dREL: A Relational Expression Language for Dictionary Methods

Abstract

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.

Lerche: Generating data file processors in Julia from EBNF grammars

“…Reliance on EBNF parser generators external to the Julia environment, for example, by calling Lark or pre-generating parsers, complicates distribution and creates a barrier to user contribution to packages. dREL (Spadaccini et al, 2012) is a relational data processing language for specifying crystallographic algorithms. The dREL LALR(1) EBNF (Hester, 2021a) was developed using Lerche to verify its correctness and conformance to LALR(1) requirements.…”

Extensions to the STAR File Syntax

“…Clearly, internet access to widely disparate and rapidly expanding information continues to be a strong driver for these requirements. To facilitate the precise identification and description of data, and their inter-relationships, a STAR-based dictionary definition language (DDL) has been developed. ,− …”

“…The changes from the original syntax are summarized separately in Appendix A in the Supporting Information. Companion papers , describe the application of the extended STAR file syntax within a semantically rich dictionary definition language (DDLm) and the purpose-built language dREL for DDLm methods scripts. Using methods expressions, DDLm can define machine-parsable and executable relationships between data items, as well as facilities for user defined types and functions.…”

Applied and implied semantics in crystallographic publishing

“…If this may seem a trivial example, there are prototype implementations that are capable of calculating the complex structure factor for any reflection vector by summing over all atoms in a unit cell based on a 10-line methods definition in a CIF dictionary [ 13 ]; again, we emphasise that none of these crystallographic concepts is built into the processing engine.…”

“…The development of software that can perform extended domain-specific calculations solely from machine-specified semantic relationships is likely to be a long-term project, but implementations such as dREL [ 13 ] demonstrate that it is feasible. How well such a project succeeds will probably depend on the perceived need for general semantic querying across several disciplines.…”