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Re: Opinions on comments as part of the content

At 10:37 08/03/2007, Brian McMahon wrote:
>A lot of good stuff in this discussion. One thing it brings out
>is the dichotomy between the "simple" approach - stick a CIF in vi,
>memorise the CIF dictionaries, stick in a few comments to remind
>other readers why we've done something that way - and the "formal"
>approach of mechanise all i/o with reference to dictionaries
>and/or stylesheets. CIF sits astride both camps, albeit somewhat
>awkwardly.  The editorial staff at the IUCr can edit and manipulate
>small-molecule CIFs pretty well, and a generation of Acta C/E
>authors can also do so, with varying levels of proficiency. The
>editorial staff at RCSB can even do it with mmCIFs, but the
>complexity of a full structure description in an mmCIF stretches
>people to the limit, and in collections of data sets, whether
>coreCIF or mmCIF, we really do need formal validation mechanisms.
Just to say that we have recently run CIFDOM over a large number of 
CIFs from Acta and applied dictionary validation. We can validate 
against enumerations, limits and data types (effectively only numb as 
char fits everything). The level of errors is very low - there are, I 
think, one or two places where there are non-numeric item values 
where they should be numb. The level of non-conformance from CIFs 
directly from crystallographic laboratories is considerably higher 
and shows evidence of hand- and template-based editing. We shall be 
making these tools public if authors wish to check at an earlier stage.


Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK

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