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EPSG codes are numeric codes associated with coordinate system definitions. For instance, EPSG:4326 is geographic WGS84, and EPSG:32611 is “UTM zone 11 North, WGS84”. The WMS protocol uses EPSG codes to describe coordinate systems. EPSG codes are published by the OGP Surveying and Positioning Committee. A list of PROJ.4 definitions corresponding to the EPSG codes can be found in the file /usr/local/share/proj/epsg. PROJECTION describes how to use these in your Mapfile.
http://spatialreference.org for a listing of spatial references and an interface to search for spatial references.
Shapefiles are simple GIS vector files containing points, lines or areas. The format was designed and published by ESRI and is widely supported in the GIS world. It is effectively the native and highest performance format for MapServer.