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The information about molecular processes is shared continuously in the form of runnable pathway collections, and biomedical ontologies provide a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Here we propose a strategy that integrates these resources by means of extended ontologies built on top of a common meta-format. Information sharing, integration and discovery are the primary features provided by the system; additionally, two current field applications of the system are reported.