1. A computer implemented method of processing clinical documentation for a multi-axial coding scheme, the method comprising: inputting clinical documentation from memory operatively coupled with a computer system, the clinical documentation comprising narrative text; executing a natural language processor on the computer system, the natural language processor configured to: segment the narrative text based on boundaries defined in the clinical documentation; sequence words in the narrative text, based on the segmented text; map the sequenced words to semantic objects in an ontology, the ontology defining classes of the semantic objects corresponding to axes of the multi-axial coding scheme and concepts of a conceptual data resource, wherein the classes of semantic objects define a hierarchical structure in the ontology, the hierarchical structure defining conditions on and relationships between the semantic objects; convert the semantic objects into characters; output, to a user interface, the characters into slots in a procedural or a diagnostic medical code, wherein the characters are positioned in the slots based on the multi-axial coding scheme and wherein in the multi-axial coding system each position of a character within the procedural or diagnostic medical code corresponds to a semi-independent axis of classification of a procedure or diagnosis; output, to the user interface, trace data that includes linking information to map characters in a selected slot in the procedural or the diagnostic medical code to particular locations in the narrative text of the clinical documentation from which the characters in the selected slot in the medical code are derived; and infer at least one of the characters in at least one of the slots in the procedural or the diagnostic medical code, wherein the inferred character is associated with a particular semantic object that is not mapped to sequenced words in the segmented text, the particular sematic object being inferred from one or more other semantic objects that are mapped to sequenced words in the segmented text.