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(79) Proposed report and recommendations to the IUCr Executive
- To: COMCIFS@iucr.org
- Subject: (79) Proposed report and recommendations to the IUCr Executive
- From: bm
- Date: Wed, 10 Dec 1997 15:49:16 GMT
D79.1 Proposed report to the EC following COMCIFS internal review
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I give below the draft of a document that I intend to submit to
the Executive Committee of the IUCr as a report on our work since we were
founded in 1993, and a proposal for changes in our continued operation.
I would welcome any suggestions for improvements and, ultimately,
the agreement of members of Comcifs to the proposal.
David
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A REPORT ON THE WORK OF COMCIFS
AND PROPOSALS FOR THE
THE FUTURE OF COMCIFS
Submitted to the Executive Committee of the IUCr
by DAVID BROWN
1997.12.10
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, coreCIF.dic-1.0, had been approved, work was well underway
on the powder and macromolecular dictionaries (pdCIF.dic and mmCIF.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 (coreCIF.dic-2.0). This was followed by the
approval of the first versions of the macromolecular dictionary
(mmCIF.dic-1.0) on 8 June 1997 and the powder dictionary (pdCIF.dic-1.0)
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)
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
will likely 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 are 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 Group do not become Comcifs policy
until approved by Comcifs.
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