Please be patient, it is being written right now!
Nils Gehlenborg / email@example.com
Functional Genomics Team / EMBL-EBI
Wellcome Trust Genome Campus
Cambridge / CB10 1SD / UK
AEX, short for "Archive Explorer", is a tree map visualization of the
content of the ArrayExpress Archive mapped to the Experimental Factor Ontology (EFO)
that enables ontogy-guided browsing and exploration to complement the keyword-based search interface of the ArrayExpress Archive.
The EFO models the relationships between experimental variables used in studies that have been deposited in ArrayExpress.
We convert the EFO into a tree and for every EFO term we determine the number of studies in the
ArrayExpress Archive annotated with this term. The resulting tree with node weights is then visualized
as the tree map. In the tree map each node of the tree is represented by a rectangle,
whose size corresponds to the node weight relative to the node weights of its siblings.
This construction efficiently provides an overview of the amount of data available for the
different terms of the EFO and can be explored either by descending down individual branches
of the EFO ("Branch Mode") or by viewing the entire EFO at different depths ("Level Mode").
It is important to note that AEX does not capture the complete content of the archive since its retrieval functionality
is limited to studies that can be mapped to ontology terms. Thus it is recommened to use the
search interface of
the ArrayExpress Archive to perform unrestricted queries for specific keywords.