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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.
>     _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:

    '_geom_special_details' core  no
    '_geom.details'         mmCIF no

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

    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.



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

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