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Re: Additional fast-track definitions

    _database_code_COD                       Aye
    _chemical_identifier_inchi               Aye
    _chemical_identifier_inchi_version       Aye
    _chemical_identifier_inchi_key           Aye
    _diffrn_radiation_wavelength_details     Aye

     -- 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, 30 Mar 2011, Brian McMahon wrote:

> Dear Colleagues
>
> Oh dear. In updating the core dictionary with the recently approved
> changes, I have discovered a number of other "fast-track" proposals that
> have been overlooked. My apologies for this; owing to an early
> misunderstanding between myself and James Hester, notification of these
> postings was not passed on to the coreDMG Chair.
>
> The relevant items are
>   _database_code_COD
>   _chemical_identifier_inchi
>   _chemical_identifier_inchi_version
>   _chemical_identifier_inchi_key
>   _diffrn_radiation_wavelength_details
>
> Full details for each proposal may be found at
>   http://www.iucr.org/resources/cif/dictionaries/new-item/cif_core
> but I'll repeat the salient points below.
>
> I'd be very grateful if you would take the trouble to vote explicitly for
> (or against) each of these items in the next few days; although our
> procedures allow acceptance by default after a 6-week period if there
> are no comments or objections I would appreciate it if we could
> manage to bundle these changes along with the others in releasing
> version 2.4.2 of the core within the next few days.
>
> I do apologise again for this oversight; it is not a good advertisement
> for the "fast-tracking" process; but the fault is entirely mine.
>
> I vote in favour of all five of the proposed new definitions.
>
> Best regards
> Brian
>
> Further details of the proposed definitions:
>
> ------------------------------------------------------------------------------
>
> _database_code_COD
>
> Definition:
>
> Identification code assigned by Crystallography Open Database (COD).
>
> Example:
>
>
> Category: database
>
> An identifier of the structure as assigned by the Crystallography Open
> Database. This was requested by Saulius Grazulis by analogy with existing
> database identifiers such as _database_code_CSD for the Cambridge Structural
> Database.
>
> ------------------------------------------------------------------------------
>
> _chemical_identifier_inchi
>
> Definition:
>
> The IUPAC International Chemical Identifier (InChI) is
> a textual identifier  for chemical substances, designed
> to provide a standard and human-readable way to
> encode molecular information and to facilitate the
> search for such information in databases and on the
> web.
>
> Example:
> 'InChI=1/C18H21NO3/c1-19-8-7-18-11-4-5-13(20)17(18)22-16-14(21-2)6-3-10(15(16)18)9-12(11)19/h3-6,11-13,17,20H,7-9H2,1-2H3/t11-,12+,13-,17-,18-/m0/s1'
> codeine
>
> Category: chemical
>
> ------------------------------------------------------------------------------
>
> _chemical_identifier_inchi_version
>
> Definition:
>
> Version of the InChI standard.
>
> Example:
> 1.02
>
> Category: chemical
>
> InChI is a changing standard. It is necessary to track the current version
> in order to parse it correctly.
>
> ------------------------------------------------------------------------------
>
> _chemical_identifier_inchi_key
>
> Definition:
>
> The 25-character hashed version of the full InChI (IUPAC
> International Chemical Identifier), designed to allow for
> easy web searches of chemical compounds.
>
> Example:
> InChIKey=OROGSEYTTFOCAN-DNJOTXNNBG 	codeine
>
> Category: _chemical_identifier_inchi_key
>
> The InChIKey is a 25-character hashed version of the full InChI, designed to
> allow for easy web searches of chemical compounds. InChIKeys consist of 14
> characters resulting from a hash of the connectivity information of the
> InChI, followed by a hyphen, followed by 8 characters resulting from a hash
> of the remaining layers of the InChI, followed by a single character
> indicating the version of InChI used, followed by single checksum character.
> There is a finite, but very small probability of finding two structures with
> the same InChIKey. However the probability for duplication of only the first
> block of 14 characters has been estimated as one duplication in 75 databases
> each containing one billion unique structures; such duplication therefore
> appears unlikely at present. Further information on the InChIKey is
> available at http://www.iupac.org/inchi/release102.html.
>
> ------------------------------------------------------------------------------
>
> _diffrn_radiation_wavelength_details
>
> Definition:
>
> Information about the determination of the radiation wavelength that is not
> conveyed completely by an enumerated value of
> _diffrn_radiation_wavelength_determination.
>
> Example:
>
>
> Category: diffrn_radiation_wavelength
>
>
>
> Any other attributes suggested by the submitter are listed here:
>
> _type                        char
>    _list                        both
>    _list_reference            '_diffrn_radiation_wavelength_id'
>
>
> When adding the recently approved _diffrn_radiation_wavelength_determination
> to the core dictionary, it was noticed that the suggested definition for
> this new data name was:
>
> The method of determination of incident wavelength.
> Further information may be provided in _diffrn_radiation_special_details
>
> However, _diffrn_radiation_special_details does not exist. This data name is
> suggested in order to fulfil that role; note that as a member of this
> category it would necessarily be looped if there are multiple wavelengths
> listed. An alternative (or perhaps complementary) approach would be to
> create a "scalar" _diffrn_radiation_details item in the parent category.
>
> ------------------------------------------------------------------------------
> _________________________________________________________________________
> Brian McMahon                                       tel: +44 1244 342878
> Research and Development Officer                    fax: +44 1244 314888
> International Union of Crystallography            e-mail:  bm@iucr.org
> 5 Abbey Square, Chester CH1 2HU, England
> _______________________________________________
> coreDMG mailing list
> coreDMG@iucr.org
> http://scripts.iucr.org/mailman/listinfo/coredmg
>
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