Additional fast-track definitions
David Brown
idbrown at mcmaster.ca
Wed Mar 30 15:04:58 BST 2011
I am in favour of all the proposed changes in Brian's email.
David Brown
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 at iucr.org
>5 Abbey Square, Chester CH1 2HU, England
>_______________________________________________
>coreDMG mailing list
>coreDMG at iucr.org
>http://scripts.iucr.org/mailman/listinfo/coredmg
>
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