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Re: Rough agenda for COMCIFS open meeting August 8th 16:45 in room516e . .
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS)" <firstname.lastname@example.org>
- Subject: Re: Rough agenda for COMCIFS open meeting August 8th 16:45 in room516e . .
- From: "Herbert J. Bernstein" <email@example.com>
- Date: Wed, 6 Aug 2014 11:28:15 -0400
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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 <firstname.lastname@example.org> 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: email@example.com [mailto:firstname.lastname@example.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. >> >> >> -- >> T +61 (02) 9717 9907 >> F +61 (02) 9717 3145 >> M +61 (04) 0249 4148 >> >> >> ________________________________ >> Email Disclaimer: www.stjude.org/emaildisclaimer >> Consultation Disclaimer: www.stjude.org/consultationdisclaimer >> >> _______________________________________________ >> comcifs mailing list >> email@example.com >> http://mailman.iucr.org/mailman/listinfo/comcifs >> > > > > -- > T +61 (02) 9717 9907 > F +61 (02) 9717 3145 > M +61 (04) 0249 4148 > > _______________________________________________ > comcifs mailing list > firstname.lastname@example.org > http://mailman.iucr.org/mailman/listinfo/comcifs > _______________________________________________ comcifs mailing list email@example.com http://mailman.iucr.org/mailman/listinfo/comcifs
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