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Re: Additional fast-track definitions for Core 2.4.2

Aye on all five -- 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 Sun, 17 Apr 2011, Brian McMahon wrote:

> Dear COMCIFS colleagues
>
> If you are wondering about the delay in publishing the recent round of
> updates to the Core dictionary, this is because, in implementing the
> recently approved changes, I discovered a number of other "fast-track"
> proposals that were overlooked, owing to an early misunderstanding
> between myself and James Hester regarding the mechanism of the approval
> process. I have subsequently asked the core dictionary management
> group to review and accept these proposals, and I now ask voting
> members of COMCIFS to complete the process by indicating their
> approval - or, of course, reservations or other comments.
>
> I shall be on vacation for the next week, but if the relevant approvals
> are received during that time, should be in a position to bundle
> these changes along with the others and release version 2.4.2 of the
> core within a few days of my return.
>
> 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 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
> _______________________________________________
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>
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