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

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. 


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.





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.



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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