Within the context of automated assembly systems, one of the challenges is ensuring that machine program logic is consistent with process planning requirements. A critical inconsistency can arise due to a lack of i) formal engineering tools and methods that link the Process and Resource domains, ii) a standard way to describe the assembly process that maintains a consistent level of granularity, and iii) transparency of the machine program logic from the perspective of the Process domain. This research demonstrates how these problems can be addressed through the use of a Product, Process, Resource (PPR) ontology. The ontology model includes a Skill model that integrates the PPR domains. Due to this, the Process can be described at many levels of granularity and, provided it is linked to the Skill model, the logical sequence relative to the machine can be validated. The approach is tested on a hydrogen fuel cell assembly system where the process is described in two different ways. Nevertheless, the query is still able to ascertain the sequence consistency and execute a check for capability. The impact of this research is to enable more effective communication between domain models and an extensible Skill model that, with implementation into industrial engineering tools, will reduce costs, time-to-market, and increase responsiveness as errors in the engineering change process are mitigated.