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Re: Backus-Naur Form for CIF

At 14:24 04/10/00 +0100, I. David Brown wrote:
>Peter Murray-Rust wrote
> > [NB I
> > have never felt happy about the *semantics* of dot and query - it 
> certainly
> > used to be possible to interpret them so that CIF processors were required
> > the to expand ? in DDLs  into default values in data files.]
>The 'Guide to CIF for Authors' makes it clear that '?' is used when the
>value is not known (i.e. it may or may not be the default).  '.' is
>interepreted as the default (if a default exists).
>In my understanding '.' is also used to indicate that the value is
>irrelevant in the current context in which case substituting the default
>value should not cause any problem.  However, '?' should never be
>substituted by the default.

My worry about defaults is that they can become regarded as "hard facts" 
after they have been inserted for the first time. XML has a tools for 
adding default attribute values, e.g.:
         <!ELEMENT molecule ANY>
         <!ATTLIST molecule convention CDATA "CML">
says that any <molecule> without a convention attribute:
  is processed as if it were:
         <molecule convention="CML">
This is fine for metadata and styling, but is perhaps dangerous for 
"experimental values".  When the file is emitted from an XML or CIF tool 
which adds defaults there will be no way of knowing whether some data were 
actually measured or whether they were defaulted. The same problem occurs 
with null values - "." is often a null-like value.

The reason that this is difficult is that it is a difficult problem :-)


>It is not easy to find where these conventions are defined and I would
>recommend that they be carefully and explicitly defined on Brian's
>revamped website.
>Dr.I.David Brown,  Professor Emeritus
>Brockhouse Institute for Materials Research,
>McMaster University, Hamilton, Ontario, Canada
>Tel: 1-(905)-525-9140 ext 24710
>Fax: 1-(905)-521-2773

Peter Murray-Rust, Director Virtual School of Molecular Sciences
Pharmaceutical Sciences, University of Nottingham, NG7 2RD, UK
Tel: +44-(0)-115-951-5087 Fax: +44-(0)-115-951-5110