology. However, OWL2 language has no sufficient
> expressiveness to represent assertions like:
> For all field F, if rot F = 0 then F is a conservative field.

It is right that OWL cannot express this, and that OMDoc can.  The question is
what you want to do with that information.  If you want to publish it on the
web, OMDoc (and then XHTML+MathML generated from it) is a good choice.  If you
want to publish it on paper, you might consider writing it down in sTeX, the
LaTeX syntax for OMDoc, as that gives you both OMDoc and high-quality PDF.  If
you want to do automated reasoning, there are various (mostly half-done)
translators from OMDoc to the native languages of proof assistants.  If you
want to do queries over the structure of a document collection, OMDoc together
with the TNTBase database is a good choice.  See
https://svn.omdoc.org/repos/jomdoc/doc/pubs/eswc-demo10/gencs-lod.pdf for a
recent publication that covers all of these topics.

Given that OWL ontologies for physics already exist (e.g. SWEET:
http://sweet.jpl.nasa.gov/2.0/) you may want to go for a combination.
Combining OMDoc with OWL ontologies is partly described in
https://svn.omdoc.org/repos/omdoc/trunk/doc/blue/foaf/mkm09.pdf, but there has
been further work done since then.  You basically have the following
* You can convert an OWL ontology to OMDoc to get started
* You can author OWL ontologies in OMDoc, which gives you additional
  expressivity, better ways of modeling modularity, and better documentation
* The OWL-compatible subset of such an ontology can be converted back to OWL.
* Ontologies implemented in OMDoc can reference existing ontologies
  implemented in OWL.
* Any OMDoc document can contain arbitrary RDFa metadata.  Those can also be
  used to establish links to existing ontologies.

2010-03-25 12:59 Herli Joaquim de Menezes <herlimenezes at gmail.com>:
> I tried to repeat some examples of this book using Eclipse Web Tools got no
> succes because some lines expressing dc: at XML code are not recognized by
> Eclipse. Should I drop Eclipse and do this from the scratch using Emacs, for
> example?

I have not worked on OMDoc with Eclipse either, but it should work.  You can
try to delete the <!DOCTYPE> declaration, if that is the problem.  As long as
the dc:* namespace is declared, everything should work.  Using the DTD is not
advisable anyway for what _you_ need, as the new ontology- and RDFa-related
facilities are currently only implemented in the work-in-progress version
OMDoc 1.3, whose DTD is not up date, or which will no longer have a DTD at
all.  But there is an up-to-date Relax NG schema at
https://svn.omdoc.org/repos/omdoc/branches/omdoc-1.3/rnc.  That is known to
work with Emacs's nxml-mode.  For detailed Eclipse questions you might want to
ask our Eclipse expert Constantin Jucovschi, who is working on an Eclipse
plugin for sTeX (see http://kwarc.info/kohlhase/submit/mkm10-stexide.pdf)

> 1.  there is no means to represent mathematical formulas in OWL

Right, but as said above it depends on what you want to do with the formulae.
If you want to do automated inference or e.g. computer algebra, you will need
OpenMath or OMDoc.  But the SWEET ontology can also represent certain
superficial characteristics of mathematical operations in OWL.

> 2.  the inference engine of OWL DL does not handle mathematical assertions
> and there is no means to handle mathematical inferences, because there is no
> way to evaluate expressions in OWL

So it seems you do need OMDoc.

> 3.  I am trying to write some piece of xml code using OmDoc and integrate by
> means of imports in OWL ontology.

Not sure how you want to do this.  But one of the OMDoc/OWL migration paths
mentioned above should help.

> Im using as reference Kohlhase's OmDoc1.2 book.

This book is somewhat outdated but still the most comprehensive overview of
the OMDoc XML syntax and tools (without certain extensions made in the
meantime).  You might also find these useful:

https://svn.omdoc.org/repos/omdoc/branches/omdoc-1.3/doc/spec (OMDoc 1.3 spec,
work in progress)
http://omdoc.org/pubs.html (OMDoc-related publications)

Finally, if a trip to Paris in July is realistic for you, we are preparing a
"content math training camp" co-located with the CICM conference
(http://cicm2010.cnam.fr/).  It will take place from July 5 to 7.  That would
be a good opportunity for getting a hands-on experience on OpenMath, OMDoc and
related tools.  The overall conference will extend to July 10 and host more
events that might be interesting for you.



Christoph Lange, Jacobs Univ. Bremen, http://kwarc.info/clange, Skype duke4701
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