J D Westbrook1, P E Bourne. 1. Rutgers, State University of New Jersey, Department of Chemistry, Piscataway 08854-8087, USA. jwest@rcsb.rutgers.edu
Abstract
MOTIVATION: Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing macromolecular structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well-characterized data domains. RESULTS: Details of the DDL, the dictionaries that have been developed, and software for reading and using this ontology are presented. AVAILABILITY: Extensive documentation, software tools and the DDL and dictionaries are available from http://ndbserver.rutgers.edu/mmcif and associated mirror sites. CONTACT: Bourne: bourne@sdsc.edu and Westbrook:jwest@rcsp.rutgers.edu
MOTIVATION: Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing macromolecular structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well-characterized data domains. RESULTS: Details of the DDL, the dictionaries that have been developed, and software for reading and using this ontology are presented. AVAILABILITY: Extensive documentation, software tools and the DDL and dictionaries are available from http://ndbserver.rutgers.edu/mmcif and associated mirror sites. CONTACT: Bourne: bourne@sdsc.edu and Westbrook:jwest@rcsp.rutgers.edu
Authors: Jurgen F Doreleijers; Steve Mading; Dimitri Maziuk; Kassandra Sojourner; Lei Yin; Jun Zhu; John L Markley; Eldon L Ulrich Journal: J Biomol NMR Date: 2003-06 Impact factor: 2.835
Authors: Thomas D Goddard; Conrad C Huang; Elaine C Meng; Eric F Pettersen; Gregory S Couch; John H Morris; Thomas E Ferrin Journal: Protein Sci Date: 2017-09-06 Impact factor: 6.725
Authors: Marek Grabowski; Karol M Langner; Marcin Cymborowski; Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Matthew D Zimmerman; Marc André Elsliger; Stephen K Burley; Wladek Minor Journal: Acta Crystallogr D Struct Biol Date: 2016-10-28 Impact factor: 7.652