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Re: Fwd: COMCIFS minutes

Sounds good to me. -- Herbert

On Sat, Aug 30, 2014 at 10:43 PM, James Hester <jamesrhester@gmail.com> 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>
> 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] 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>
>>> 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
>>>>> F +61 (02) 9717 3145
>>>>> M +61 (04) 0249 4148
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> comcifs mailing list
>>>>> comcifs@iucr.org
>>>>> 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
>>>> Ph: (848) 445-4290 Fax: (732) 445-4320
>>>> _______________________________________________
>>>> comcifs mailing list
>>>> comcifs@iucr.org
>>>> http://mailman.iucr.org/mailman/listinfo/comcifs
>>>
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>>
>> --
>>
>> 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
>
>
>
>
> --
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
>
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