Computer implemented systems and methods of processing clinical documentation for a multi-axial coding scheme include inputting clinical documentation from memory operatively coupled with a computer system, and executing a natural language processor configured to process narrative text in the clinical documentation. The processor segments the narrative text based on boundaries defined in the clinical documentation, sequences words in the narrative text based on the segmentation, and maps the sequenced words to semantic objects in an ontology database. The ontology defines classes of semantic objects and relationships between them, corresponding to the multi-axial coding scheme. The semantic objects are converted into characters and output into slots in a medical code, with the characters positioned in the slots based on the multi-axial coding scheme.