DDLm: a new dictionary definition language.

A previous paper [Spadaccini and Hall J. Chem. Inf. Model. doi:10.1021/ci300074v] details extensions to the STAR File [Hall J. Chem. Inf. Comput. Sci. 1991, 31, 326-333] syntax that will improve the exchange and archiving of electronic data. This paper describes a dictionary definition language (DDLm) for defining STAR File data items in a domain dictionary. A dictionary that defines the ontology and vocabulary of a discipline is built with DDLm, which is itself implemented in STAR, and is extensible and machine parsable. The DDLm is semantically rich and highly specific; provides strong data typing, data enumerations, and ranges; enables relationship keys between data items; and uses imbedded methods written in dREL [Spadaccini et al. J. Chem. Inf. Model. doi:10.1021/ci300076w] for data validation and evaluation and for refining data definitions. It promotes the modular definition of the discipline ontology and reuse through the ability to import definitions from other local and remote dictionaries, thus encouraging the sharing of data dictionaries within and across domains.

dREL: a relational expression language for dictionary methods.

The provision of precise metadata is an important but a largely underrated challenge for modern science [Nature 2009, 461, 145]. We describe here a dictionary methods language dREL that has been designed to enable complex data relationships to be expressed as formulaic scripts in data dictionaries written in DDLm [Spadaccini and Hall J. Chem. Inf. Model.2012 doi:10.1021/ci300075z]. dREL describes data relationships in a simple but powerful canonical form that is easy to read and understand and can be executed computationally to evaluate or validate data. The execution of dREL expressions is not a substitute for traditional scientific computation; it is to provide precise data dependency information to domain-specific definitions and a means for cross-validating data. Some scientific fields apply conventional programming languages to methods scripts but these tend to inhibit both dictionary development and accessibility. dREL removes the programming barrier and encourages the production of the metadata needed for seamless data archiving and exchange in science.

Extensions to the STAR File syntax.

The STAR File [Hall J. Chem. Inf. Comput. Sci. 1991, 31, 326-333; Hall and Spadaccini J. Chem. Inf. Comput. Sci. 1994, 34, 505-508] format represents a universal language adopted for electronic data and metadata exchange in the molecular-structure sciences [Hall et al. Acta Crystallogr. Sect. A 1991, 47, 655-685; International Tables for International Tables for Crystallography. Vol. G: Definition and exchange of crystallographic data; Springer: Dordrecht, The Netherlands, 2005; Allen et al. J. Chem. Inf. Comput. Sci. 1995, 35, 412-427] and used by the International Union for Crystallography for publication submissions and database depositions. This paper describes an extended STAR syntax that facilitates richer and more specific data definition and typing and a commensurate improvement in precise data description.