Updating COMCIFS' approach to dictionaries

Peter Murray-Rust pm286 at cam.ac.uk
Mon Feb 20 08:50:30 GMT 2012

I approve of the general purpose here. Some details will need to be refined
as we progress.

On Mon, Feb 20, 2012 at 1:16 AM, James Hester <jamesrhester at gmail.com>wrote:

> >>Dear COMCIFS members,
> I would appreciate hearing any thoughts on the issue discussed below.
> I therefore envisage three levels of COMCIFS engagement with dictionaries:
> (i) The Core CIF dictionary together with other small add-on
> dictionaries continue to be treated as before, with active COMCIFS
> approval required;

I agree. There is enough software and usage that the core dictionary must
be managed carefully

> >>(ii) Dictionaries that are submitted by organisations recognised
> by COMCIFS as being competent are given automatic COMCIFS approval
> (this would presumably apply, for example. to the PDB).  These
> dictionaries are expected to maintain ontological agreement with other
> IUCr dictionaries, and may require some technical editing;

I also agree with this. I have started to promote the dictionary approach
in other areas  of physical science (computational chemistry, NMR
spectroscopy). We ran a meeting here a month ago and BrianM presented the
IUCr approach. It is seen as a shining light for others to follow.

We face the problem of "one true dictionary" against several local
dictionaries without central direction. We are currently starting with
one-dictionary-per-code (e.g. NWChem, Gaussian, etc.) - a bottom up
approach - and also a single core dictionary with terms which are common to
all experiments.

Currently we do not have organizations of the same initiative and coherence
as IUCr/CIF so (iii) represents the starting point

> >>(iii) COMCIFS offers syntactical checks and advice to dictionaries not
> covered by (i) and (ii)

I think this will become common on the web outside crystallography. Like
Herbert I would insist on namespaces. If there are two names for the same
concept in different local dictionaries it's far better than having no
local dictionaries. And the maintainers of those could agree that the names
are synonyms and create a term in an uber-dictionary. We are going to have
to deal with aliases, sameAs, etc. I don't think they should be encouraged,
but it's primarily a social problem. The web has tools to address it

>>COMCIFS would also allow inclusion of any syntactically correct
dictionaries in the central register maintained by the IUCr at the

> disgression of the COMCIFS secretary, provided it is clear that
> these dictionaries do not necessarily mesh with IUCr-sponsored
> dictionaries.
> Fully agreed. It's how the world is developing.


Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
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