Mathematics and Scientific Markup

Abstract

The development of e-Science (cyberScience, Grid, etc.) is starting to become a reality with formalised data resources, services on demand, domain-specific search engines, digital repositories, etc. Increasingly STM information will be contained in compound XML documents, representing scientific communication (articles, theses, repository entries, etc.). In physical sciences such as chemistry, materials science, engineering, physics, earth sciences, these “datuments” [1] normally contain hypertext, graphics, tables, graphs and numerical data, mathematical objects and relationships. In addition they may also contain domain-specific content such as chemical formula and reactions, thermodynamic and mechanical properties, electric, magnetic and optical properties.

Among the domain-specific languages, CML (Chemical Markup Language) is the oldest and broadest, and is now being actively used for publishing by the Royal Society of Chemistry (Project Prospect [2]) which gives an idea of what chemistry in datuments can look like. CML has had to develop the domain-specific objects (molecules, atoms, bonds, spectra, crystallography, etc.) and the relationships between them. However, due to the text-based nature of early XML, it has also had to design an implement domain-independent infrastructure which can support much of physical science. Originally called STMML [3] it supports data types (float, integer, complex, etc.), data structures (arrays, lists, matrices, etc.), geometrical concepts (points, planes, lines, etc.) and scientific units of measurement. In addition CML bases much of its flexibility one usercreated dictionaries (ontologies) which are hyperlinked from objects in the datuments.