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Minutes of 2021 COMCIFS meeting
- To: comcifs@iucr.org, cif-developers@iucr.org, coredmg@iucr.org
- Subject: Minutes of 2021 COMCIFS meeting
- From: Brian McMahon <bm@iucr.org>
- Date: Tue, 21 Sep 2021 10:39:04 +0100
Committee for the Maintenance of the CIF Standard (COMCIFS) Meeting Online 31 August 2021 12:00 UTC Present: James Hester* (Chair), Herbert Bernstein*, John Bollinger*, Saulius Grazulis, Mike Hoyland, James Kaduk, Brian McMahon*, Andrius Merkys, Peter Murray-Rust, Brian Toby, Antanas Vaitkus, John Westbrook*, Simon Westrip * Voting members 1. COMCIFS report last triennium -------------------------------- The triennial report for 2017-2021 (a four-year period on account of the postponement of the IUCr XXV Congress) was circulated beforehand and will be published as part of the Congress Report in Acta Crystallographica Section A. 2. Any questions/discussion of report ------------------------------------- There were no comments. Among the items noted were that submissions to the wwPDB in CIF format were now mandatory, that work on the second edition of International Tables Volume G was progressing, that collaboration between COMCIFS and the NeXus International Advisory Committee (NIAC) continued to be fruitful, and that there was contact with European efforts around materials modelling (EMMO and OPTIMADE). 3. Actions arising from CommDat meeting 25th August --------------------------------------------------- COMCIFS works closely with the IUCr Committee on Data (CommDat), and noted the following activities discussed at the CommDat post-Congress meeting. The high-pressure community have been working for some time on a CIF dictionary, and are keen to make progress with this. The quantum crystallography community also sees a need to capture details of non-spherical atomic form factors in a CIF format (as evidenced by Dylan Jayatilaka's keynote talk at the Congress and a presentation by Simon Grabowsky and Krzysztof Wozniak at the pre-Congress CommDat workshop on chemical crystallography). The Commission on Powder Diffraction held an online meeting after the Congress to discuss further developments of the pdCIF dictionary and applications. Their priority is to facilitate validation of powder structure determinations submitted to IUCr journals, but they also see a need to capture all details of serial refinements across ranges of temperature and pressure; and the desirability of working with instrument vendors to improve the capture of raw data direct from the diffractometer to CIF. The Commission on Electron Crystallography would also like to see CIF dictionary extensions to capture special aspects of electron diffraction. Many members of the Commission also work with nanoED, a European academic consortium that has agreed placements at the Chester office with two students or postdocs to learn about the formal aspects of CIF. It was also noted that links to CIF dictionaries, templates and example files on the IUCr web site used ftp-based URIs. These were no longer fetched by current web browsers. Brian McMahon (BM) undertook to replace these by http(s)-based URLs, and would review the best way to provide location information in the CIF dictionary register. 4. Revitalising COMCIFS ----------------------- 4.1 Discussion of ideas ----------------------- While acknowledging that the mmCIF/PDBx family of dictionaries was keeping track effectively with developments in biological macromolecular structural science, James Hester (JH) reflected that other areas under COMCIFS supervision had plateaued for much of the past decade. He felt that there was a need for COMCIFS to be, and to be seen to be, more productive in extending CIF standards to novel techniques and scientific growth areas. In addition to the initiatives discussed by CommDat, he gave neutron diffraction and the squeeze algorithm as examples of areas where new definitions and procedures were required. He did note that dictionaries were now being developed on GitHub, permitting access to a larger group of people. His early suggestion (on the COMCIFS email list) that it might be useful to have a technical advisory committee separate from the dictionary content developers had not found favour - it was generally felt that technical implementation and domain knowledge should be intimately coupled. He did identify the problem that the machinery of COMCIFS was opaque to the outside world, and that some mechanism was needed to make it as easy as possible for people to engage with COMCIFS activities when new standards were desired. He invited further input on ways to revitalise the work of the Committee. Herbert Bernstein (HJB) argued that the most important step was to provide clear step-by-step instructions (on the IUCr web or in print) on how to go about creating a new dictionary. He also suggested considering the ANSI/ISO model where standards creators are required to review the status of the standard on a fixed cycle; but emphasised that the engagement of stakeholders was more important than the specific process adopted. Peter Murray-Rust (PMR) considered the CIF dictionary effort outstanding, and used it as a model in his current molecular and plant science activities. He felt it was important to identify "hot spots" where people were actively developing ontologies, and saw materials science as an area where there was much current activity. He also recommended getting CIF identifiers into WikiData, and has already worked with Saulius Grazulis (SG) and Antanas Vaitkus (AV) on putting COD identifiers there. This would put crystallography in front of many more people through the distributed nature of WikiData. JH mentioned the European Materials Modelling Council (EMMC) as a materials science initiative that he had engaged with, and PMR referred to the BIG-MAP (Battery Interface Genome – Materials Acceleration Platform) and Material Genome projects, but pointed out that such initiatives tended to flourish during a period of supported funding, but had limited longevity. SG reported that he had had very positive experiences with GitHub and similar collaborative platforms in developing standards (OPTIMADE) and in software development, and that the use of a familiar community platform could allow IUCr to attract other groups with an interest in developing standards to work within a common development environment. [JH demonstrated some aspects of the existing COMCIFS GitHub implementation, which allowed this sort of discussion and peer review for the current suite of CIF dictionaries and their conversion to DDLm.] If COMCIFS were seen to be inclusive towards new ideas, that would encourage other groups to look to COMCIFS for authority, consistency and expert guidance. JH agreed on the merits of GitHub, but saw a need for documentation to help new users to use it to best advantage. He also made the point that as GitHub used version control, it was possible to allow experimentation by anyone interested in contributing, thus creating a more inclusive and welcoming environment. JH reviewed some ideas he had presented to the IUCr Executive Committee: * Topic-focused virtual workshops * IUCr contribution to conference/sabbatical for completion of CIF work * Lightweight newsletter for mailing lists (e.g. quarterly, with details of recent GitHub activity) * Training modules for dictionary authors * Formalised and published governance procedures * Commissions take responsibility for dictionaries He now thought that simple guidelines and how-to's might usefully take the place of unduly formalised governance procedures. HJB cautioned against a system that relied solely on Commissions, because of the danger of activities behind closed doors that could stifle wider community input. JH argued that the Commission was at least answerable to the Executive Committee. But there was general agreement that any development activity should be carried out on a platform such as GitHub, where openness was a feature and any interested contributors from the wider community could provide input. It was felt that COMCIFS would liaise with a sponsoring Commission and would provide guidance on setting up a GitHub site linked within the framework of COMCIFS activities. BM pointed out that there was a historic diversity of dictionary-building projects - some Commissions (Aperiodic Crystals, Magnetic Structures) had proven very effective; other dictionaries (electron density, topology) had arisen from focussed groups of individual programmers. This suggested some ongoing flexibility in the composition of dictionary working groups; but Commission liaison was worthwhile where that seemed useful or appropriate; and the idea of a common family of GitHub sites would give a more complete and coherent picture of overall activities. He also suggested (1) that journal editors should also be brought into working groups to design a new table of mandatory experimental data items that would inform the publication requirements to be met by a new dictionary; and (2) some form of roadmap be published on the CIF website to show what areas of structural science had existing CIF dictionaries, where these were under revision or construction, and what areas were barren and had potential for future ontology development. John Westbrook (JW) agreed that publishers (and relevant repositories) were key players who should be involved in new developments. Another aspect of diversity was the variety of stakeholders who might have different requirements as a new area of CIF was developed, and so it was essential that any working groups sought to engage with and represent all of these diverse (and sometimes conflicting) requirements. He made the point that (from a repository viewpoint) collecting the data was dependent on the software actually in use within the community that was going to support the desired standards. JW also emphasised that the experience of the mmCIF community was that greatest productivity flowed from small or medium-sized working groups able to work together on a regular basis. Asynchronous (email-based) discussion was not very productive where complex requirements needed to be understood and agreed. A model where people can be brought together, focus on the immediate requirements, and revisit progress on a timescale where enough time has been allowed to develop code, but not so much that details get forgotten, has worked effectively. SG thought the idea of a lightweight newsletter for developers a good one, but pointed out the potential usefulness of the the IUCr Newsletter for periodically carrying news on data standardisation to a much wider community. He also pointed out that email-led development could work well, provided the discussion was led and directed by a skilled project leader. Returning to the problems faced by groups new to CIF of getting up to speed on how to create a dictionary, he recommended that COMCIFS publish contact details of members who could act as mentors to people coming freshly to the field. Jim Kaduk (JK) reviewed the status of the powder dictionary. While the immediate priority was to encourage more authors to submit structure determinations based on powder to IUCr journals (through fine-tuning of checkCIF procedures), he felt the pdCIF dictionary needed to be reviewed so as better to handle CIFs with mixtures and/or quantum mechanical calculations. It was also the case that parametric experiments were much more important than when the pdCIF dictionary was first published, and new experimental metadata were needed to describe current practice. He volunteered to explore these issues. JH suggested this could be the basis of a focussed workshop. JK indicated that authors of the most widespread packages (GSAS, TOPAS, FullProf) would be among the stakeholders that one needed to engage. 4.2 Next steps -------------- JH would consider the discussion and circulate to the group a summary of suggestions on moving forward. BM would update ftp: based links on the IUCr website. BM would think about a suitable visual indication of established CIF ontologies, ones under development, and areas requiring new standards. 5. Any other business --------------------- None was raised. The meeting concluded at 13:00 UTC. Brian McMahon Secretary
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