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Re: Rough agenda for COMCIFS open meeting August 8th 16:45 in room516e . .

Dear Colleagues,

  At the moment, the formal specification of the extended STAR syntax
is only available from the ACS for $35.This is not a good idea for
something we would want people to use, and, as James notes, we don't
really need the nesting yet, so, for the moment I would suggest we
keep things simple and flat, and drop back to un-nested save frames
for the new dictionaries.

  Regards,
    Herbert

On Wed, Aug 6, 2014 at 8:26 AM, James Hester <jamesrhester@gmail.com> wrote:
> The format of the draft dictionaries indeed varies from the CIF2 syntax in
> the ways John has indicated.  Because the Perth group undertook this work,
> they used their tools and therefore the syntax corresponds to their
> published STAR2 syntax rather than the slightly different CIF2 syntax.
> Clearly any final document approved by us must correspond to our agreed
> standard and all the variations from our syntax identified by John can be
> automatically fixed.
>
> The issue of nested save frames is an interesting one which we should
> discuss. DDL2 dictionaries use save frames to present definitions within a
> single data block, and DDLm (as published by the Perth group) follows this
> practice but also allows the save frames to be nested.  The main reason for
> nesting, as I understand it, is that this enforces good dictionary
> construction when reading and editing the dictionary, as child definitions
> are forced to lie within the parent category together with their siblings.
> It may also simplify the implementation of dictionary tools that build an
> inheritance model out of these nested categories, and we should bear in mind
> that the dictionary tools provided to us by the Perth group at last years'
> workshop assume that categories will be nested.
>
> On the other hand, this nesting duplicates information contained within the
> definitions themselves so un-nesting the save frames (as done in DDL2) has
> no implications for dictionary semantics.
>
> James
>
>
> On Wed, Aug 6, 2014 at 1:08 PM, Bollinger, John C
> <John.Bollinger@stjude.org> wrote:
>>
>> Dear COMCIFS members,
>>
>>
>>
>> I was looking at the draft of the DDLm-format Core dictionary that James
>> pointed us toward, and I find that it does not comply with the CIF2 format
>> we approved (as I understand that).  It has at least these issues:
>>
>>
>>
>> 1. As a trivial matter, it does not start with the *required* CIF version
>> comment.
>>
>> 2. As a somewhat more serious matter, it uses incorrect list and table
>> syntax throughout (specifically, it delimits list elements and table items
>> with commas instead of with whitespace).
>>
>> 3. As a very serious matter, it relies on nested save frames.  I can and
>> have prepared a revised draft with the above issues fixed, but I am
>> uncertain about the correct fix for this one, for CIF 2.0 as we approved it
>> does not support the semantics the file seems to be trying to express.
>>
>>
>>
>> I have not checked the DDLm-format mmCIF dictionary, but I suppose it will
>> have the same issues.
>>
>>
>>
>>
>>
>> John
>>
>>
>>
>> From: comcifs-bounces@iucr.org [mailto:comcifs-bounces@iucr.org] On Behalf
>> Of James Hester
>> Sent: Monday, July 28, 2014 10:08 PM
>> To: Discussion list of the IUCr Committee for the Maintenance of the CIF
>> Standard (COMCIFS)
>> Subject: Rough agenda for COMCIFS open meeting August 8th 16:45 in room
>> 516e . .
>>
>>
>>
>> Dear COMCIFS members,
>>
>> Please find below an agenda and some background information for the
>> meeting in Montreal.  Let me know if there are any other items that need
>> discussion.
>>
>> James.
>>
>> ===============================
>>
>> 0. Introductory comments (J Hester)
>>
>> 1. Report on CIF-NeXuS interaction (H Bernstein)
>>
>> 2. Discussion and possible approval of new data citation data items (B
>> McMahon)
>>
>> 3. Dictionaries under construction: magCIF (J Hester or B Campbell if
>> available)
>>
>> 4. Plan for next triennium (J Hester)
>>
>>  - managing CIF2/DDLm introduction
>>
>>  - funding request to IUCr executive
>>
>>  - interactions with DDDWG
>>
>> 5. Report on meeting with IUCr executive (if anything to report) (J
>> Hester)
>>
>> 6. Any other project updates (CIFAPI? wwPDB?)
>>
>> 7. Discussion, hopefully leading to decision: "that all new dictionaries
>> accepted by COMCIFS use DDLm, and that COMCIFS updates existing dictionaries
>> to DDLm as soon as possible."
>>
>> 8. Any other business
>>
>>
>>
>> Supplementary information
>>
>> (1) Herbert may wish to supply links to background material
>>
>> (2) See my previous email today
>>
>> (7) The Perth group has been busy producing draft DDLm versions of the
>> DDL1/2 dictionaries for your ontological pleasure.  All current
>> COMCIFS-administered dictionaries have been completed and may be perused at
>> https://github.com/COMCIFS/cif_core. The ddl.dic file found in that
>> directory contains the definitions of the DDLm attributes themselves.  As a
>> rough plan, DDLm dictionaries for which DMGs are functioning will be passed
>> through those DMGs for approval before becoming official.
>>
>>
>>
>> Feel free to discuss (7) on this mailing list ahead of time.
>>
>>
>> --
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>> M +61 (04) 0249 4148
>>
>>
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>
>
>
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