Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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
=====================================================
_______________________________________________
ddlm-group mailing list
ddlm-group@iucr.org
http://scripts.iucr.org/mailman/listinfo/ddlm-group

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Council for Science (admitted 1947). Member of CODATA, the ICSU Committee on Data. Member of ICSTI, the International Council for Scientific and Technical Information. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

ICSU Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.