Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract ONDEX enables data from diverse biological data sets to be linked, integrated and visualized 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 (see G6G Abstract Number 20121), TRANSPATH (see G6G Abstract Number 20121), CHEBI, Gene Ontology (GO), KEGG, Drastic, Enzyme Nomenclature, Pathway Tools Pathway Genomes (PGDBs) (see G6G Abstract Number 20236), Plant Ontology, and Medical Subject Headings Vocabulary (MeSH) together with associated sequence data where available.

The imported data may be utilized 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 Frontend 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, an advanced filter is available to import 'microarray expression' level data to globally analyze 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).

It can also filter out unattached nodes (ones with No edges or relations) for the problem under consideration and provides labeled, organized graphs that may also be manipulated through the user interface.

ONDEX Features/Capabilities include:

Potential applications for ONDEX arise in many areas of analysis, including the support of microarray analysis, metabolomics, gene annotation, database curation, metabolic engineering, as well as modeling and simulation of biological systems.

The ONDEX Backend --

1) Data Import - import and extraction of biological networks currently from the numerous databases and generic exchange formats.

2) Data Integration -

3) Text mining -

4) Sequence analysis -

5) TAVERNA/GRID workflow support -

The ONDEX Frontend --

1) Data import/export -

2) Graph visualization -

3) Graph analysis -

System Requirements

ONDEX requires Java SE Runtime Environment (JRE) 6 Update 10 or later to be installed (available on Windows, Linux and 64-bit Intel Macs). The minimum memory requirement is 1GB (depending on the size of datasets to be analyzed).


The ONDEX Suite was developed by a large number of contributors. Most are associated with Rothamsted Research. See the complete list of contributors at the link below.

Manufacturer Web Site ONDEX Suite

Price Contact manufacturer.

G6G Abstract Number 20300

G6G Manufacturer Number 102307