In Snow Owl maps can be created as a Map type reference set or as a''' Mapping set'''. When you are defining a map, you are linking components from one terminology (as the source) to components with similar meaning from another terminology (which would be called the mapping target). Both types - Mapping sets and Map type reference sets - are representing cross-links between terminologies, which option you chose depends on your requirements.

Map type reference sets are a SNOMED CT standard mapping SNOMED as the source to a specified target terminology. Simple maps represent one-to-one relationships. Complex maps and extended maps allow mappings from to multiple codes in the target scheme and defining rules (e.g. ICD-10-AM map). These maps can be exported in RF1 or RF 2 format, but also as a text file with specific delimiter characters that can be used in Excel.

Mapping sets are not constricted to SNOMED CT. They can be used to create cross-links between two non-SCT terminologies (e.g. here is an example of a map between local codes and LOINC). They also allow associating components from different terminologies. In this example, SNOMED concepts are mapped to ATC, ICD-10 or local codes in the same mapping set, which would not be possible in a reference set. MS can be exported as Excel files, but not in RF1 or RF2.

Automapping is useful to map an external code system to SNOMED CT. For example, clinical terms from an Excel spreadsheet can be mapped to SNOMED CT, and then used to create a map type reference set. Automapping is based on lexical similarity, frequency of use and a customizable search profile.