Figure 1

Databases and ontologies for information on genes, pathways and phenotypes. The diagram shows the information flow from genes to phenotypes via pathways. There are a large number of databases storing gene expression and other genomic data, with most of them species specific that include links to a phenotype ontology term. In addition, there is a large number of phenotype ontologies that are not organism specific, such as a mammalian phenotype ontology and the cellular phenotype ontology (CMPO). There exist a few databases providing genotype to phenotype links, although most of this information is covered by species specific genomic databases. There are many small-scale species specific or pathway-type specific databases and a few large general pathway databases (KEGG, Pathway Commons, REACTOME). Pathway ontologies exist but are not widely used yet. Although in general there are good links among genes and pathways and genes and phenotypes, associations between pathways and phenotypes are lacking