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


On Thursday, January 27, 2011 6:53 AM, John Westbrook wrote:

>I am trying to understand the mapping of the proposed items to a simple
>example from the mmCIF dictionary.   Could you provide an example using
>the proposed DDL for how the following alias would be represented.
>
>save__geom.details
>     _item_description.description
>;              A description of geometry not covered by the
>                existing data names in the GEOM categories, such as
>                least-squares planes.
>;
>     _item.name                  '_geom.details'
>     _item.category_id             geom
>     _item.mandatory_code          no
>     _item_aliases.alias_name    '_geom_special_details'
>     _item_aliases.dictionary      cif_core.dic
>     _item_aliases.version         2.0.1
>     _item_type.code               text
>      save_


So, it looks like despite converging on an agreed form for the DDLm changes we have been discussing, Herbert and I may still have divergent visions for their use.  As far as I intend, and even as I interpret the proposed formal changes, "ensembles" are distinct from and on top of aliases.  You can have aliases without ensembles, but not ensembles without aliases.  As such, this is how I think the above alias, plus an alias to the DDL2 mmCIF definition, would be modeled in a DDLm dictionary:

save_geom.details
[...]
loop_
    _alias.definition_id
    _alias.xref_code
    _alias.deprecated
    '_geom_special_details' core  no
    '_geom.details'         mmCIF no
[...]
save_


That references items in the existing, dictionary-wide dictionary_xref category:

loop_
    _dictionary_xref.code
    _dictionary_xref.name
    _dictionary_xref.date
    _dictionary_xref.format
    _dictionary_xref.uri
    core   cif_core.dic  '29-Jun-2010'  DDL1  ftp://ftp.iucr.org/pub/cif_core.dic
    mmCIF  cif_mm.dic    '27-Jun-2005'  DDL2  ftp://ftp.iucr.org/pub/cif_mm.dic


Currently _dictionary_xref.format (values 'DDL1' and 'DDL2' above) is defined as having type 'Text', meaning that it is not intended to be machine-interpretable.  It is an open question whether that item should be redefined to be a 'Code' drawing on a controlled vocabulary of format codes.

You will also note that in the most recent version of the proposal there is no analog of _item_alias.version.  An earlier version of the proposal did contain such an analog (_alias.dictionary_version), and anyone who thinks it important to have that is welcome to make a case for reintroducing it.  I would not oppose such a move.

Anyway, having defined aliases as shown above, a dictionary author might choose to associate them with one or more ensembles as Herbert demonstrated.  The meaning of any particular ensemble can be dictionary-specific, but the proposal on the table presumes some kind of official set of particular ensemble IDs with centrally defined meaning.


Regards,

John

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






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