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Re: Please advise regarding a design of CIF dictionaries for materialproperties
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
- Subject: Re: Please advise regarding a design of CIF dictionaries for materialproperties
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Wed, 28 Sep 2011 10:54:37 -0400 (EDT)
- In-Reply-To: <4E832F86.6080805@ibt.lt>
- References: <4E832F86.6080805@ibt.lt>
Dear Colleagues, The example CIF itself looks intutive and clear, so the difficuly, if any, seems to lie in expressing this structure in the dictionary. As a DDL2 dictionary, it would be easy, just change the last underscore in each tag to a period, define a category for the part to the left of the period, and the part to the right is a column name. There would be one data block, a lot of save frames, and there is a past practice in DDL2 dictionaries of gathering information about a lot or related tags into a common save frame for some master parent tag and just putting minimal information on the individual tags in their own save frames. I highly recommend taking a look at the mmCIF dictionary or the pdbx dictionary. If that is followed as a model, then when we do the move of those to DDLm this new dictionary should move forward with minimal fuss. If we start retooling DDL1 for what is really a DDL2 issue, I fear we would be borrowing trouble. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 28 Sep 2011, Saulius Grazulis wrote: > Dear COMCIFS members, > > I have a question about the design of domain-specific CIF dictionaries > and would like to ask for your advise (and please accept my apologies > and let me know if there is a better mailing list to ask for such > questions). > > I am currently participating in the design of CIF dictionary for the > Material Properties Open Database (MPOD) that intends to store all > published experimentally measured crystal properties, such as elasticity > tensors, dielectric permeability and so forth. All in all there should > be about 50 different tensors. > > Each tensor can be measured at different temperatures or pressures. To > preset data convenietly, for both humans and computers, we curretnly > plan to put each tensors' measurements into a separate loop. Since tag > names may not be repeated int the same data block, we will have to > define similar measurement condition tags for each tensor: > > _prop_elastic_stiffness_temperature > _prop_piezoelectric_temperature > > (_prop_ is a prefix registered for MPOD in the IUCr prefix list). > > Now, although this is only a small overhead in CIFs, it would be an > overkill to specify all these tags separately in a dictionary. Thus, I > would like to "contract" the definition of all > _prop_<property>_temperature tags into one dictionary datablock: > > data_prop_temperature > loop_ > _name '_prop_elastic_stiffness_temperature' > '_prop_piezoelectric_temperature' > # Other names will follow and may be added in the future releases > # of the dictionary > _type numb > _type_conditions esd > _category prop # or prop_temperature ? or prop_elastic? > _list both > _description > ; > Specifies measurement temperature of a property in Kelvins. > ; > _example > ; > Please see below in this mail... > ; > > Now, my questions are -- is there a problem if: > > a) tags of the same property are split into several loops in data CIFs? > > b) one dictionary data block describes names that are potentially in > different categories (but otherwise have the same characteristics)? For > example, would the dictionary entry above be considered correct if we > declare _prop_elastic_stiffness_temperature to be in > 'prop_elastic_stiffness' category, and _prop_piezoelectric_temperature > to be in 'prop_piezoelectric' category, and still have one dictionary > datablock to specify their properties? > > b') or the category is so inclusive that it describes data spanning > several loops (like '_prop_' category in the above example)? > > c) data_... block name in the dictionary no longer matches tag name. I > guess this should not be a problem... Is it? > > d) would it break anything if category name is not the prefix of the tag > (e.g. declaring _prop_piezoelectric_temperature to have category > _prop_temperature, to describe all temperature tags in one data block)? > > e) Any other anticipated problems? > > Sincerely yours, > Saulius > > PS. We have toyed with two other representations, one putting all > tensors into one loop, but they seem much worse (would require lots of > '.' fields and would result in severely denormalised relational tables). > > PPS: data examples with the proposed tags: > >> The CIF would look like >> >> loop_ >> _prop_elastic_stiffness_label >> _prop_elastic_stiffness_temperature >> _prop_elastic_stiffness_c11 >> _prop_elastic_stiffness_c12 >> _prop_elastic_stiffness_c13 >> _prop_elastic_stiffness_c22 >> _prop_elastic_stiffness_c23 >> _prop_elastic_stiffness_c33 >> _prop_elastic_stiffness_c44 >> _prop_elastic_stiffness_c55 >> _prop_elastic_stiffness_c66 >> Copper 273 375.1 -48.5 -48.5 375.1 -48.5 375.1 101.4 101.4 101.4 >> Copper 293 375.1 -48.5 -48.5 375.1 -48.5 375.1 101.4 101.4 101.4 >> Copper 313 375.1 -48.5 -48.5 375.1 -48.5 375.1 101.4 101.4 101.4 >> >> loop_ >> _prop_piezoelectric_label >> _prop_piezoelectric_temperature >> _prop_piezoelectric_frequency >> _prop_piezoelectric_d15 >> _prop_piezoelectric_d16 >> _prop_piezoelectric_d21 >> PIN-PMN-PT 100.0 ? 2190 1022 511 >> PIN-PMN-PT 100.0 ? 2190 1022 511 >> PIN-PMN-PT 100.0 ? 2190 1022 511 >> >> and so on. > > S.G. > > -- > Dr. Saulius Gra?ulis > Institute of Biotechnology, Graiciuno 8 > LT-02241 Vilnius, Lietuva (Lithuania) > fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 > mobile: (+370-684)-49802, (+370-614)-36366 > _______________________________________________ > comcifs mailing list > comcifs@iucr.org > http://scripts.iucr.org/mailman/listinfo/comcifs >
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