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Self-described CIF proposal
- Subject: Self-described CIF proposal
- From: Joe Krahn <krahn@xxxxxxxxxxxxx>
- Date: Wed, 28 May 2008 12:21:07 -0400
CIF relies on dictionaries to parse data correctly. The underlying STAR format does not have a well-defined system for representing general-purpose data, and leaves these details to a higher-level specification. My proposal is to define a "self-described CIF" format. I mentioned this before, but there was not a lot of interest. I assume that this is because most CIF developers are working with standardized databases, where dealing with non-standard self-described data is difficult. Experimentalists often need to store general-purpose data that cannot always be handled by trying to create a dictionary that covers all possible needs. In my opinion, STAR should be flexible enough to represent data in a manner similar to NetCDF. The general syntax can be that a CIF data block can contain save-frames that represent data in the same manner as save-frames within a dictionary. Dictionary data that is not in a save-frame will have to be contained in a special save frame, which could be named "dictionary", or some form of 'un-named' tag such as a single underscore. As simple example of user-defined data, this could be inserted in a data block that includes a mass for each atom, but also uses the dictionary for everything else. To avoid conflicts, non-standard values used in the context of a standard dictionary could all require a "[user]" prefix. data_XXX save__atom_site.[user]mass _item_description.description 'Atomic mass for this atom.' _item_type.code float _item_units.code 'unified_atomic_mass' save_ ... For dictionary-oriented data, this idea can still be useful for tagging a data block with the matching dictionary, for example: data_XXX save_dictionary _dictionary.title mmcif_std.dic _dictionary.version 2.0.10 save_ ... Current mmCIF files contain "_audit_conform" entries, but it seems more useful to have a general mechanism rather than identifying the dictionary within dictionary-defined fields. Of course, this could also be done with some sort of formatted comment on the first or second line of the file. I think this should be a fairly simple extension to CIF. If CIF developers don't want to change CIF, this idea could also be implemented as an alternative STAR implementation, or it could be explicitly defined as a CIF extension rather than a change to CIF itself. Joe Krahn _______________________________________________ cif-developers mailing list cif-developers@iucr.org http://scripts.iucr.org/mailman/listinfo/cif-developers
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