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Re: Adding datanames covering database information

Hi James,
      I only looked at a small part of this but in the line for RCSBthe word 'STructural' should be 'Structural'.
      Hope all is well.  Will we see you in Toronto?
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On Thu, 28 Jun 2018, James Hester wrote:
> Please see below some draft definitions for a new database_related category, as foreshadowed in> my email of April 12th.? Feel free to comment. If any databases have been left off the initial> list below, feel free to suggest additions.> > Note that I have chosen not to make these datanames aliases of the DATABASE_2 datanames in> mmCIF, as the new category has a different key.> > James.> =============================================================> #> #?Draft definitions for a new DATABASE_RELATED category> #> > save_DATABASE_RELATED> _definition.id????????? DATABASE_RELATED> _definition.class?????? Loop> _definition.scope?????? Category> _definition.update????? 2018-06-29> _description.text> ;> > ??? A category of items recording entries in databases that describe> ??? the same or related data. Databases wishing to insert their own> ??? canonical codes when archiving and delivering data blocks should> ??? use items from the DATABASE category.> ???> ;> _name.category_id?????? PUBLICATION> _name.object_id???????? DATABASE_RELATED> _category_key.name????? '_database_related.id'> save_> > save_database_related.id> _definition.id????????? '_database_related.id'> _definition.update????? 2018-06-29> _description.text> ;> ?????? An identifer for this database reference> ;> _name.category_id?????? database_related> _name.object_id???????? id> _type.purpose?????????? Key> _type.source??????????? Recorded> _type.container???????? Single> _type.contents????????? Text> save_> > save_database_related.database_id> _definition.id????????? '_database_related.database_id'> _definition.update????? 2018-06-29> _description.text> ;> ?????? An identifier for the database that contains the> ?????? related dataset.> ;> _name.category_id?????? database_related> _name.object_id???????? database_id> _type.purpose?????????? State> _type.source??????????? Recorded> _type.container???????? Single> _type.contents????????? Text> _import.get [{'save':database_list 'file':templ_enum.cif}]> save_> > save_database_related.database_code> _definition.id????????? '_database_related.database_code'> _definition.update????? 2018-06-29> _description.text> ;> ?????? The code used by the database referred to in> ?????? _database_related.database_id to identify the> ?????? related dataset.> ;> _name.category_id?????? database_related> _name.object_id???????? database_code> _type.purpose?????????? Encode> _type.source??????????? Recorded> _type.container???????? Single> _type.contents????????? Text> > save_> > save_database_related.relation> _definition.id????????? '_database_related.relation'> _definition.update????? 2018-06-29> _description.text> ;> ?????? The general relationship of the data in the data block> ?????? to the dataset referred to in the database.> ;> _name.category_id?????? database_related> _name.object_id???????? relation> _type.purpose?????????? State> _type.source??????????? Recorded> _type.container???????? Single> _type.contents????????? Text> loop_> ?? _enumeration_set.state> ?? _enumeration_set.details> ?? Identical?????????? 'The dataset contents are identical'> ?? Subset????????????? 'The dataset contents are a proper subset of the contents of the data block'> ?? Superset??????????? 'The dataset contents include the contents of the data block'> ?? Derived???????????? 'The dataset contents are derivable from the contents of the data block'> ?? Common????????????? 'The dataset contents share a common source'> save_> > save_database_related.special_details> _definition.id????????? '_database_related.special_details'> _definition.update????? 2018-06-29> _description.text??????????????????????> ;> ??? Information about the external dataset and relationship not encoded> ??? elsewhere.> ;> _name.category_id?????????????????????? database_related> _name.object_id???????????????????????? special_details> _type.purpose?????????????????????????? Describe> _type.source??????????????????????????? Recorded> _type.container???????????????????????? Single> _type.contents????????????????????????? Text> > save_> > > #> # Contents to be added to templ_enum.cif listing database codes> #> > > save_database_list> loop_> ??? _enumeration_set.state> ??? _enumeration_set.detail> ??? CAS????????? 'Chemical Abstracts'> ??? COD????????? 'Crystallographic Open Database'> ??? CSD????????? 'Cambridge Structural Database'> ??? ICSD???????? 'Inorganic Crystal Structure Database'> ??? MDF????????? 'MetalsData File'> ??? NDB????????? 'Nucleic Acid Database'> ??? PDB????????? 'Protein Data Bank'> ??? PDF????????? 'PowderDiffraction File (JCPDS/ICDD)'> ??? RCSB???????? 'Research Collaboratory for STructural Bioinformatics'> ??? EBI????????? 'European Bioinformatics Institute'> save_> > > On 12 April 2018 at 15:59, James Hester <jamesrhester@gmail.com> wrote:>       Dear Core CIF users and experts,> > The current core CIF provides the DATABASE and DATABASE_CODE categories for identifying a> database entry corresponding to the structure contained in the data block, for a variety> of pre-determined databases.? These are both Set categories, that is, their datanames can> only take a single value in a single data block.? This restriction is reasonable if the> database content for that entry is seen as coincident with the data block contents, as> has been the case for structural databases.> > However, it is possible for multiple entries from a single database to be more broadly> relevant to the contents of a data block. For example, multiple structures may correspond> to a single topology.? So I would like you to consider the creation of a (looped)> DATABASE_RELATED category that would simply list entry codes for databases in the same> way as CITATION simply lists literature references.? Other categories in other dictionaries> may then reference these entries for their own uses.? This is not intended to replace the> current DATABASE categories, which would still be preferred for use by structural> databases upon deposition and delivery of CIF files.? The new category would instead align> with the mmCIF DATABASE_2 category.> > The proposed data names are as follows, with short summaries of their meanings:> > _database_related.id?????????? 'An arbitrary identifier for this entry'> _database_related.database_id??????????? 'An identifier for the database from an enumerated list (e.g. CCDC,> PDB, ICSD, COD ...)> _database_related.reference?? 'A code used by the database given in> _database_related.database_id'> _database_related.relation ? ?? 'The way in which the database entry is related to the contents> of the data block, from an enumerated list. Initial suggestions include> "identical","component","derived","common source" '> _database_related.special_details?? 'Optional free-form description of the relationship> between this entry and the data block contents"> ?> An example of use in a data file would then be:> > loop_> _database_related.id?????????> _database_related.database_id????????> _database_related.reference?> _database_related.relation ? ?> _database_related.special_details> 1??? COD????????????? 1234?????????????????? identical??????????????????????????? 'As deposited structure'> 2??? COD????????????? 6789?????????????????? 'common source'??????????? 'Curated version of this structure'> 3??? CCDC??????????? qrst-12?????????????? 'common source'??????????? 'Curatedversion of this structure'> 4??? ICSD????????????? lll-ppp???????????????? . ??????????????????????? ? ? ? ? ? ? ? ? 'An earlier version of the structure with missing H atoms'> > Please provide your thoughts on this general scheme, and any further data names that you> think might be useful in this context.? If there are no objections, I will prepare formal> definitions and advise this group when they are ready for inclusion.> > best wishes,> James Hester.> --> T +61 (02) 9717 9907> F +61 (02) 9717 3145> M +61 (04) 0249 4148> > > > > --> T +61 (02) 9717 9907> F +61 (02) 9717 3145> M +61 (04) 0249 4148> >_______________________________________________coreDMG mailing listcoreDMG@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/coredmg

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