ONDEX

ONDEX enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. ONDEX can be used in a number of important application areas such as transcription analysis, protein interaction analysis, data mining and text mining. Data may be imported through a number of ‘parsers’ of public-domain and other databases such as TRANSFAC, TRANSPATH, BRENDA, GO, KEGG, Drastic, ENZYME, Pathway Tools Pathway Genomes (PGDBs), Cell Ontology, and Medical Subject Headings Vocabulary (MeSH) together with associated sequence data where available. The imported data may be utilised with the data mining features and specific applications or extensions of the ONDEX framework. The ONDEX Frontend is an example of an ONDEX application package and this displays the data as a set of linked graphs with the nodes representing a data object and the edges (or links between the nodes) representing a relationship between the two nodes. ‘Filters’ are provided through the Frontend to select specific classes of data and relations between them to a selectable depth of linkage. In addition, a powerful filter is available to import microarray expression level data to globally analyse the relations between the different genes being expressed.

ONDEX is able to handle very large graphs and is able to represent many hundreds of thousands of data items, examine them for potential relationships through identifying equivalent concepts (data type), filter out unattached nodes (ones with no edges or relations) for the problem under consideration and provides labelled, organised graphs that may also be manipulated through the user interface.

Citation: Köhler, J. et al. (2006) Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 22(11):1383-1390. PMID: 16533819