Online Validation and Comparison of Molfile and CML Molecular Atom-Connection Descriptors

Abstract

We describe an online resource in the form of this journal article for comparing the molecular constitution of molecule descriptors expressed as either the MDL Molfile or CML (Chemical Markup Language, an XML language). The resource comprises a set of server-based tools for validating molecule descriptors expressed in either CML or MDL Molfile syntax, and for comparing the constitutional identity of any two molecules so described. We discuss the issues of how XML Schema-based validation compares with non-XML-based formats such as the molecular Molfile. This system serves to exemplify a component of a concept we call the Chemical Semantic Web, in which journal articles such as this one can be used as a (re)usable and integrated molecular resource.