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

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.

   -- HJB

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  2011-01-26
;
     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.

;
    _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 2011-01-21
     _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.
;
     _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_

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.
;
     _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 2:29 PM -0600 1/26/11, Bollinger, John C wrote:
>On Wednesday, January 26, 2011 11:34 AM, Herbert J. Bernstein wrote:
>
>>OK, so we need to pick a non-conflicting name for the tag that gives
>>the unifying identifier that will satisfy John W.'s concerns and
>>James's concerns, but that will not preclude John B. and David's
>>preference to allow the presentation to be unified with the
>>xref_code.  How about "ensemble_id".  This is a distinct concept
>>from the identifier of the dictionary itself, because one
>>dictionary can contain multiple ensembles and one ensemble
>>can span multiple dictionaries.
>
>Ok, that makes sense.
>
>>  Here is my modified version of John B.' proposal:
>
>I think we are close here.  There are a couple of additions I would 
>like to see to Herbert's version of the proposal, however.  Rather 
>than quote the whole thing, I include it verbatim below, with my 
>additions at the bottom and additional commentary following:
>
>
>1) Deprecate _alias.dictionary_uri.
>
>2) Add as a of subcategory of alias, alias_ensemble with the following
>tags:
>
>_alias_ensemble.definition_id
>      a tag identifier belonging to an ensemble
>_alias_ensemble.ensemble_id
>      a code identifying an ensemble of tags to which the tag belongs
>_alias_ensemble.xref_code
>
>All of these tags are members of the composite key of the sub
>category, so that it is possible to have a physical dictionary
>the same tag in multiple ensembles, or to break out this subcategory
>as a master index running over all tags alias giving both the
>physical dictionaries from which they are taken and and the
>ensembles to which they belong.
>
>3) Add tag
>
>_alias.xref_code
>
>to the alias category
>
>_alias.xref_code specifies the physical dictionary from which the
>preferred definition of the tag alias has been taken, or is null
>if the current dictionary is the primary definer of the tag alias.
>This tag is the parent of _alias_ensemble.xref_code.  There are
>some technical issues on use of the join mechanism, and which
>tags are keys, but they can be resolved if the flattened version
>is truly desired.
>
>
>4) Add tag:
>
>_alias.deprecated: Specifies whether use of the alias is deprecated.
>      _type.purpose     State
>      _type.container   Single
>      _type.contents    YesorNo
>
>5) Modify the definition of _dictionary_xref.format by changing its
>_type.contents attribute to "Code".
>
>6) Deprecate _definition.xref_code (its purpose will be served via
>the alias mechanism)
>
>
>----
>JCB Adds:
>----
>
>7) In the ALIAS category, replace attribute _category_key.generic with:
>     _category_key.primitive [ '_alias.xref_code' '_alias.definition_id' ]
>
>This is still appropriate, inasmuch data names are not guaranteed to 
>be globally unique across all dictionaries.  For that matter, if it 
>were inappropriate here then there would be no need for 
>_alias_ensemble.xref_code, as no _alias.definition_id could be 
>associated with more than one xref_code, and that one would be 
>specified by _alias.xref_code.
>
>
>8) Modify the description of the DICTIONARY_XREF category to: "The 
>DICTIONARY_XREF attributes identify and describe logical or physical 
>dictionaries to which items in the current dictionary are 
>cross-referenced using the _definition.xref_code or _alias.xref_code 
>attribute."
>
>I still think the concept of a logical dictionary is a sound and 
>useful one, even alongside Herbert's _alias_ensemble idea.  This 
>wording change accommodates the concept without requiring any new 
>attributes.  Be it known, however, that if we agree to this then 
>corresponding slight adjustments may be needed to the definitions of 
>some of the other existing attributes in the DICTIONARY_XREF 
>category.  I think those can be discussed later, when and if the 
>time comes.
>
>Naturally, if _definition.xref_code were removed instead of 
>deprecated, then this definition should not refer to it.
>
>========
>
>
>I can live with deprecating _definition.xref_code and 
>_alias.definition_uri, though my preference is still to remove them. 
>Inasmuch as, to my knowledge, DDLm has so far been published and 
>distributed only in draft / for-comments form, it will indeed be a 
>new standard when it eventually is accepted by COMCIFS.  Those 
>developers and dictionary authors already working with the draft 
>should be doing so with the understanding that it is subject to 
>change.  Also, I suspect we will consider further 
>possibly-disruptive changes before we are done, and I am loathe to 
>set a precedent that compatibility with the draft is a supremely 
>compelling concern.
>
>Nevertheless, deprecation vs. removal of these attributes is too 
>small a detail to be hung up over.  When we are ready to vote on the 
>overall proposal, I would prefer to vote separately on that question 
>-- separately for each attribute, in fact.  In the mean time, let's 
>proceed.
>
>Question to consider: should there be a means in the DDL to identify 
>the significance of a particular ensemble, at least for the benefit 
>of humans?  That might take a form as simple as a dictionary-scoped 
>ENSEMBLE category, with attributes _ensemble.ensemble_id and 
>_ensemble.description.
>
>I note also that Herbert did not bring forward my proposed 
>_alias.dictionary_version attribute into his version of the 
>proposal, nor have I added it back to this version.  I see only 
>limited potential use for it, and I am not prepared to argue for it. 
>Others of you may think differently, however.
>
>
>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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>ddlm-group mailing list
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>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
                  [email protected]
=====================================================
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