The appropriate categorisation of written information by health professionals is very important to guarantee its accessibility. Unfortunately, the information technology tools that support professionals on that task imply a heavy workload, so that the responsibility for categorising the written content is often delegated to administrative staff. Well-known health ontologies such as SNOMED-CT or MeSH provide a representation of the clinical contents to be used by the information systems. This research proposes a computer based method to automatically extract and code the diagnostics, procedures and treatments according to health ontologies. A Knowledge Management System based on an extended version of Drupal is used to implement and evaluate this proposal. Results provide a positive evidence on the application of the method to support medical professionals.