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Re: Absence of _item.category_id or _item_linked.parent_name in somemmcif definitions

Hi all,

If there are no objections from the group, I propose to create a revised version of
the PDBx/mmCIF dictionary that localizes all of the content for each data item
within that items' definition section (save__item.name).   The historical style
of dictionary composition that consolidates information within parent items
has been a source of confusion and aggravation for many mmCIf adopters.

Regards,

John


On 12/21/12 7:35 AM, yayahjb wrote:
> Dear Colleagues,
>
>    This is not a matter of something being missing from the mmCIF dictionary.
> John W. tried explaining this a few years ago.  I'll give it a shot this time,
> but in view of the continuing problems in reading the DDL2 dictionaries,
> I will also suggest a change.  In this case, even though as a technical matter
> it ain't broke, as a practical human engineering matter, something is broke
> so we _should_ fix it.
>
>    In the mmcif dictionary, the definitions of individual tags are _not_
> in general completely contained in a single save frame.  For example,
> as James notes, the category and parent name for  _atom_site_anisotrop.id
> are explicitlygiven in a loops in the _atom_site.id save frame:
>
>        loop_
>      _item.name
>      _item.category_id
>      _item.mandatory_code
>                 '_atom_site.id'                 atom_site            yes
>                 '_atom_site_anisotrop.id'       atom_site_anisotrop  yes
>                 '_geom_angle.atom_site_id_1'    geom_angle           yes
> ...
>
>      loop_
>      _item_linked.child_name
>      _item_linked.parent_name
>                 '_atom_site_anisotrop.id'       '_atom_site.id'
>                 '_geom_angle.atom_site_id_1'    '_atom_site.id'
> ...
>
> The two alternatives to this approach would be ether to move the
> information from the parent save frames to the children, or to duplicate
> the information.  Duplication may help in readability, but it is a maintenance
> headache.  The DDLm solution of only requiring/allowing specification
> of parents, rather than children would be similar to moving this linking
> information from loops in the parents into the children in DDL2.
>
>    My suggestion would be to move to the DDLm approach in the DDL2
> dictionaries, of putting the parent information with the children, rather
> than the children information with the parents in the formal dictionary,
> without duplication to minimize maintenance problems, but that Brian's
> nice formatting program be modified to gather the child information
> so that it is printed with the parent information as well as with each
> child to help people in reading these dictionaries.
>
>    I would suggest doing the same for the DDLm dictionaires:  provide
> print formatting tools to gather child information relating to a parent
> to put with the parent as a useful index.
>
>    Regards,
>      Herbert
>
>
>
> On 12/21/12 1:26 AM, James Hester wrote:
>> I will have a stab at this, although somebody with more experience of the mmCIF development process may wish to comment further.
>>
>> As far as I can tell, programmatically the only way to fix the 'missing parent' problem you identify is indeed to go through the
>> entire dictionary processing 'item_linked.parent_name' and '_item_linked.child_name' loops, which are usually found at the top of
>> the pointer tree (in this case in the _atom_site save frame).  This same save frame also contains a list of category ids for each
>> of the 'id' values.  My approach in PyCIFRW is to repopulate the individual definitions when ingesting the dictionary, to save
>> time later.  The PyCIFRW code and comments for this can be found at
>> https://bitbucket.org/jamesrhester/pycifrw/src/78576030f75bb4f8cb52d84a60e603815ad38afb/pycifrw/CifFile.nw?at=stable
>> starting at line 839, with lines 854-862 describing and discussing your issue.  Note also subsequent lines discussing PDBX.
>>
>> There is a school of thought that the category name is 'implicit' in a DDL2 dataname or save frame name, however IT Vol G states
>> that this is conventional rather than required so I prefer (like you it seems) never to assume this unless given no alternative.
>>
>> An mmCIF/PDB person may wish to comment on the philosophical reasons behind these decisions, which I gather have something to do
>> with taking a relational database view of a CIF file.
>>
>> all the best,
>> James.
>>
>> On Thu, Dec 20, 2012 at 1:32 PM, Richard Gildea <rgildea@gmail.com <mailto:rgildea@gmail.com>> wrote:
>>
>>     Dear All,
>>
>>     Certain definitions in the mmcif dictionary (e.g.
>>     _atom_site_anisotrop.id <http://atom_site_anisotrop.id>) do not
>>     contain the items _item.category_id or _item_linked.parent_name.
>>     Without these data items, how is it possible to identify
>>     programmatically that _atom_site_anisotrop.id
>>     <http://atom_site_anisotrop.id> belongs to the
>>     _atom_site_anisotrop category and that it is a pointer to
>>     _atom_site.id <http://atom_site.id> (without examining every save
>>     frame?
>>
>>     For quick reference here is the definition in question:
>>
>>     save__atom_site_anisotrop.id  <http://save__atom_site_anisotrop.id>
>>          _item_description.description
>>     ;              This data item is a pointer to _atom_site.id  <http://atom_site.id>  in the ATOM_SITE
>>                     category.
>>     ;
>>          _item.name  <http://item.name>                   '_atom_site_anisotrop.id  <http://atom_site_anisotrop.id>'
>>          _item.mandatory_code          yes
>>          _item_aliases.alias_name    '_atom_site_aniso_label'
>>          _item_aliases.dictionary      cif_core.dic
>>          _item_aliases.version         2.0.1
>>           save_
>>
>>     Cheers,
>>
>>     Richard
>>
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>>
>>
>>
>>
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-- 

John Westbrook, Ph.D.
RCSB, Protein Data Bank
Rutgers, The State University of New Jersey
Department of Chemistry and Chemical Biology
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
e-mail: jwest@rcsb.rutgers.edu
Ph: (848) 445-4290 Fax: (732) 445-4320
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