Dear Colleagues, I have been asked by Mike Dacombe to submit an annual report for Comcifs for 1999. I enclose below my draft of the report for your comments in case I have missed out something important or misrepresented an issue. Please let me have any comments as soon as possible. The deadline for submission of the report is the end of February. David keep on scrolling - the report is below. ***************************************************** Dr.I.David Brown, Professor Emeritus Brockhouse Institute for Materials Research, McMaster University, Hamilton, Ontario, Canada Tel: 1-(905)-525-9140 ext 24710 Fax: 1-(905)-521-2773 firstname.lastname@example.org ***************************************************** Annual Report of Comcifs to the Executive Committee of the IUCr Annual Report for 1999 Submitted by I.D.Brown 1. Introduction 1999 saw important developments in the operation of Comcifs. The Glasgow congress of the IUCr not only provided the first opportunity for the triennial review of membership under the terms of reference approved in 1998, it was the occasion for the first formal meeting of Comcifs since its appointment in 1993. The Comcifs meeting at Glasgow had two components, an open meeting which outlined some of the problems facing CIF, and a closed meeting in which we developed a strategy to deal with these problems. Details are given below. 2. Membership The membership of Comcifs consists of a small number of voting members appointed by the Executive Committee of the IUCr and an unlimited number of non-voting members added at the discretion of the chair. The non-voting members comprise all those with an interest in the development of CIF who request to be placed on the Comcifs discussion list. Both kinds of members are fully involved in the work of Comcifs, but approval of new CIF dictionaries and policies is restricted to the voting members. The voting membership approved by the Executive Committee consists of: David Brown (chair) Brian McMahon (secretary) Helen Berman Herbert Bernstein Paul Edgington Syd Hall Gotzon Madariaga This is a reduction of one in the number of voting members from the previous Comcifs. 3. Meeting in Glasgow This meeting provided an opportunity for direct discussion of the issues facing CIF. To address the problems (described individually in the sections below) four subcommittees were established. These are: Dictionary Definition Language (DDL) Development Committee Publicity and Outreach Committee Software Development Committee Dictionary Review Committee Details of their terms of reference and membership are given below. 4. CIF Dictionaries Approval was given on 1999.3.22 to version 2.1 of the Core CIF dictionary. By the end of the year several dictionaries were close to being submitted for approval. These are: Macromolecular CIF dictionary Version 2 Modulated Structure CIF Image CIF Symmetry CIF In addition, dictionaries are in preparation for: Diffuse Scattering Electron Densities Small Angle Scattering Magnetic Structures Graphics Each of the approved dictionaries (core, macromolecular and powder dictionaries) has a Dictionary Maintenance Group whose job is to update the dictionary and present the revisions to Comcifs for approval. Following the meeting in Glasgow a Dictionary Review Committee (membership: Brown, McMahon, John Westbrook) was appointed to ensure that each dictionary submitted to Comcifs for approval received a detailed review. When satisfied that the dictionary complies with Comcifs policy this committee recommends to the voting members of Comcifs that the dictionary be approved. 5. The future of the Dictionary Definition Language The CIF dictionaries, like the CIFs themselves, are written as STAR files whose semantics are defined by a Dictionary Definition Language (DDL). Currently two different versions are in use: DDL1 is used for the core and powder diffraction CIF dictionaries and DDL2 is used for the macromolecular dictionary. DDL2 is more prescriptive and less permissive than DDL1, but this has been deemed necessary for the projected applications of the macromolecular CIF. Dictionaries written in different DDLs (and hence CIFs written using these dictionaries) are not compatible, an arrangement that is not viable in the long term. Further, if CIF is to remain competitive with other file structures being developed for the web (e.g., XML, ASN.1), it will need increased functionality. The possibilities were demonstrated by Hall who showed how one can code algebraic relations between different items into a CIF dictionary. This development can be likened to the addition of verbs to a CIF dictionary that currently only contains nouns. Such a development would greatly increase the power of CIF editors and simplify crystallographic programming. Following the Glasgow meeting a DDL Development Committee was appointed (Westbrook, Hall) and charged with making recommendations for a version of DDL that is upwardly compatible with DDL1 and DDL2 and which will provide for the inclusion of algebraic expressions and other algorithmic methods. 6. Concatenation of Dictionaries McMahon, Bernstein and Westbrook presented a proposal to Comcifs for a protocol that allows different CIF dictionaries to be concatenated. This simplifies the structure of specialised dictionaries since they do not need to duplicate the definitions of items that appear in other dictionaries. It also makes it easier for users to define any local items included in their CIFs. An early approval of this protocol is anticipated. 7. Software CIF is a powerful crystallographic language, but an electronic language is of little use without the software to manipulate it. Comcifs has identified the lack of software as a major impediment in the adoption of CIF causing many potential users to turn to less suitable languages for which there is good software support. Most users continue to see CIF as merely a format for submission of experimental results rather than as a language for manipulating crystallographic ideas. An urgent need is a CIF editor and browser to simplify the process of reading, constructing and modifying CIFs. Two editors are under development: an editor based on DDL2 is being developed by the Protein Databank (PDB) to simplify the preparation of submissions to the PDB, and an editor based on DDL1 is being developed at the Cambridge Crystallographic Data Centre to help in the preparations of submissions to the Cambridge Structural Database and to crystallographic journals. Both editors will be useful for preparing submissions to Acta Cryst. B. C and D and will be a pivotal tool in the mooted all-electronic structure journal. Lack of software is currently a serious impediment to the full exploitation of the potential of CIF. Following the Glasgow Congress a Software Development Committee (Bernstein, Westbrook and Edgington) was appointed to review the current state of CIF software and make recommendations for its improvement. 8. Publicity CIF needs to be advertised and promoted at a time when the internet is expanding and standards are rapidly changing, otherwise we may lose our advantage through ignorance of the potential of the language. It is essential that all branches of the crystallographic community move to a common, or at least compatible, electronic language. CIF has been tailored to the community and provides the flexibility and functionality that the community needs. It is essential that this message be heard and understood across the crystallographic world. Following the Glasgow Congress a Publicity and Outreach Committee (Berman, Hall, McMahon) was appointed and charged with ensuring that the virtues of CIF are widely disseminated and that software developers are encouraged to incorporate CIF into their programs. 9. Interoperability The rise of the World Wide Web and other Internet protocols has fuelled new developments in information interchange. Abstraction of information about information (so-called metadata) now allows for richer and more structured exchange mechanisms between and across disciplines. Some of the initiatives in areas related to crystallography include Chemical Markup Language (CML - a DTD for describing chemical structures within SGML or XML documents), macromolecular structure descriptions in terms of CORBA objects and RDF (Resource Description Framework) schemas. In addition, the embedding in CIFs of external objects tagged by MIME type (an Internet standard for defining types of data files) and the provision of appropriate MIME types for CIF documents allow easier manipulation of crystallographic data within the current Web protocols. There are also arguments for formalising CIF within the ANSI or ISO standards frameworks. In addition to these very general extensions, a number of disciplines related to various areas of crystallography are developing their own data vocabularies; often it is mutually helpful to work towards common data structures, expressed in STAR of CIF formalisms or at least in terms of related database schemas. Members and consultants of COMCIFS are actively involved in all these areas, and their work is an important element of ensuring that CIF is relevant in the wider context of information provision. 10. Intellectual Property Ownership of CIF by the IUCr is essential to prevent the development of incompatible CIF dialects. That ownership needs to be publicised and the standards enforced. On the other hand, the IUCr wishes to see the standard widely used and does not wish to discourage the use of CIF by implied threats of legal action for software that inadvertently fails to follow the standard. Various methods of protecting our interest have been suggested such as registering CIF as a service mark, providing a set of legal guidelines for the use of CIF, and providing software to certify that a document or program claiming to be CIF compliant is actually CIF compliant. The Executive Secretary of the IUCr was requested to proceed with registering appropriate service marks, and Bernstein and Phil Bourne were appointed as an ad hoc committee to lead a further discussion on this topic. 11. Acknowledgement I would like to thank the members of Comcifs for their dedication and hard work. In particular I would like to thank the secretary, Brian McMahon, for maintaining the internet connections that allow Comcifs to function.
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