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

[peter murray-r. <pm...@ca...>]

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=20
a mess and intend to change almost all of them to=20
"any".  Basically we cannot predict what we are=20
going to want as content and it is currently too=20
constraining. I'd like comments on this!

I can easily changes this in schema25. I am=20
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
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>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