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Re: [ddlm-group] DDLm aliases (subject changed). .. .
- To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
- Subject: Re: [ddlm-group] DDLm aliases (subject changed). .. .
- From: John Westbrook <jwest@rcsb.rutgers.edu>
- Date: Thu, 27 Jan 2011 07:52:47 -0500
- In-Reply-To: <a06240800c9668e1faa7c@[192.168.2.102]>
- References: <AANLkTi=ATdNovWFiecEwDrbtMdTwZ7guvYuBCGrdnb-i@mail.gmail.com> <8F77913624F7524AACD2A92EAF3BFA54166D7D1EDE@SJMEMXMBS11.stjude.sjcrh.local > <4D404DAA.8070804@mcmaster.ca> <a06240802c96600c48956@[192.168.2.102]> <8F77913624F7524AACD2A92EAF3BFA54166D7D1EE1@SJMEMXMBS11.stjude.sjcrh.local ><a06240800c9668e1faa7c@[192.168.2.102]>
Hi Herbert, 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_ Thanks, John On 1/26/11 10:49 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. > > -- HJB > > save_definition.xref_code > _definition.id '_definition.xref_code' > _definition.update 2011-01-26 > _definition.class Attribute > _description.text > ; > Code identifying the equivalent definition in the dictionary > referenced by the DICTIONARY_XREF attributes. > > Use of _definition.xref_code is deprecated in favor of > use of _alias.xref_code > ; > _name.category_id definition > _name.object_id xref_code > _type.purpose Identify > _type.container Single > _type.contents Code > save_ > > save_ALIAS > > _definition.id alias > _definition.scope Category > _definition.class List > _definition.update 2011-01-26 > _description.text > ; > The attributes used to specify the aliased names of definitions. > Every tag has an implicit alias to itself with a null > _alias.xref_code to allow use of the primary tag in > the ALIAS_ENSEMBLE category. > ; > _category.parent_id ddl_attr > _category_key.primitive ['_alias.definition_id', > '_alias.xref_code'] > save_ > > > save_alias.definition_id > _definition.id '_alias.definition_id' > _definition.class Attribute > _definition.update 2006-11-16 > _description.text > ; > Identifier tag of an aliased definition. > ; > _name.category_id alias > _name.object_id definition_id > _type.purpose Key > _type.container Single > _type.contents Tag > save_ > > save_alias.deprecated > _definition.id '_alias.deprecated' > _definition.class Attribute > _definition.update 2006-11-16 > _description.text > ; > Specifies whether use of the alias is deprecated > ; > _name.category_id alias > _name.object_id definition_id > _type.purpose STATE > _type.container Single > _type.contents YesorNo > _enumeration.default No > save_ > > > save_alias.dictionary_uri > _definition.id '_alias.dictionary_uri' > _definition.update 2011-01-26 > _definition.class Attribute > _description.text > ; > Dictionary URI in which the aliased definition belongs. > _alias.dictionary_uri is deprecated in favor if > _alias.xref_code > ; > _name.category_id alias > _name.object_id dictionary_uri > _type.purpose Identify > _type.container Single > _type.contents Uri > save_ > > save_alias.xref_code > _definition.id '_alias.xref_code' > _definition.update 2011-01-26 > _definition.class Attribute > _description.text > ; > Code identifying the dictionary containing the primary > definition of the dictionary as given in the > DICTIONARY_XREF category. > > ; > _name.category_id definition > _name.object_id xref_code > _name.linked_item_id '_dictionary_xref.code' > _type.purpose Key > _type.container Single > _type.contents Code > save_ > > > > > save_ENSEMBLE > > _definition.id ensemble > _definition.scope Category > _definition.class List > _definition.update 2011-01-26 > ; > Data items used to describe the ensemble identifiers > used in this dictionary. Data items in this category > are NOT used as attributes of individual data items. > > See linked item _alias_ensemble.ensemble_id. > ; > _category.parent_id ddl_attr > _category_key.generic '_ensemble.id' > > save_ > > save_ensemble.id > _definition.id '_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. > ; > _name.category_id ensemble > _name.object_id code > _type.purpose Key > _type.container Single > _type.contents Code > > save_ > > save_ensemble.description > _definition.id '_ensemble.description' > _definition.class Attribute > _definition.update 2011-01-26 > _description.text > ; > A description of the ensemble > ; > _name.category_id ensemble > _name.object_id code > _type.purpose Describe > _type.container Single > _type.contents Text > > > save_ > > save_ALIAS_ENSEMBLE > > _definition.id alias_ensemble > _definition.scope Category > _definition.class List > _definition.update 2011-01-26 > ; > The attributes used to specify the ensemble of > tags to which a given tag belong. > > A given tag may belong to multiple ensembles > and may be cited against multiple dictionaries. > > ; > _category.parent_id alias > _category.parent_join Yes > _category_key.primitive ['_alias_ensemble.ensemble_id', > '_alias_ensemble.definition_id', > '_alias_ensemble.xref_code'] > save_ > > save_alias_ensemble.definition_id > _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. > ; > _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_ > > save_alias_ensemble.ensemble_id > _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. > ; > _name.category_id alias_ensemble > _name.object_id code > _name.linked_item_id '_ensemble.id' > _type.purpose Key > _type.container Single > _type.contents Code > > save_ > > > save_alias_ensemble.xref_code > _definition.id '_alias_ensemble.xref_code' > _definition.class Attribute > _definition.update 2011-01-21 > _description.text > ; > A code identifying the actual dictionary, > virtual dictionary or other logical grouping > to which the identifier tag belongs. > ; > _name.category_id alias_ensemble > _name.object_id code > _name.linked_item_id '_dictionary_xref.code' > _type.purpose Key > _type.container Single > _type.contents Code > save_ > > > > > At 2:29 PM -0600 1/26/11, Bollinger, John C wrote: >> On Wednesday, January 26, 2011 11:34 AM, Herbert J. Bernstein wrote: >> >>> OK, so we need to pick a non-conflicting name for the tag that gives >>> the unifying identifier that will satisfy John W.'s concerns and >>> James's concerns, but that will not preclude John B. and David's >>> preference to allow the presentation to be unified with the >>> xref_code. How about "ensemble_id". This is a distinct concept >> >from the identifier of the dictionary itself, because one >>> dictionary can contain multiple ensembles and one ensemble >>> can span multiple dictionaries. >> >> Ok, that makes sense. >> >>> Here is my modified version of John B.' proposal: >> >> I think we are close here. There are a couple of additions I would >> like to see to Herbert's version of the proposal, however. Rather >> than quote the whole thing, I include it verbatim below, with my >> additions at the bottom and additional commentary following: >> >> >> 1) Deprecate _alias.dictionary_uri. >> >> 2) Add as a of subcategory of alias, alias_ensemble with the following >> tags: >> >> _alias_ensemble.definition_id >> a tag identifier belonging to an ensemble >> _alias_ensemble.ensemble_id >> a code identifying an ensemble of tags to which the tag belongs >> _alias_ensemble.xref_code >> >> All of these tags are members of the composite key of the sub >> category, so that it is possible to have a physical dictionary >> the same tag in multiple ensembles, or to break out this subcategory >> as a master index running over all tags alias giving both the >> physical dictionaries from which they are taken and and the >> ensembles to which they belong. >> >> 3) Add tag >> >> _alias.xref_code >> >> to the alias category >> >> _alias.xref_code specifies the physical dictionary from which the >> preferred definition of the tag alias has been taken, or is null >> if the current dictionary is the primary definer of the tag alias. >> This tag is the parent of _alias_ensemble.xref_code. There are >> some technical issues on use of the join mechanism, and which >> tags are keys, but they can be resolved if the flattened version >> is truly desired. >> >> >> 4) Add tag: >> >> _alias.deprecated: Specifies whether use of the alias is deprecated. >> _type.purpose State >> _type.container Single >> _type.contents YesorNo >> >> 5) Modify the definition of _dictionary_xref.format by changing its >> _type.contents attribute to "Code". >> >> 6) Deprecate _definition.xref_code (its purpose will be served via >> the alias mechanism) >> >> >> ---- >> JCB Adds: >> ---- >> >> 7) In the ALIAS category, replace attribute _category_key.generic with: >> _category_key.primitive [ '_alias.xref_code' '_alias.definition_id' ] >> >> This is still appropriate, inasmuch data names are not guaranteed to >> be globally unique across all dictionaries. For that matter, if it >> were inappropriate here then there would be no need for >> _alias_ensemble.xref_code, as no _alias.definition_id could be >> associated with more than one xref_code, and that one would be >> specified by _alias.xref_code. >> >> >> 8) 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 _definition.xref_code or _alias.xref_code >> attribute." >> >> I still think the concept of a logical dictionary is a sound and >> useful one, even alongside Herbert's _alias_ensemble idea. This >> wording change accommodates the concept without requiring any new >> attributes. Be it known, however, that if we agree to this then >> corresponding slight adjustments may be needed to the definitions of >> some of the other existing attributes in the DICTIONARY_XREF >> category. I think those can be discussed later, when and if the >> time comes. >> >> Naturally, if _definition.xref_code were removed instead of >> deprecated, then this definition should not refer to it. >> >> ======== >> >> >> I can live with deprecating _definition.xref_code and >> _alias.definition_uri, though my preference is still to remove them. >> Inasmuch as, to my knowledge, DDLm has so far been published and >> distributed only in draft / for-comments form, it will indeed be a >> new standard when it eventually is accepted by COMCIFS. Those >> developers and dictionary authors already working with the draft >> should be doing so with the understanding that it is subject to >> change. Also, I suspect we will consider further >> possibly-disruptive changes before we are done, and I am loathe to >> set a precedent that compatibility with the draft is a supremely >> compelling concern. >> >> Nevertheless, deprecation vs. removal of these attributes is too >> small a detail to be hung up over. When we are ready to vote on the >> overall proposal, I would prefer to vote separately on that question >> -- separately for each attribute, in fact. In the mean time, let's >> proceed. >> >> Question to consider: should there be a means in the DDL to identify >> the significance of a particular ensemble, at least for the benefit >> of humans? That might take a form as simple as a dictionary-scoped >> ENSEMBLE category, with attributes _ensemble.ensemble_id and >> _ensemble.description. >> >> I note also that Herbert did not bring forward my proposed >> _alias.dictionary_version attribute into his version of the >> proposal, nor have I added it back to this version. I see only >> limited potential use for it, and I am not prepared to argue for it. >> Others of you may think differently, however. >> >> >> 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 >> ddlm-group@iucr.org >> http://scripts.iucr.org/mailman/listinfo/ddlm-group > > -- ****************************************************************** John Westbrook, Ph.D. Rutgers, The State University of New Jersey Department of Chemistry and Chemical Biology 610 Taylor Road Piscataway, NJ 08854-8087 e-mail: jwest@rcsb.rutgers.edu Ph: (732) 445-4290 Fax: (732) 445-4320 ****************************************************************** _______________________________________________ ddlm-group mailing list ddlm-group@iucr.org http://scripts.iucr.org/mailman/listinfo/ddlm-group
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