Re: Draft namespace recommendations

• To: "Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS)" <comcifs@iucr.org>
• Subject: Re: Draft namespace recommendations
• From: =?windows-1252?Q?Saulius_Gra=9Eulis?= <grazulis@ibt.lt>
• Date: Wed, 17 Jul 2013 15:31:35 +0300
• In-Reply-To: <51E675AB.7080202@gmail.com>
• References: <CAM+dB2eWdo5Hn0nMJ98O_dXN72jhmVGCPUjxugK+whEz9-AoRg@mail.gmail.com><CAM+dB2fQuEZpRENz+AXRSGQEWVA3OY2XLVbD08ToO9scUa6WMw@mail.gmail.com><51E675AB.7080202@gmail.com>

Dear COMCIFS members,

On 2013-07-17 13:44, yayahjb wrote:
>   _IUCR::atom_site.occupancy
> as equivalent to
>   _atom_site.occupancy
> when the discipline is know to be IUCR

If I correctly understand the current namespace proposal and its
suggested enhancements, the datablock like:

data_1
   _audit.discipline SAXS
   _refine_ls_goodness_of_fit_all 1.01
#end_data_1

would mean that, for the sake of example, the
'_refine_ls_goodness_of_fit' is defined in the discipline (aka
namespace) "SAXS", would be described in a dictionary different from the
cif_core.dic, and might have different type, constraints and meaning
from the data item described in cif_core.dic?

I so, I see a bit of a problem if the '_audit.discipline' gets lost at
some stage (and the practice shows data items do get lost, for one
reason or another ;). In such case, the '_refine_ls_goodness_of_fit_all
1.01' data item will be mis-interpreted as stemming from the IUCr
discipline. This might be a minor annoyance for CIFs used as processing
intermediates, but and unpleasant headache for archive-stored data.

In general, if the new mechanism encourage the use of the same data
names for different purposes in different disciplines, an ambiguity will
arise if the _audit.discipline tag is lost or not provided. And given
the current situation with the _audit_conform_dict_*, this could be
quite likely. Do you think this is a serious problem?

The current prefix-based mechanism is immune to the _audit_* tag loss --
one can always figure out, with some work, the dictionaries that
describe _pdbx_ or _cod_ tags.

Regards,
Saulius

-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556
mobile: (+370-684)-49802, (+370-614)-36366
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