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Items for the Agenda of the COMCIFS closed meeting
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <firstname.lastname@example.org>
- Subject: Items for the Agenda of the COMCIFS closed meeting
- From: David Brown <email@example.com>
- Date: Mon, 21 Mar 2005 15:17:15 -0500
To members of COMCIFS ITEMS FOR DISCUSSION AT THE CLOSED COMCIFS MEETING IN FLORENCE I would like to place the following two topics on the agenda for the closed meetings in Florence. I welcome suggestions for other agenda items. 1. What is the role of CIF in the current rapidly changing world of information technology? 2. How can we make transparent the boundary between CIFs written with DDL1 dictionaries and those written with DDL2? David Brown +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ COMMENTS OF THESE ITEMS 1. FUTURE DIRECTION OF CIF It should be no surprise that an information technology language adopted in 1990 needs to be reviewed after fifteen years of operation. The rapid advances in the field and the introduction of XML make such a review more than timely. A further urgency is added by the need to ensure that incremental changes that we make in the dictionaries and other documents are compatible with future directions of crystallographic information technology. Two current problems illustrate how this impacts on dictionary structures. 1. Is it better to have a semantically meaningless item as the _list_reference (DDL1) or _category_key (DDL2) to label each line in a loop, or should we use semantically meaningful items (such as _atom_site_label) that are already present? The former solution allows a more straightforward programming and avoids possible conflicts between the information technology and crystallographic use of the item, but the latter leaves the CIF less cluttered and easier for humans to follow because the links are more readily followed by eye. The current revision of the core dictionary needs an answer to this question, because the answer will affect future CIF data structures. 2. Should there be rules defining the relationships that are allowed to be expressed by parent-child links? These links have been developed in an ad hoc way, but as we move towards more advanced data structures, we may find that we have developed links that are impossible to manipulate. One way of exploring the logic of the linked structures is to use the ResourceDescriptionFramework (RDF) which is being developed as part of the Semantic Web (see http://www.w3.org/RDF/ and http://www.w3.org/RDF/FAQ ). This scheme expresses the parent-child links as a graph making it easier to trace the logic. Another possibility is to use the Unified Modeling Language ( www.uml.org ). 2. THE CONVERGENCE OF DDL1 AND DDL2 As interest focuses on software that explores the interactions of small and large molecules, the incompatibility between the Dictionary Definition Language 1 (DDL1) and DDL2 is becoming a hindrance. CoreCIF is designed for use with small molecules and is written in DDL1 but mmCIF designed for reporting macromolecules is written using DDL2. While most of the features of the two standards are similar, there are two significant differences: Firstly DDL2 has a tighter structure designed to make automatic computer manipulation of the information easier, secondly the names given to the data items have a different structure. As the similarities between the two languages are far greater than their differences, it should be possible to achieve some convergence; already the core dictionary is evolving towards the DDL2 standard, but a complete convergence would require major reworking of some dictionaries. Convergence can be achieved in different ways. One way is to ensure that software is able to validate CIFs against both DDL1 and DDL2 dictionaries, and since the dictionaries contain synonyms of the data names (alternative data names for items with essentially the same definition, listed under _related_item (DDL1) and _item_aliases.alias_name (DDL2)), any character string used to represent a particular data name should be recognized by software that takes note of any alias names present regardless of the dictionary or version being used. Since all the items in the coreCIF dictionary appear (transformed to DDL2) in the mmCIF dictionary with their original DDL1 data names given as aliases, mmCIF software should be able to read coreCIFs without difficulty. mmCIF aliases are currently not present in the coreCIF dictionary but could easily be added. Alternatively, a DDL2 version of the coreCIF dictionary could be separated out and used as an alternative to the DDL1 core dictionary.
begin:vcard fn:I.David Brown n:Brown;I.David org:McMaster University;Brockhouse Institute for Materials Research adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada email;internet:firstname.lastname@example.org title:Professor Emeritus tel;work:+905 525 9140 x 24710 tel;fax:+905 521 2773 version:2.1 end:vcard
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