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Re: [ddlm-group] DDLm aliases (subject changed). .. .. .

Except for not changing Yes to No on the parent joint issue,
here is a revised version of the suggested DDLm changes incorporating
John B.'s revisions.   The _dictionary_xref.format Tag vs. Code
issue needs to be settled.  Pleas review.  Comments, corrections and
suggestions much appreciated.

   Regards,
     Herbert

save_definition.xref_code
      _definition.id             '_definition.xref_code'
      _definition.update           2011-01-26
      _definition.class            Attribute
      _description.text
;
       Code identifying the equivalent definition in the dictionary
       referenced by the DICTIONARY_XREF attributes.

       Use of _definition.xref_code is deprecated in favor of
       use of _alias.xref_code
;
      _name.category_id            definition
      _name.object_id              xref_code
      _type.purpose                Identify   
      _type.container              Single
      _type.contents               Code
       save_

save_ALIAS

      _definition.id               alias
      _definition.scope            Category
      _definition.class            List
      _definition.update           2011-01-26
      _description.text
;
       The attributes used to specify the aliased names of definitions.
       Every tag has an implicit alias to itself with a null
       _alias.xref_code to allow use of the primary tag in
       the ALIAS_ENSEMBLE category.
;
      _category.parent_id          ddl_attr
      _category_key.primitive      ['_alias.definition_id',
                                    '_alias.xref_code']
       save_


save_alias.definition_id
      _definition.id             '_alias.definition_id'
      _definition.class            Attribute
      _definition.update           2006-11-16
      _description.text
;
       Identifier tag of an aliased definition.
;
      _name.category_id            alias
      _name.object_id              definition_id
      _type.purpose                Key   
      _type.container              Single
      _type.contents               Tag
       save_

save_alias.deprecated
      _definition.id             '_alias.deprecated'
      _definition.class            Attribute
      _definition.update           2006-11-16
      _description.text
;
       Specifies whether use of the alias is deprecated
;
      _name.category_id            alias
      _name.object_id              definition_id
      _type.purpose                STATE
      _type.container              Single
      _type.contents               YesorNo
      _enumeration.default         No
       save_


save_alias.dictionary_uri
      _definition.id             '_alias.dictionary_uri'
      _definition.update           2011-01-26
      _definition.class            Attribute
      _description.text
;
       Dictionary URI in which the aliased definition belongs.
       _alias.dictionary_uri is deprecated in favor if
       _alias.xref_code
;
      _name.category_id            alias
      _name.object_id              dictionary_uri
      _type.purpose                Identify   
      _type.container              Single
      _type.contents               Uri
       save_

save_alias.xref_code
      _definition.id             '_alias.xref_code'
      _definition.update           2011-01-26
      _definition.class            Attribute
      _description.text
;
       Code identifying the dictionary containing the primary
       definition of the dictionary as given in the
       DICTIONARY_XREF category.

;
      _name.category_id            definition
      _name.object_id              xref_code
      _name.linked_item_id         '_dictionary_xref.code'
      _type.purpose                Key
      _type.container              Single
      _type.contents               Code
       save_


save_ENSEMBLE

    _definition.id      ensemble
    _definition.scope   Category
    _definition.class   List
    _definition.update  2011-01-26
;
     Data items used to describe the ensemble identifiers
     used in this dictionary.  Data items in this category
     are NOT used as attributes of individual data items.

     See linked item _alias_ensemble.ensemble_id.
;
     _category.parent_id ddl_attr
     _category_key.generic  '_ensemble.id'

     save_

save_ensemble.id
      _definition.id   '_ensemble.id'
      _definition.class  Attribute
      _definition.update 2011-01-26
      _description.text
;
      A code identifying an ensemble of related tags.
      To help ensure that dictionaries can be merged,
      each code should either begin with an IUCr-registered
      prefix or, if not prefixed, have been approved
      by COMCIFS.  The special prefix 'local_' may be
      use for purely internal purposes of an organization.
;
      _name.category_id ensemble
      _name.object_id   code
      _type.purpose     Key
      _type.container   Single
      _type.contents    Code

     save_

save_ensemble.description
      _definition.id   '_ensemble.description'
      _definition.class  Attribute
      _definition.update 2011-01-26
      _description.text
;
      A description of the ensemble
;
      _name.category_id ensemble
      _name.object_id   code
      _type.purpose     Describe
      _type.container   Single
      _type.contents    Text


     save_

save_ALIAS_ENSEMBLE

     _definition.id      alias_ensemble
     _definition.scope   Category
     _definition.class   List
     _definition.update  2011-01-27
;
      The attributes used to specify the ensemble of
      tags to which a given tag belong.

      A given tag may belong to multiple ensembles
      and may be cited against multiple dictionaries.

      Note that _alias_ensemble.ensemble_id is a compoent
      of the key of ALIAS_ENSEMBLE.  If the denormalized
      join presentation is used to bring the object
      id's of this child category up into the parent
      ALIAS category, then _alias.ensemble_id will
      we used as an implicit addition to the key of
      the denormalized ALIAS category.

;
     _category.parent_id  alias
     _category.parent_join  Yes
     _category_key.primitive  ['_alias_ensemble.ensemble_id',
                               '_alias_ensemble.definition_id',
                               '_alias_ensemble.xref_code']
      save_

save_alias_ensemble.definition_id
      _definition.id   '_alias_ensemble.definition_id'
      _definition.class  Attribute
      _definition.update 2011-01-27
      _description.text
;
      Together with _alias_ensemble.xref_code, identifies
      an alias belonging to an ensemble.  An alias may
      belong to any number of ensembles, including zero.

;
      _name.category_id alias_ensemble
      _name.object_id   definition_id
      _name.linked_item_id  '_alias.definition_id'
      _type.purpose     Key
      _type.container   Single
      _type.contents    Tag
       save_

save_alias_ensemble.ensemble_id
      _definition.id   '_alias_ensemble.ensemble_id'
      _definition.class  Attribute
      _definition.update 2011-01-27
      _description.text
;
      Identifies an ensemble to which the alias
      identified by _alias_ensemble.definition_id
      and _alias_ensemble.xref_code ) belongs.

      A pointer to _ensemble.id
;
      _name.category_id alias_ensemble
      _name.object_id   code
      _name.linked_item_id  '_ensemble.id'
      _type.purpose     Key
      _type.container   Single
      _type.contents    Code

     save_


save_alias_ensemble.xref_code
      _definition.id   '_alias_ensemble.xref_code'
      _definition.class  Attribute
      _definition.update 2011-01-21
      _description.text
;
      A code identifying the actual dictionary,
      virtual dictionary or other logical grouping
      to which the identifier tag belongs.
;
      _name.category_id alias_ensemble
      _name.object_id   code
      _name.linked_item_id  '_dictionary_xref.code'
      _type.purpose     Key
      _type.container   Single
      _type.contents    Code
       save_





At 9:34 AM -0600 1/27/11, Bollinger, John C wrote:
>On Wednesday, January 26, 2011 9:50 PM, Herbert J. Bernstein wrote:
>
>>So, to pull it all together, see below.  Please review and see
>>what I have missed, mistyped  or failed to convert from some
>>earlier incarnation.  Comments, corrections and suggestions
>>greatly appreciated.
>>
>>I have not yet included the type change for _dictionary_xref.format
>>because I am not sure a single word code would be sufficient
>>to describe the format of any given dictionary, so for the moment
>>it is still Text.
>
>Herbert's latest version looks good to me.  See below for comments 
>and tentative corrections:
>
>[...]
>
>>save_ALIAS_ENSEMBLE
>>
>>     _definition.id      alias_ensemble
>>     _definition.scope   Category
>[...]
>>     _category.parent_id  alias
>>     _category.parent_join  Yes
>>     _category_key.primitive  ['_alias_ensemble.ensemble_id',
>>                               '_alias_ensemble.definition_id',
>>                               '_alias_ensemble.xref_code']
>>      save_
>
>
>As I understand the use of _category.parent_join, I think its value 
>for this category needs to be 'No', because the parent category has 
>a different (narrower) key structure.
>
>
>>save_alias_ensemble.definition_id
>>      _definition.id   '_alias_ensemble.definition_id'
>>      _definition.class  Attribute
>>      _definition.update 2011-01-21
>>      _description.text
>>;
>>      Identifier tag of a definition associated with
>>      an xref code by which to group this tag with
>>      other tags.
>>
>>      A given tag may belong to multiple ensembles
>>      and may be cited against multiple dictionaries.
>>
>>      Note that the tag does not have to be a valid
>>      tag under DDLm tag construction rules, but
>>      it should be a valid tag under the rules of
>>      some DDL.
>>;
>
>I would prefer to describe this a bit differently:
>;
>      Together with _alias_ensemble.xref_code, identifies
>      an alias belonging to an ensemble.  An alias may
>      belong to any number of ensembles, including zero.
>;
>
>I omit the bit about tag construction rules, as no DDL yet proposed 
>defines any such rules; allowable tags are defined by CIF.  As James 
>earlier observed, DDLm can define any tag allowed by CIF, even if 
>that name is not in the subset addressable by dREL.  Similarly, DDL1 
>and DDL2 can both define any data name allowed by CIF1, which 
>collectively are a subset of those allowed by CIF2.  See also below.
>
>>      _name.category_id alias_ensemble
>>      _name.object_id   definition_id>     _name.linked_item_id 
>>'_alias.definition_id'
>>      _type.purpose     Key
>>      _type.container   Single
>>      _type.contents    Code
>>       save_
>
>Shouldn't this item's _type.contents be 'Tag' to agree with the 
>linked item's?  Alternatively, if 'Tag' signifies something more 
>specific than "data name allowed by CIF2" then perhaps 
>_alias.definition_id needs to be changed instead.  I presume that 
>these questions are related to the comments about DDL tag 
>construction rules in this item's proposed description.
>
>
>>save_alias_ensemble.ensemble_id
>>      _definition.id   '_alias_ensemble.ensemble_id'
>>      _definition.class  Attribute
>>      _definition.update 2011-01-26
>>      _description.text
>>;
>>      A code identifying an ensemble of related tags.
>>      To help ensure that dictionaries can be merged,
>>      each code should either begin with an IUCr-registered
>>      prefix or if not prefixed, have been approved
>>      by COMCIFS.  The special prefix 'local_' may be
>>      use for purely internal purposes of an organization.
>>;
>[...]
>
>Is it needful or appropriate to repeat the definition text of the 
>linked item here?  As long as we do adopt the ENSEMBLE category, the 
>importance of _alias_ensemble.ensemble_id is primarily that it 
>associates an alias with one of the ensembles defined elsewhere in 
>the dictionary.  I suggest this alternative description text:
>
>;
>      Identifies an ensemble to which the alias identified by ( 
>_alias_ensemble.definition_id, _alias_ensemble.xref_code ) belongs.
>;
>
>
>Regards,
>
>John
>
>--
>John C. Bollinger, Ph.D.
>Department of Structural Biology
>St. Jude Children's Research Hospital
>
>
>
>
>
>Email Disclaimer:  www.stjude.org/emaildisclaimer
>
>_______________________________________________
>ddlm-group mailing list
>ddlm-group@iucr.org
>http://scripts.iucr.org/mailman/listinfo/ddlm-group


-- 
=====================================================
  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
=====================================================
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