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

This can be made to work, but for my uses, there are
some minor issues:

1.  I will be grouping the primary DDLm tag.  With the
_definition.xref_code removed, the primary DDLm tag
will have to be aliased; and

2.  With multiple xref codes for a given tag (e.g.
DDL2 and DDLm), it would be more appropriate to
normalize and put the tags and xref codes into
a sub-category, rather than to keep repeating the
same tag.  This would have the advantage of allowing
the alias category to return to a non-compound key
and would also allow all the grouping of
tags in a dictionary to be gathered on a separate
block, if desired.

For these reasons, I suggest

1.  Leave _alias.dictionary_uri, but deprecate it in
favor of:

2.  Create an ALIAS_XREF category with the
following tags, forming a composite key

     a tag identifier belonging to a group
     a code identifying a real or virtual dictionary
or other logical groups of tags to which the tag 

The other tags that John proposes for David's uses
actually fit better in terms of normalization in this sub-
category, than on the top level, but that is a decision
for David to make.  I am happy either way.

The addition to the ddl dictionary would be:


   _definition.id      alias_xref
   _definition.scope   Category
   _definition.class   List
   _definition.update  2011-01-21
    The attributes used to specify the actual dictionary,
    virtual dictionary, or other logical grouping of
    tags indicated by an xref code to which a given tag belong.

    The default xref code under which all tags for which
    no xref group is defined is the one specified by
    a null value.

    _category.parent_id  alias
    _category_key.primitive  ['_alias_xref.definition_id',

     _definition.id   '_alias_xref.definition_id'
     _definition.class  Attribute
     _definition.update 2011-01-21
     Identifier tag of a definition associated with
     an xref code by which to group this tag with
     other tags.  A single tags may be associated
     with multiple xref codes.  An xref code does
     not have to be associated with a particular
     dictionary, nor with a particular DDL format.

     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_xref
     _name.object_id   definition_id
     _type.purpose     Key
     _type.container   Single
     _type.contents    Code

     _definition.id   '_alias_xref.xref_code'
     _definition.class  Attribute
     _definition.update 2011-01-21
     A code identifying the actual dictionary,
     virtual dictionary or other logical grouping
     to which the identifier tag belongs.
     _name.category_id alias_xref
     _name.object_id   code
     _type.purpose     Key
     _type.container   Single
     _type.contents    Code

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


On Fri, 21 Jan 2011, Bollinger, John C wrote:

> On Friday, January 21, 2011 8:57 AM, David Brown wrote:
> [...]
>> I would like to know exactly what I am voting on.  There seems to be 
>> general agreement on the information that is needed for an alias, the 
>> only dispute is the format in which it will appear.  If the various 
>> pieces of information I listed each had their own item, this would be 
>> agreeable and we could delegate someone to come up with the requisit 
>> DDLm save frames, but if this information is to be included, explicitly 
>> or implicitly, in a smaller number of items, then I would like to see 
>> the definitions and descriptions so that I could understand how each 
>> piece of information would be retrieved.  John B, can you supply us 
>> with an example of what your normalized item(s) would look like?
> Indeed, here is the formal proposal I promised, at the end of which is 
> an example:
> Proposal: Extended Alias Attributes
> ===================================
> Introduction / Rationale
> ------------------------
> This proposal aims primarily to provide all the ALIAS attributes that several members of this group have recently agreed are needed (at least in principle).  However, attributes that are properties of dictionaries rather than of individual data names are normalized out of the ALIAS category and into the DICTIONARY_XREF category.  The description of the DICTIONARY_XREF category is slightly modified to be explicitly consistent with this usage and with the concept of referencing logical dictionaries that have no independent physical manifestation.
> Proposed Actions
> ----------------
> 1) Replace _alias.dictionary_uri with:
> _alias.xref_code: Specifies a code that identifies the logical or physical dictionary in which the alias is defined.  This serves to categorize and fully identify the alias.
>    _type.purpose     Identify
>    _type.container   Single
>    _type.contents    Code
> 2) Add these attributes:
> _alias.dictionary_version: Specifies the first version of the
> dictionary identified by _alias.xref_code that defines the alias.
>    _type.purpose     Identify
>    _type.container   Single
>    _type.contents    Code
> _alias.deprecated: Specifies whether use of the alias is deprecated.
>    _type.purpose     State
>    _type.container   Single
>    _type.contents    YesorNo
> 3) In the ALIAS category, replace attribute _category_key.generic with:
>    _category_key.primitive [ '_alias.xref_code' '_alias.definition_id' ]
> 4) Modify the definition of _dictionary_xref.format by changing its 
> _type.contents attribute to "Code".
> 5) Remove _definition.xref_code (its purpose will be served via the 
> alias mechanism)
> 6) 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 _alias.xref_code attribute."
> Comments
> --------
> Here is the resulting correspondence between DDLm data names and David's 
> list of alias attributes:
> "The tag" -> _alias.definition_id (unchanged by this proposal)
> "the dictionary in which it appears" -> a row/instance of 
> DICTIONARY_XREF, identified by _alias.xref_code (added by this proposal)
> "the version of this dictionary" -> _alias.dictionary_version (added by 
> this proposal)
> "the DDL in which the dictionary is written" -> _dictionary_xref.format 
> (type attributes modified by this proposal)
> "a flag to indicate whether the dataname is deprecated" -> 
> _alias.deprecated (added by this proposal)
> "a pointer to where the named dictionary can be found" -> 
> _dictionary_xref.uri (unchanged by this proposal)
> Although this proposal chooses the existing DICTIONARY_XREF category as 
> the normalized location for alias attributes that depend only on 
> dictionary, it would also be possible to instead introduce a new, 
> parallel category for this purpose.  If the _definition.xref_code is 
> merged into the alias feature as I propose, however, then 
> DICTIONARY_XREF no longer has any other purpose.  On the other hand, it 
> is not essential to drop _definition.xref_code.
> As in my previous proposal concerning _alias.dictionary_uri, the key for 
> the ALIAS category is expended to a compound one containing the 
> dictionary identifier and the data name.  This allows one data name's 
> appearances in multiple dictionaries all to be aliased to the same 
> defined name, without implying that all possible definitions of the name 
> are aliased.  Essentially, it scopes the alias to the dictionary in 
> which it appears.  DDL2's similar ITEM_ALIASES category is keyed not 
> only to name and dictionary identifier, but also to dictionary version; 
> the last seems needless, even in DDL2, because we can assume that once 
> introduced into a dictionary, data names are not removed or incompatibly 
> changed.
> The type attributes of _dictionary.xref_format are changed so that this 
> attribute represents a computer-interpretable code describing at least 
> the DDL compliance level of the referenced dictionary.  Allowed values 
> could be defined so that they encompass other information as well, very 
> much like the proposed tag_style might do.  It might be desirable for 
> DDLm to enumerate allowed values for this attribute, but it would be 
> more flexible to have an external register, such as Herbert proposed for 
> tag_style.  I presently take no position on the best course in that 
> regard, but this proposal does not provide enumerated values.
> This proposal is offered for comment.  Although I would be willing to 
> have a vote on it as it stands, it could likely be improved.  I am open 
> to changing some of the details if that will contribute to broader 
> acceptance.
> Example
> -------
> loop_
>    _dictionary_xref.code
>    _dictionary_xref.date
>    _dictionary_xref.format
>    _dictionary_xref.name
>    _dictionary_xref.uri
>    core  '2010-Jun-29'  DDL1  cif_core.dic  ftp://ftp.iucr.org/pub/cif_core.dic
>    mmcif '2005-Jun-27'  DDL2  mmcif_std.dic ftp://ftp.iucr.org/pub/cif_mm.dic
> [...]
> save_diffrn_standards.decay_percent
>    _definition.id             '_diffrn_standards.decay_percent'
> [...]
>    loop_
>        _alias.xref_code
>        _alias.definition_id
>        _alias.dictionary_version
>        _alias.deprecated
>        core  '_diffrn_standards_decay_%' . no
>        mmcif '_diffrn_standards.decay_%' . no
> save_
> 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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