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In this paper, we address the problem of negotiation process in a multi-agents system by using ontologies. Therefore, we present an ontology solution based on the knowledge management system for semantic heterogeneity. The proposed solution prevents the misunderstanding during the negotiation process though the agents' communications. Our approach aims to make the agents able to understand each other when using these ontologies. Thus, we propose a general architecture for Negotiation process which uses ontology-based knowledge management system (NOKMS). This architecture consists of three layers: the negotiation layer (NL) that describes the negotiation process between the initiator static agents (ISAs) and the participant mobile agents (PMAs) by using suitable ontologies, the Semantic Layer (SEL) contains the semantic translator which uses in the case of misunderstanding of the sent messages between the agents, and the last one is the knowledge management systems layer (KMSL) which bases on the intelligent knowledge base (IKB) to give the flexibility to our negotiation ontology. Finally, we present a case study which applies our architecture on the multimodal transport information system (MTIS) project where we will show tow scenarios applicable: the first uses our negotiation ontology architecture in one transport system, and the second applies this architecture on the multi-transport systems. These cases studies show that the proposed NOKMS improves the execution of negotiation process in multi-agents systems in order to satisfy the transport customers.