The Combechem e-Science project has demonstrated the advantages of using Semantic Web technology, in particular RDF and the associated triplestores, to describe and link diverse and complex chemical information, covering the whole process of the generation of chemical knowledge from inception in the synthetic chemistry laboratory, through analysis of the materials made which generates physical measurements, computations based on this data to develop interpretations, and the subsequent dissemination of the knowledge gained. The RDF descriptions employed allow for a uniform description of chemical data in a wide variety of forms including multimedia, and of the chemical processes both in the laboratory and in model building. The project successfully adopted a strategy of capturing semantic annotations ‘at source’ and establishing schema and ontologies based closely on current operational practice in order to facilitate implementation and adoption. We illustrate this in the contexts of the synthetic organic chemistry laboratory with chemists at the bench, computational chemistry for modelling data, and the linking of chemical publications to the underlying results and data to provide the appropriate provenance. The resulting ‘Semantic Data Grid’ comprises tens of millions of RDF triples across multiple stores representing complex chains of derived data with associated provenance.