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

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:


>    _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.

>     _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.

>     _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.



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

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