[Date Prev][Date Next][Date Index]
(84) Procedural matters: terms of reference, discussion lists, DMGs
- To: COMCIFS@iucr
- Subject: (84) Procedural matters: terms of reference, discussion lists, DMGs
- Cc: execsec@iucr.org
Dear Colleagues This mailing is essentially on procedural matters. All members have approved the Report to the Executive Committee, which I print in its final form at the end. Paula Fitzgerald (PMDF) has some reservations about the manner in which business is and will be conducted, and I present these below as responses to item D79.1. Paula and Peter Murray-Rust (PMR) had some comments on the suggestion that we replace the current system of periodic digests with an email discussion group, which are tabled under item D83.1. Acceptance of the report implies acceptance of the delegation of maintenance of existing dictionaries to Dictionary Management Groups (DMG), and I list in item D84.1 the existing de facto DMGs for the core and mmCIF dictionaries. Brian Toby is in the process of establishing a powder DMG. D79.1 Report to the IUCr Executive Committee -------------------------------------------- PMDF> My biggest problem with the way that COMCIFS does business is that I PMDF> find it burdensome to try and resolve such complicated technical PMDF> issues via email. Brian McMahon does yeoman's work in collating and PMDF> redistributing the various input that he receives, but my response when I PMDF> get yet another 897 line COMCIFS mailing from Brian is to say "Oh dear, PMDF> I'll read that tomorrow." Sometimes tomorrow comes, often it does not - PMDF> at least not anywhere near tomorrow. PMDF> PMDF> I have no objection to the report in terms of the structure of the PMDF> committee, which is all that it really addresses. It does not address PMDF> the operating mechanics of the committee, and that is where I would like PMDF> to see changes. This is a committee that should meet, in person, at least PMDF> once a year. These meetings could be coordinated with an appropriate PMDF> national or international crystallography meeting, or with one of the PMDF> several CIF workshops that have been occurring in the past few years. It PMDF> is in sitting face to face in a room, with the knowledge that time is PMDF> limited, and (most usefully) with access to computers, that we could PMDF> efficiently deal with the business that the committee has in front of it. PMDF> PMDF> I am genuinely of the opinion that many decisions that COMCIFS makes PMDF> are adversely influenced by the volume of email that must be absorbed to PMDF> do an adequate job of weighing the issues at hand. I am often PMDF> the last to vote, because I find it so hard to sit down and dig my PMDF> way through all of the email. There must be a more efficient way of PMDF> going through the issues that we must deal with; I think a face-to-face PMDF> discussion once a year would be a major step in the right direction. PMDF> PMDF> On a somewhat related issue (the fact that the report addresses structure PMDF> of the committee but not its operations) - you state "Minor changes to PMDF> the dictionaries will likely be made in a piecemeal fashion, and COMCIFS PMDF> will have to ensure that these changes conform to existing rules and PMDF> practices." And yet the proposed new structure for COMCIFS says PMDF> nothing about how this is to be handled. I don't think that PMDF> dictionary changes should be made piecemeal. If we are serious in our PMDF> policy that changes require COMCIFS review for technical soundness, PMDF> followed by community review for content, followed by COMCIFS review for PMDF> final approval, this must be done according to a schedule. This is PMDF> particularly relevant for community review - if we can convince the PMDF> community that we are serious when we propose annual extensions and PMDF> corrections to the dictionary, and that we will stick to that timetable, PMDF> the whole effort will be much more credible. D83.1 Discussion group versus moderated digest ---------------------------------------------- PMR> With a discplined community and a perceptive moderator the discussion-group PMR> mode is *extremely* effective. This is the way that all XML groups work and PMR> they cover a huge amount of ground very rapidly and thoroughly. If members PMR> stray off topic a brief word from the 'chair' is always effective and in PMR> the 10000 (sic) messages I have read there have been no flame wars PMR> PMR> In more public discussion (e.g. PMR> http://www.lists.ic.ac.uk/hypermail/xml-dev) which I moderate there has PMR> been extremely good discipline even though no-one is part of a formal PMR> process. PMR> PMR> The CIF community is very well disciplined and I think the group would PMR> benefit from having a more rapid turnround with clear moderation if topics PMR> stray. The chair would summarise from time to time as appropriate and also PMR> pose questions which should be addressed - e.g. PMR> - should we have BNF's for CIF PMR> - if so, should there be one for each variant PMR> - should there be a formal list of non-BNF validity constraints PMR> etc. PMR> PMR> Each member can then reply to any given question and with good discipline PMR> this is easy to summarise. PMR> PMR> I also think that the more that the proceedings are open to the community PMR> (perhaps read-only except by invitation) the more there is a feeling of PMR> communal ownership. 'Casual' posters can then send mail to the chair who PMR> can repost it - this is what I do for WWW groups that I'm not a member of. PMR> PMR> Hypermailing the list is extremely effective in searching back for things PMR> (e.g. the mmCIF list or XML-DEV - see above). PMDF> I would like to reiterate [the] comments that ... PMDF> this committee could get its business done with much greater PMDF> dispatch were we to actually meet, face-to-face, on some regular PMDF> schedule. But short of that, I also think that the committee's PMDF> business would be easier to keep up with if we operated via a list server PMDF> rather than via the moderated mailings that are our current mode of PMDF> communication. Much as I applaud Brian's efforts in assembling and PMDF> editing these mailings, I find that they make *very* daunting reading, PMDF> and I often shy away from investigating their contents just because of PMDF> the volume of material involved. I think a list-based discussion would be PMDF> much more immediate, and would tend to draw input from more of the members PMDF> of the group. D84.1 Approval of membership of Dictionary Maintenance Groups ------------------------------------------------------------- The current memberships of the Dictionary Management Groups and a summary of their modus operandi are listed below, and they shall be considered as formally approved unless active objections are lodged. Core: David Brown Syd Hall Ton Spek (U. Utrecht) Paul Edgington Brian McMahon Consultant: John Westbrook Business is conducted through the restricted coredmg list (coredmg@iucr.org) archived at http://www.iucr.org/iucr-top/lists/coredmg/ . mmCIF: Helen Berman Paula Fitzgerald John Westbrook Herbert Bernstein Editorial Board: Frank Allen Phil Bourne Kim Henrick Andy Howard Joel Sussman Dale Tronrud Proposed extensions to the dictionary are refereed by the editorial board and approved by the executive group to a published schedule. There is also a public mailing list mmciflist@ndbserver.rutgers.edu, archived at http://ndbserver.rutgers.edu/NDB/mmcif/resources/mail/index.html and also at http://www.iucr.org/iucr-top/cif/mmcif/ndb/resources/mail/index.html . As mentioned above, work is in hand to establish a formal powder DMG. -- Regards Brian ============================================================================== A REPORT ON THE WORK OF COMCIFS AND PROPOSALS FOR THE FUTURE OF COMCIFS Submitted to the Executive Committee of the IUCr by DAVID BROWN Chair, COMCIFS 1998.5.7 1. INTRODUCTION The Crystallographic Information File (CIF) uses the STAR file structure (Hall, 1991, J. Chem. Inf. Comp. Sci. 31, 326-333). STAR is patented by the International Union of Crystallography (IUCr), and the CIF dictionaries that implement the CIF standard are copyright by the IUCr. The purpose of the patent and copyright is to ensure that ownership and the rights to maintain the standard are retained by the IUCr. The Executive Committee of the IUCr has appointed the sub-committee COMCIFS to approve and maintain the CIF dictionaries. The first CIF dictionary, the core version 1, was prepared by an ad hoc committee and was approved by the Executive in 1990 [Acta Cryst. (1991) A47, 655-685]. Subsequently further ad hoc committees were established to prepare dictionaries for crystallographic powder data and macromolecular structures. In August 1992 the Executive of the IUCr decided to appoint a sub-committee to be known as COMCIFS (Committee for the Maintenance of the CIF Standard) to take on the responsibility for maintaining the CIF standard. The first committee was appointed early in 1993 and COMCIFS held its first and only meeting at the IUCr Congress in Beijing in August of that year. By the time that COMCIFS was appointed, a number of important decisions had already been taken. The first core version of the CIF dictionary, cif_core_1.0.dic, had been approved, work was well under way on the powder and macromolecular dictionaries (cif_pd.dic and cif_mm.dic respectively), and the concept of storing the CIF dictionaries themselves as STAR files had been accepted. This required the construction of a dictionary definition language (DDL) but the maintenance of the DDL dictionary was not part of COMCIFS mandate. There are currently two DDLs. Most CIF dictionaries use DDL1 but the macromolecular dictionary uses the more structured DDL2. 2. TERMS OF REFERENCE The terms of reference of COMCIFS as stated in the original letters of appointment were: "1. To receive and examine all proposed amendments and extensions to the CIF standard. In particular to ratify proposed data names, ensure that data structures conform to the basic CIF specifications, and to ensure that the definitions of data items are clear and unambiguous. "2. To ensure that adequate current documentation of the CIF standard is available to potential users in both printed and machine-readable forms. "3. To ensure that all accepted amendments and extensions to the CIF standard are announced in an appropriate publication or news item in an IUCr publication. "Further, COMCIFS is to be a stand alone committee of the IUCr. It is not associated directly with any of the Commissions or Working Groups that were involved in the origination of CIF. The Executive requested that membership of COMCIFS be kept as small as possible and be restricted to those with acknowledged technical expertise in the areas of 1-3 above. Initial membership was by invitation of the chairman [at that time Frank Allen], with further co-option and replacement being the responsibility of the Committee itself with IUCr approval. COMCIFS reports directly to the IUCr Executive Committee through the Executive Secretary." 3. HISTORY Since its founding, COMCIFS has been working to bring three dictionaries to approval. Even before the founding of COMCIFS, Acta Crystallographica C had committed itself to the use of CIFs for the submission of papers describing crystal structure determinations and in recent years all papers have been submitted as electronic CIFs. As a result of this experience, a number of changes were required to the core dictionary. These were approved on 12 November 1996 as version 2.0 of the core dictionary (cif_core_2.0.dic). This was followed by the approval of the first versions of the macromolecular dictionary (cif_mm_1.0.dic) on 8 June 1997 and the powder dictionary (cif_pd_1.0.dic) on 9 July 1997. The International Center for Diffraction Data is committed to using pdCIF for the Powder Data File, and both the Protein Databank and the Nucleic Acid Databank are committed to using mmCIF. Modifications are being proposed to these approved CIF dictionaries and we expect new versions to appear in the next year or two. In addition work is in progress for dictionaries covering area detectors (raising problems of how to store large arrays of primary data), electron densities, modulated structures, symmetry, and diffuse scattering. Technical discussions are under way on how best to represent images, how to combine binary data with CIFs and how to link different CIF dictionaries. Current dictionaries and drafts of dictionaries under development are available on the IUCr web pages, and all approved dictionaries will appear in hardcopy in the proposed volume G of International Tables for Crystallography. 4. CURRENT MEMBERSHIP The current membership, which can conveniently be classified into three categories, is: Full Members ------------ I. D. Brown (Chair), McMaster University (idbrown@mcmaster.ca) S. R. Hall, Univ. Western Australia (syd@crystal.uwa.edu.au) P. R. Edgington, CCDC (edgington@ccdc.cam.ac.uk) P. M. D. Fitzgerald, Merck Research Laboratories (paula_fitzgerald@merck.com) B. H. Toby, Reactor Radiation Division, NIST (Brian.Toby@NIST.GOV) G. Madariaga, Univ. Pais Vasco, Bilbao (wmpmameg@lg.ehu.es) M. Spackman, Univ. New England (mspackman@metz.une.edu.au) B. McMahon (Coordinating Secretary), IUCr (bm@iucr.org) Consultants ----------- A. Authier (authier@lmcp.jussieu.fr) (Commission on Crystallographic Nomenclature) G. M. Sheldrick (gsheldr@ibm.gwdg.de) P. Murray-Rust (pmr1716@ggr.co.uk) P. E. Bourne (bourne@sdsc.edu) E. Ulrich (elu@nmrfam.wisc.edu) (NMR Databank) O. Ritter (o.ritter@bnl.gov) (Protein Data Bank) H. Berman (berman@dnarna.rutgers.edu) (IUCr Database Committee) Auditors -------- E.N.Baker (Ted.Baker@aukland.ac.nz) (IUCr President) N.Spadaccini (nick@cs.uwa.edu.au) (STAR/DDL1) J.Westbrook (jwest@rutchem.rutgers.edu) (DDL2) H. Bernstein (yaya@bernstein-plus-sons.com) (CIFtbx/Fortran programming) A.Hammersley (hammersl@esrf.fr) (Crystallographic Binary File) H.Flack (Howard.Flack@cryst.unige.ch) (Chair of EPC) T.Proffen (proffen@rsc.anu.edu.au) (Diffuse Scattering CIF) F.Bernstein (bernstein@bnl.gov) (PDB editorial style) J. Faber (faber@icdd.com) (International Center for Diffraction Data) Full members, consultants and auditors all receive the mailings that constitute the business of COMCIFS (see below). Full members are required to vote on matters put to a vote, and must therefore accept responsibility for the decisions made by COMCIFS. This implies a commitment of time. Consultants usually represent a particular constituency and are expected to take part in discussions relevant to that constituency. They may also comment on other matters, but are free to ignore items that lie outside their constituency. Auditors, who are not strictly members of COMCIFS, have no responsibilities but may contribute to any of the discussions. Anyone may ask to become an auditor. 5. CURRENT MODE OF OPERATION COMCIFS does not hold formal meetings. All business is conducted by email. Comments are sent to the Secretary (Brian McMahon) who includes them in the circulars that constitute the record of COMCIFS' business. These circulars, which are sent to full members, consultants and auditors, raise matters for discussion and include any comments received by the Secretary. Usually matters are resolved by consensus, but where this cannot be achieved, a formal vote is called. Only the full members have voting privileges. About 15 circulars are issued each year. COMCIFS is not directly involved in the preparation of new dictionaries. This is carried out by working groups, of whom at least one member is usually a full member of COMCIFS. The working groups are encouraged to consult widely in the field and this is done, inter alia, through electronic discussion groups, workshops, conferences or by posting the current draft of the dictionary on the web. When a working group has completed a draft it is referred to COMCIFS who may return it with comments for further work, or approve it provisionally for more widespread circulation and comment. After appropriate discussion in the community, the draft is presented to COMCIFS for final approval. Only full members may vote and all full members are required to vote on the adoption of new dictionaries. 6. FUTURE ROLE OF COMCIFS In its first four years, COMCIFS has been concerned with establishing general policies for CIFs in response to the questions raised by the working groups, and much of its energies have been devoted to getting the first versions of the powder and macromolecular dictionaries approved. In addition it has given advice to working groups that are starting the process of drafting other dictionaries. In the future, COMCIFS work is likely to change. More effort will be spent in maintaining existing dictionaries in response to a much increased user community. As more software is written to read, write and manipulate CIFs, and as more organisations commit themselves to the use of CIF, we can expect an increasing number of requests for changes and additions to the dictionaries. We need to find ways of addressing these requests in a timely manner. Minor changes to the dictionaries may be made in a piecemeal fashion, and COMCIFS will have to ensure that these changes conform to existing rules and practice. About half the Commissions of the IUCr have responsibilities for fields which overlap with COMCIFS. Some form of formal liaison with these Commissions may be desirable. Such links already exist with the Commission on Crystallographic Nomenclature and informal links have been made with other Commissions. Other organisations such as the crystal structure databases and equipment manufacturers may also wish to have a voice in COMCIFS discussions. We need to find the most effective way to involve these groups in COMCIFS' deliberations. PROPOSALS FOR A NEW STRUCTURE FOR COMCIFS As a result of our experience thus far, we propose the following revised terms of reference for COMCIFS. I. THE PURPOSE OF COMCIFS The purpose of COMCIFS is to maintain the integrity of the crystallographic file structure (CIF) on behalf of the International Union of Crystallography (IUCr). This purpose includes, but is not limited to, the following activities. 1. To establish policies defining the use of the Crystallographic Information File. 2. To receive and examine all proposed amendments and extensions to the CIF standard. In particular, to ratify proposed data names, to ensure that the data structures conform to the basic CIF specifications, and to ensure that the definitions of data items are clear and unambiguous and conform to accepted IUCr usage. 3. To ensure that all accepted amendments and extensions to the CIF standard are announced in an appropriate publication or news item in an IUCr publication. 4. To ensure that adequate current documentation of the CIF standard is available to potential users in both printed and machine-readable forms. 5. To coordinate with other organisations proposing CIF related dictionaries using STAR files to ensure maximum compatibility between CIFs and related file structures. 6. To coordinate with other crystallographic organisations proposing non-CIF standards to ensure maximum compatibility. 7. To coordinate with writers of software intended to read and write CIFs. 8. To ensure that those using CIF are aware of its ownership by the IUCr and the conditions under which it may be used. II. MEMBERSHIP OF COMCIFS 1. Voting members COMCIFS should consist of about 6 voting members appointed by the Executive Committee of the IUCr on the recommendation of COMCIFS. Membership would normally be for a three year renewable term. A membership slate will be presented to the Executive Committee of the IUCr for approval following each IUCr Congress. Voting members will be knowledgeable in the area of electronic manipulation of information and representative of the various fields of crystallography. COMCIFS will have a chair and secretary appointed by the Executive Committee. The secretary need not be a voting member. 2. Observers Observers are individuals nominated by and representing other organisations, or individuals wishing to participate in, or be aware of, COMCIFS business. They will receive all COMCIFS mailings and are free to comment on any Comcifs business. Observers will have no vote. Observers are appointed at the discretion of the chair of COMCIFS. There is no limit to the number of observers that may be appointed. III. ORGANISATION OF COMCIFS 1. Comcifs is accountable to the Executive Committee of the IUCr and reports through the Executive Secretary. 2. Dictionary Maintenance Groups For each approved cif dictionary, COMCIFS will appoint a Dictionary Maintenance Group (DMG) to make recommendations on revisions to the dictionary. Membership of each DMG will be approved by COMCIFS. The groups will establish their own mode of operation, but will be expected to consult widely with the community served by the dictionary and to refer back to COMCIFS any matters that involve a change in current COMCIFS policy. 3. Working Groups Working Groups may be established by the Chair to report to COMCIFS on particular matters, including (but not limited to) the production of draft dictionaries in areas not currently covered by CIF dictionaries. The mandate of a working group ends when its report has been received by COMCIFS. 4. COMCIFS Policy Decisions of the DMGs and Working Groups do not become COMCIFS policy until approved by COMCIFS. ==============================================================================
- Prev by Date: (83) Discussion mode; BNF; mmCIF extensions from EBI
- Index(es):