Re: [cml/ccml-discuss] conditions/metadata in CMLSpect

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

At 11:59 13/06/2006, Stefan Kuhn wrote:
>Am Thursday 08 June 2006 23:03 schrieben Sie:
> > At 13:29 08/06/2006, Stefan Kuhn wrote:
> > >Dear Peter,
> > >thanks a lot for clarification. If we want to have substanceList in
> > > spectrum (I think it would be good), this needs to go into the schema,
> > > right? Would you do this? I feel a bit too unexperienced to do the
> > > change.
> > >Stefan
> >
> > I am now almost convinced that content models are
> > a mess and intend to change almost all of them to
> > "any".  Basically we cannot predict what we are
> > going to want as content and it is currently too
> > constraining. I'd like comments on this!
>
>My humble comments: I am afraid the whole CML project could get somehow
>invalid when not having strict content models. Isn't it a main point of CML
>to try to come up with a valid model? I see it is hard to do this, but=
 still
>worth trying. Furthermore: Wouldn't the jumbo application loose much of its
>use when the content model is too lazy?
>Stefan

There will be validation but it is not done with=20
the W3C approach - but a mixture of Schematron=20
and other approaches. The attributes are more important than the content=
 model

Cheers

> >
> > I can easily changes this in schema25. I am
> > wondering what we need for schema24?
> >
> > P.
> >
> > >Am Thursday 08 June 2006 10:21 schrieb peter murray-rust:
> > > > At 10:32 01/06/2006, Stefan Kuhn wrote:
> > > > Thanks very much - sorry for the delay...
> > > >
> > > > There are some important general points
> > > > here.  CML does not directly provide markup for
> > > > most chemical concepts, but enables users to
> > > > create dictionaries describing to concept. These
> > > > dictionaries can have any of the dataTypes that
> > > > CML allows - scalar, matrix, array, substance,
> > > > condition, parameter, etc. For example Bruker
> > > > often include several hundred concepts in their
> > > > file and I would expect a Bruker-NMR dictionary
> > > > to manage them. Most of the concepts below can be managed in this=
 way.
> > > >
> > > > The exceptions are:
> > > > * when a concept has a new data type. This might
> > > > happen for (say) 3- dimensional data, 3rd rank tensor, etc.
> > > > * when the data are fundamental to the
> > > > algorithmic processing and interpretation of the
> > > > information. I am not sure that there is anything
> > > > required for spectra. For example NMR frequency -
> > > > which is required to convert between Hz and ppm -
> > > > is only required for NMR spectra. We need to
> > > > avoid vocabulary pollution. Here there is a real
> > > > need for an NMR dictionary which contains core concepts.
> > > >
> > > > >Hi all, hi Peter, we (Tobias and me) come across
> > > > >some problems with metadata (or sort of) in
> > > > >CMLSpect, starting from what is defined as
> > > > >conditions in NMRShiftDB. I try to translate
> > > > >them to CML entries. The conditons are: -
> > > > >Temperature: Fine, can become an entry in conditionList
> > > >
> > > > Yes.
> > > >
> > > > >  - Field strength: Similar, only problem:
> > > > > cmlDict does not seem to have an entry for
> > > > > field strength, similar to temperature.
> > > >
> > > > Correct. Please add it! The idea of the
> > > > dictionaries is that they can be created by the
> > > > community and this looks like an excellent example.
> > > >
> > > > >Or did I miss this. - Solvent: Is this a condition?
> > > >
> > > > I suggest substanceList/substance. This is what
> > > > we do in reaction and several of your concerns are similar
> > > >
> > > > >  It does not really have a unit. In CMLReact,
> > > > >
> > > > >  substance is used for solvents. solventList is
> > > > > currently not an entry in the schema for CMLSpect. Should we have=
 it?
> > > >
> > > > we should certainly have substanceList - this
> > > > could contain things like TMS as well
> > > >
> > > > >  Are there other substances for spectra than solvent?
> > > >
> > > > That's up to you. anything that is important
> > > >
> > > > >Or should it go in metadata? - Assignment method
> > > > >(COSY, HMBC etc): This would be a metadata, right?
> > > >
> > > > Probably.
> > > >
> > > > >  Or is metadata more for non-chemical stuff
> > > > > like "measured by", "which lab" etc.?
> > > >
> > > > Have a look at the comp chem examples. I think there are a lot of
> > > > similarities
> > > >
> > > > >  Ok, I hope this feedback has some value.
> > > > > Stefan -- Stefan Kuhn M. A. Cologne University
> > > > > BioInformatics Center
> > > > > (http://www.cubic.uni-koeln.de) Z=C3=BClpicher Str.
> > > > > 47, 50674 Cologne Tel:
> > > > > +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
> > > > > My public PGP key is available at http://pgp.mit.edu
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >_______________________________________________
> > > > >cml-discuss mailing list
> > > > >cml...@li...
> > > > >https://lists.sourceforge.net/lists/listinfo/cml-discuss
> > > >
> > > > Peter Murray-Rust
> > > > Unilever Centre for Molecular Sciences Informatics
> > > > University of Cambridge,
> > > > Lensfield Road,  Cambridge CB2 1EW, UK
> > > > +44-1223-763069
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > cml-discuss mailing list
> > > > cml...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/cml-discuss
> > >
> > >--
> > >Stefan Kuhn M. A.
> > >Cologne University BioInformatics Center=
 (http://www.cubic.uni-koeln.de)
> > >Z=FClpicher Str. 47, 50674 Cologne
> > >Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
> > >My public PGP key is available at http://pgp.mit.edu
> > >
> > >
> > >_______________________________________________
> > >cml-discuss mailing list
> > >cml...@li...
> > >https://lists.sourceforge.net/lists/listinfo/cml-discuss
> >
> > Peter Murray-Rust
> > Unilever Centre for Molecular Sciences Informatics
> > University of Cambridge,
> > Lensfield Road,  Cambridge CB2 1EW, UK
> > +44-1223-763069
>
>--
>Stefan Kuhn M. A.
>Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
>Z=FClpicher Str. 47, 50674 Cologne
>Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
>My public PGP key is available at http://pgp.mit.edu
>
>
>_______________________________________________
>cml-discuss mailing list
>cml...@li...
>https://lists.sourceforge.net/lists/listinfo/cml-discuss

Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069=20