Right click on Model databases to Import SBML file(.xml) or to Import spreadsheets(.xls), you can import a metabolic model in SBML/spreadsheet format as described in Metabolic Models.
You can directly edit/update the content of the imported model.
Right click on Reference databases to Import database(.xls), you can import a reference database provided in Reference Databases to create your own reference database.
You can add the information about metabolites and reactions described in a model to the reference database by right clicking on the metabolic model.
A draft reconstruction can be generated by mapping a blank reconstruction outputed by GBKParser, containing gene information only, to a reference reconstruction. You just simply right click on the blank reconstruction to Draft a reconstruction
GEMsME will extract the reactions whose associated orthologous genes can be mapped to the reference reconstruction once the list of orthologous-gene pairs is available.