Information about these data can be found at: http://bgee.unil.ch/?page=documentation

Files structure: 

current/			Files to download for the current Bgee release

bgee_vXX/ 			Files to download for a previous Bgee release

affymetrix_data/ 		our filtered dataset of Affymetrix data (low quality and redundant chips removed, see http://bgee.unil.ch/?page=documentation#sectionDataAnalysis); Note that all these data come from GEO or ArrayExpress; this directory is always the most up-to-date (not versioned between releases)
...............cel_files/	Affymetrix data for which the raw CEL files were available, organized by experiments. The CEL files are compressed using gzip. Note that an experiment can be both in this directory and in the mas5_files directory if it included both types of files, for different samples. 
...............mas5_files/	Affymetrix data for which only the processed MAS5 files were available, organized by experiments; these files have been standardized (standardization of the calls, probesets ordered, etc.). Note that an experiment can be both in this directory and in the cel_files directory if it included both types of files, for different samples.

general/ 			Various files to download that are not versioned between releases (e.g., the HOM ontology)
........ontologies/		Ontologies created by Bgee: HOG, vHOG, HOM
ontologies
...................HOM_ontology/		The different versions of the HOM ontology
........homolonto/		Homolonto software and source code

external_data/			Data generated for the use of other databases