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

[Stefan K. <ste...@un...>]

Dear Peter,
thanks a lot for clarification. If we want to have substanceList in spect=
rum=20
(I think it would be good), this needs to go into the schema, right? Woul=
d=20
you do this? I feel a bit too unexperienced to do the change.
Stefan

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
> >
> >
> >
> >
> >_______________________________________________
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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
>
>
>
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--=20
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