[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Fwd: COMCIFS minutes

Hi James,

Thanks for making the clarification.

Regards,

John


On 8/30/14, 10:43 PM, James Hester wrote:
> Dear COMCIFS members,
>
> The minutes do state that the DDLm requirement relates only to *new* dictionaries, so on the basis of the minutes there is no
> requirement to do anything with current DDL2 dictionaries at all. I agree that there was a clear intention at the meeting to avoid
> any impediments to wwPDB working in DDL2, including any requirement that the mmCIF dictionary should be presented in DDLm form
> before a DDL2->DDLm lossless translation was possible.
>
> Please advise if the following text for the last paragraph in section 7 is OK:
>
> "It was agreed that any new dictionary submitted for COMCIFS approval should have a canonical DDLm version. This would not preclude
> development of a dictionary using DDL1, but the reference version upon acceptance would be DDLm. Given the DDL2 to DDLm translation
> issues identified above, and the need to avoid impediments to the wwPDB working with DDL2, any requirement for a canonical DDLm form
> for current DDL2 dictionaries (particularly mmCIF) would be subject to the successful completion of the work described in the
> previous paragraph".
>
> James.
>
>
>
> On Sat, Aug 30, 2014 at 12:08 AM, John Westbrook <jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>> wrote:
>
>     John
>
>     The minutes in section 7. do not include the condition -  *subject to the aforementioned updates to DDLm being implemented*.
>     only the statement ..
>
>
>     ... It was agreed that any new dictionary submitted for COMCIFS approval should have a canonical DDLm version. This would not
>     preclude development of a dictionary using DDL1, but the reference version upon acceptance would be DDLm ..
>
>     If this condition is added then I do not have a problem with the statement although I would prefer that it also include
>     a statement that owing to the intended semantic equivalence of dictionary metadata this would statement would not
>     represent an impediment to ongoing DDL2 dictionary developments by wwPDB.
>
>
>     Btw.  DDL2 has had methods from its initial release that we use internally within PDB.
>
>     Regards,
>
>     John
>
>
>     On 8/29/14, 9:50 AM, Bollinger, John C wrote:
>
>         As the minutes show, we agreed to ensure that DDLm had at least the same representational capability of DDL2, which it
>         currently does not.  We did not discuss modifying DDL2, and although we could indeed add methods to DDL2, but doing so is
>         unnecessary, and I am inclined to avoid it.
>
>         My recollection is that we did agree to exactly what the minutes say, *subject to the aforementioned updates to DDLm being
>         implemented*.  Then there will be one canonical representation for (future) dictionaries, with the ability to automatically
>         create derived dictionary documents in either DDL1 or (especially) DDL2 formalism.
>
>
>         John
>
>         -----Original Message-----
>         From: comcifs-bounces@iucr.org <mailto:comcifs-bounces@iucr.org> [mailto:comcifs-bounces@iucr.__org
>         <mailto:comcifs-bounces@iucr.org>] On Behalf Of Herbert J. Bernstein
>         Sent: Friday, August 29, 2014 7:30 AM
>         To: John Westbrook; Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS)
>         Subject: Re: Fwd: COMCIFS minutes. .
>
>         But, I thought we agree to ensure the lossless translation of dictionaries between DDL2 and DDLm, so there is no reason not
>         to have DDLm reference dictionaries -- for mmCIF and imgCIF they would be
>         essentially the same as the DDL2 dictionaries.   in fact the only
>         thing that is currently missing on the DDL2 side are the methods.  I suspect we can add them in them in to DDL2 a
>         non-conflicting manner.
>         That would leave only the cleanup on the DDLm side we agreed to to have full interoperability.
>
>         On Fri, Aug 29, 2014 at 8:10 AM, John Westbrook <jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>> wrote:
>
>             Hi James,
>
>             I do not believe that we agreed to the following with respect to DDL2
>             -
>
>             ... It was agreed that any new dictionary submitted for COMCIFS
>             approval should have a canonical DDLm version. This would not preclude
>             development of a dictionary using DDL1, but the reference version upon
>             acceptance would be DDLm ...
>
>             Until lossless software translation of dictionaries is possible then I
>             do not think that this is a reasonable requirement.
>
>             John
>
>
>             On 8/28/14, 9:39 PM, James Hester wrote:
>
>
>                 Dear COMCIFS,
>
>                 Please find attached some draft minutes from our meeting in Montreal.
>                 Would those who were present please check them and advise Brian or
>                 myself of any errors or omissions.
>
>                 thanks,
>                 James.
>
>
>                 --
>                 T +61 (02) 9717 9907 <tel:%2B61%20%2802%29%209717%209907>
>                 F +61 (02) 9717 3145 <tel:%2B61%20%2802%29%209717%203145>
>                 M +61 (04) 0249 4148 <tel:%2B61%20%2804%29%200249%204148>
>
>
>                 _________________________________________________
>                 comcifs mailing list
>                 comcifs@iucr.org <mailto:comcifs@iucr.org>
>                 http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>
>
>
>             --
>
>             John Westbrook, Ph.D.
>             RCSB, Protein Data Bank
>             Rutgers, The State University of New Jersey Department of Chemistry
>             and Chemical Biology
>             174 Frelinghuysen Rd
>             Piscataway, NJ 08854-8087
>             e-mail: jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>
>             Ph: (848) 445-4290 <tel:%28848%29%20445-4290> Fax: (732) 445-4320 <tel:%28732%29%20445-4320>
>             _________________________________________________
>             comcifs mailing list
>             comcifs@iucr.org <mailto:comcifs@iucr.org>
>             http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>
>
>         _________________________________________________
>         comcifs mailing list
>         comcifs@iucr.org <mailto:comcifs@iucr.org>
>         http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>
>
>
>         Email Disclaimer: www.stjude.org/emaildisclaimer <http://www.stjude.org/emaildisclaimer>
>         Consultation Disclaimer: www.stjude.org/__consultationdisclaimer <http://www.stjude.org/consultationdisclaimer>
>
>         _________________________________________________
>         comcifs mailing list
>         comcifs@iucr.org <mailto:comcifs@iucr.org>
>         http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>
>
>
>     --
>
>     John Westbrook, Ph.D.
>     RCSB, Protein Data Bank
>     Rutgers, The State University of New Jersey
>     Department of Chemistry and Chemical Biology
>     174 Frelinghuysen Rd
>     Piscataway, NJ 08854-8087
>     e-mail: jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>
>     Ph: (848) 445-4290 <tel:%28848%29%20445-4290> Fax: (732) 445-4320 <tel:%28732%29%20445-4320>
>     _________________________________________________
>     comcifs mailing list
>     comcifs@iucr.org <mailto:comcifs@iucr.org>
>     http://mailman.iucr.org/__mailman/listinfo/comcifs <http://mailman.iucr.org/mailman/listinfo/comcifs>
>
>
>
>
> --
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148

-- 

John Westbrook, Ph.D.
RCSB, Protein Data Bank
Rutgers, The State University of New Jersey
Department of Chemistry and Chemical Biology
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
e-mail: jwest@rcsb.rutgers.edu
Ph: (848) 445-4290 Fax: (732) 445-4320
_______________________________________________
comcifs mailing list
comcifs@iucr.org
http://mailman.iucr.org/mailman/listinfo/comcifs

Reply to: [list | sender only]