Additional fast-track definitions for Core 2.4.2

jim kaduk kaduk at polycrystallography.com
Thu Apr 21 16:12:37 BST 2011


I strongly support the InChI items.   
 
I have mixed feelings about the -database_code_COD, because I think that that
database is misguided.  Because others use it, I will support an item pointing
to database identifiers in it.
 
I support _diffrn_radiation_wavelength_details.
 
Jim Kaduk 
 

 On April 17, 2011 at 11:52 AM Brian McMahon <bm at iucr.org> 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 at iucr.org
 > _______________________________________________
 > comcifs mailing list
 > comcifs at iucr.org
 > http://scripts.iucr.org/mailman/listinfo/comcifs
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