A computer-implemented method, integrating cognitive processes into the management of physical automated systems, for generating a deployment for a physical automated system based on system knowledge, the method comprising: 1.1 receiving user inputs comprising engineering documents and records of human-computer interactions; 1.2 extracting (210, 115A) knowledge data from the user inputs; 1.3 generating (215, 115B) a knowledge representation comprising facts and rules related to the physical automated system based at least in part of the knowledge data; 1.4 using an automated reasoning engine to generate a set of actions executable by an automation engineering system based on the knowledge representation; 1.5 generating a deployment of the automated system based at least in part on the set of actions and implementing the automated system deployment on the physical automated system; and 1.6 using the automated reasoning engine to generate and provide a feedback to a user to enable refinement of the user inputs for future generation of deployment for the physical automated system; 1.7 wherein the engineering documents comprise one or more of e-mails, manuals, and webpages, and the method further comprises: 1.8 automatically retrieving the engineering documents from one or more databases; and 1.9 wherein the knowledge representation is generated by applying one or more machines learning models to the knowledge data to generate the facts and rules related to the automated system, and by applying an inductive programming model to generate one or more rules based on the knowledge data; 1.10 generating executable code based on the one or more rules; and 1.11 using the executable code to generate the facts and rules related to the automated system; wherein 1.12 after deployment is made, changes to requirements of the automated system are transmitted back to the automation engineering system and when new equipment is installed or replaced, the knowledge extraction component receives system input from the automated system and the automation engineering system reprograms the automated system by deploying a new automation code after validation and approval by an engineer. 1.1 receiving user inputs comprising engineering documents and records of human-computer interactions; 1.2 extracting (210, 115A) knowledge data from the user inputs; 1.3 generating (215, 115B) a knowledge representation comprising facts and rules related to the physical automated system based at least in part of the knowledge data; 1.4 using an automated reasoning engine to generate a set of actions executable by an automation engineering system based on the knowledge representation; 1.5 generating a deployment of the automated system based at least in part on the set of actions and implementing the automated system deployment on the physical automated system; and 1.6 using the automated reasoning engine to generate and provide a feedback to a user to enable refinement of the user inputs for future generation of deployment for the physical automated system; 1.7 wherein the engineering documents comprise one or more of e-mails, manuals, and webpages, and the method further comprises: 1.8 automatically retrieving the engineering documents from one or more databases; and 1.9 wherein the knowledge representation is generated by applying one or more machines learning models to the knowledge data to generate the facts and rules related to the automated system, and by applying an inductive programming model to generate one or more rules based on the knowledge data; 1.10 generating executable code based on the one or more rules; and 1.11 using the executable code to generate the facts and rules related to the automated system; wherein 1.12 after deployment is made, changes to requirements of the automated system are transmitted back to the automation engineering system and when new equipment is installed or replaced, the knowledge extraction component receives system input from the automated system and the automation engineering system reprograms the automated system by deploying a new automation code after validation and approval by an engineer.