International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 2.4, p. 51

Section 2.4.10. Conclusion

F. H. Allen,a* J. M. Barnard,b A. P. F. Cookb and S. R. Hallc

aCambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, England,bBCI Ltd, 46 Uppergate Road, Stannington, Sheffield S6 6BX, England, and cSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia
Correspondence e-mail:  allen@ccdc.cam.ac.uk

2.4.10. Conclusion

| top | pdf |

The present proliferation of formats for chemical applications tends to inhibit and complicate the exchange and use of chemical data. Many widely used chemical formats have a finite half-life because they are inflexible and not readily extensible. Others offer universality [e.g. Abstract Syntax Notation 1 (ISO, 2002a[link],b[link]); Dalby et al. (1992[link]); see http://www.daylight.com/smiles/ ] but lack visual simplicity, generality or machine readability. Nevertheless, the Molecular Information File approach has these properties but needs significantly more development to be a viable exchange approach for mainstream chemistry. The MIF dictionary enables chemical data items to be defined at high precision and this offers real benefits for the creation of a domain ontology in this field.

Herein we have outlined the basic MIF approach and provided definitions for an initial core of data items that are fundamental for the representation of 2D and 3D chemical structures and 2D substructures. These core data items cover most of the basic chemical data-exchange requirements of molecular modelling and database applications, but are clearly only a first step towards the level of chemical data exchange needed. Future MIF developments in applications software and, particularly, in data definitions are expected to encompass other aspects of chemistry. These developments will need the collaborative involvement and support of subject specialists from both academia and industry.

References

ISO (2002a). ISO/IEC 8824-1. Abstract Syntax Notation One (ASN.1). Specification of basic notation. Geneva: International Organization for Standardization.
ISO (2002b). ISO/IEC 8825-1. ASN.1 encoding rules. Specification of Basic Encoding Rules (BER), Canonical Encoding Rules (CER) and Distinguished Encoding Rules (DER). Geneva: International Organization for Standardization.
Dalby, A., Nourse, J. G., Hounshell, W. D., Gushurst, A. K. I., Grier, D. L., Leland, B. A. & Laufer, J. (1992). Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J. Chem. Inf. Comput. Sci. 32, 244–255.








































to end of page
to top of page