Within a CyberGIS environment, the development of effective mechanisms to encode metadata for spatial analytical methods and to track the provenance of operations is a key requirement. Spatial weights are a fundamental element in a wide range of spatial analysis methods that deal with testing for and estimating models with spatial autocorrelation. They form the link between the data structure in a GIS and the spatial analysis methods. Over time, the number of formats for spatial weights implemented in software has proliferated, without any standard or easy interoperability. In this paper, we propose a flexible format that provides a way to ensure interoperability within a cyberinfrastructure environment. We illustrate the format with an application of a spatial weights web service, which is part of an evolving spatial analytical workbench. We describe an approach to embed provenance in spatial weights structures and illustrate the performance of the web service by means of a number of small experiments.