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Re: [ddlm-group] DDLm aliases (subject changed). .. .. .
- To: "'email@example.com'" <firstname.lastname@example.org>, Group finalising DDLm and associated dictionaries <email@example.com>
- Subject: Re: [ddlm-group] DDLm aliases (subject changed). .. .. .
- From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
- Date: Thu, 27 Jan 2011 11:03:28 -0600
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- References: <AANLkTi=ATdNovWFiecEwDrbtMdTwZ7guvYuBCGrdnbemail@example.com><8F77913624F7524AACD2A92EAF3BFA54166D7D1EDE@SJMEMXMBS11.stjude.sjcrh.local ><4D404DAA.firstname.lastname@example.org> <email@example.com><8F77913624F7524AACD2A92EAF3BFA54166D7D1EE1@SJMEMXMBS11.stjude.sjcrh.local ><firstname.lastname@example.org><4D416A9F.email@example.com>
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 Email Disclaimer: www.stjude.org/emaildisclaimer _______________________________________________ ddlm-group mailing list firstname.lastname@example.org http://scripts.iucr.org/mailman/listinfo/ddlm-group
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- Re: [ddlm-group] DDLm aliases (subject changed). .. .. . (Herbert J. Bernstein)
- Re: [ddlm-group] DDLm aliases (subject changed) (James Hester)
- Re: [ddlm-group] DDLm aliases (subject changed). . (David Brown)
- Re: [ddlm-group] DDLm aliases (subject changed). . (Herbert J. Bernstein)
- Re: [ddlm-group] DDLm aliases (subject changed). .. . (Herbert J. Bernstein)
- Re: [ddlm-group] DDLm aliases (subject changed). .. . (John Westbrook)
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