About the Experimental Factor Ontology
If you'd like to cite EFO please use the following publication:
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling Sample Variables with an Experimental Factor Ontology. Bioinformatics 2010, 26(8):1112-1118 PDF
If you are citing the ontology used in an analysis we would recommend you also cite the version of the ontology you are using, if appropriate. The version information can be found in the release notes and in the ontology metadata stored in the versionInfo property in the OWL file.