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Re: [ddlm-group] Objectives of CIF2 syntax discussion. .. .. .

On Thursday, January 20, 2011 1:26 PM, David Brown wrote:


>The aliases should contain the following information: The tag, the dictionary in which it appears, the version of this dictionary, the DDL in which the dictionary is written (a given dictionaray may be written using different DDLs as for example the symmetry dictinoary was written in DDL2 and parts converted to DDL1), a flag to indicate whether the dataname is deprecated (needed for writing files) and a pointer to where the named dictionary can be found.  This may be a public archive or a local file that in turn points either to a local source or the public archive depending on the local institution.  There may be rare occasions when someone may want to write a program to produce a CIF in an earlier version that is compatible with software that is unaware of the later datanames.

I agree that all the information David specifies should be associated with each alias.  As I was preparing to suggest that some of the dictionary details he specified be normalized into their own category, I came across the DICTIONARY_XREF category, which already does that.  We could thereby reduce the attributes of each alias to name, xref_code, [DDL,] (first) dictionary version, deprecation flag.  I bracket DDL because I think it might better be added to DICTIONARY_XREF than to ALIAS, but we should have it one place or the other.

My discovery of DICTIONARY_XREF got me looking at its current uses, however, and I am now wondering whether _definition.xref_code serves a distinct purpose from the ALIAS items.  From the current definitions, it looks like these cover the same concept, differing only in whether the data name in the external dictionary is the same as the one the current dictionary.  Is there some other distinction?  Otherwise, do we need _definition.xref_code?


John C. Bollinger, Ph.D.
Department of Structural Biology
St. Jude Children's Research Hospital

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