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

Dear John,

   The definition_id most certainly does not exhibit the tag
style.  For example, there is no way to distinguish DDLm
tag style from DDL2 or DDL2 tag style from context.  That
is intentionally inherent in the design of DDLm.

   As for defining a hypothetical URI, that can break,
or each least time-out programs trying to get additional
information about an aliased tag from that URI.  URIs
should be for things that really exist on the web,
not a substitute for a tag that really defines something
different, in this case the style of tags.

   We already do something very similar to this with
alternate conformers and with NMR model numbers.  It
really is a simply concept for organizing information
that belongs in groups, in this case the group of
DDL1 or DDL2 or DDLm or ... style tags.  It solves
a very real problem for me with imgCIF.  It does
not harm to anybody else.  If nobody uses it in
another dictionary, it still would have been a useful
addition to DDLm.

   In the end, I suspect that both core and mmCIF DDLm
dictionaries will be built this way, because it
make it simpler and clearer and allows multi-purpose
dictionaries to be self-contained and avoid the 
maintenance headache David spotted.

   Having one tag to nominate a preferred alias tag
by tag is quite a clerical burden.  Having one style
to select is a lot less work.

   Regards,
     Herbert

=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya@dowling.edu
=====================================================

On Wed, 19 Jan 2011, Bollinger, John C wrote:

>
> On Wednesday, January 19, 2011 12:04 PM, Herbert J. Bernstein wrote:
>>   That was very helpful.  You want to maintain one dictionary that will dynamically act as a DDL1, DDL2 or DDLm dictionary. Fair enough.  But then shouldn'e the information on what alias is intended for what style of output simply be in the alias tags.  It is not really a matter of which dictionary it come from, but of which of several alternate styles of tags it conforms to.
>>
>>   Right now the alias category has 2 tags,
>>
>>   _alias.definition_id
>>   _alias.dictionary_uri
>>
>> We could both do what we need to do without conflicting if there were a third tag
>>
>>   _alias.tag_style
>>
>> which would simply be a character string, such as DDL1, DDL2, DDLm, 
>> my_new_style, ... which could be used to tie together the style of tags 
>> to be used for a particular dictionary use, both for validation of 
>> input and for generation of output.  If no particular style had been 
>> specified, the save frame name would win.  This would bring the data on 
>> which are DDL1 names and which are DDL2 names for the core values 
>> neatly together on one core dictionary without having to know if any 
>> other dictionaries were DDL1 style and which are DDL2 style.  The DDLm 
>> dictionary would have all the information right there and would not 
>> even need to refer to the older dictionaries on most cases to work with 
>> DDL1 and DDL2 data files.
>
> _alias.tag_style seems redundant to me.  For one thing, 
> _alias.definition_id will inherently exhibit the tag style.  Moreover, 
> the "tag style" in the DDL-version sense is both well known and 
> electronically available, given _alias.dictionary_uri, at least for 
> official and registered dictionaries.  A program that cared generically 
> about tag type could use either or both of those to determine it 
> dynamically while processing the dictionary.  Moreover, there is in 
> general no particular reason to expect not to find multiple aliases of 
> the same tag type, whether defined in the same or in different 
> dictionaries.
>
> If you want to select, for instance, Core data names vs. mmCIF data 
> names then then _alias.dictionary_uri gives you that directly.  It works 
> even among multiple alternative names for the same concept defined in 
> different dictionaries using the same data name convention.  Moderately 
> clever software could even make selection by dictionary URI work for 
> merged dictionaries, provided it was given information about the 
> constituent dictionaries.
>
> There does, however, appear to be a possible need for a tag by which to 
> nominate a preferred alias among several defined in the same external 
> dictionary.  The preference doesn't matter when reading CIF input, but 
> it does potentially matter when choosing a tag for output.  We could 
> rely on order of appearance in the alias list, but until now loop 
> packets have been order-independent.
>
>>   For my work, this would be just as effective as the import ... as ... 
>> or my method_alias suggestion in allowing me to use CIF1 tags that are 
>> >illegal under CIF2 without requiring us to allow those names as valid 
>> tags in DDLm dictionaries.
>>
>>   Could you accept _alias.tag_style, and perhaps allowing 
>> _alias.dictionary_uri to be omitted when not really needed?  This would 
>> be a big help >to me in then making a DDLm imgCIF dictionary that could 
>> not only replace the DDL2 dictionary, but could also, for the first 
>> time provide a DDL1 >version of all imgCIF tags.  I could even then 
>> automatically produce valid DDL1 and DDL2 dictionaries from the DDLm 
>> dictionary source, making thr >DDLm dictionary the only version that I 
>> would have to maintain.
>
> For this particular purpose, how about defining a URI to represent the 
> hypothetical DDL1 imgCIF dictionary, and using that with 
> _alias.dictionary_uri to achieve your objective?  The resulting 
> dictionary would even be more informative about the nature of the 
> aliases than a tag style could make it.  That approach would be no 
> harder to code for, as it simply substitutes one data name and set of 
> constants for another.
>
>
> Regards,
>
> John
>
> --
> John C. Bollinger, Ph.D.
> Department of Structural Biology
> St. Jude Children's Research Hospital
>
>
> Email Disclaimer:  www.stjude.org/emaildisclaimer
>
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