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ONDEX Features
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 modelling and simulation of biological systems.
THE ONDEX BACKEND
Data Import
- import and extraction of biological networks currently from the following databases and generic exchange formats:
Data Integration
- integration of different combinations of imported databases
- identify and map identical entities between different biological networks/databases
- generate new relations between integrated data
- always keep track of equivalent data
- evidence tracking where the source of integrated data as well as evidence for generated mappings between entries of different databases is tracked and always available
Text mining
- concept based information extraction from free text
- relation mining
- support for basic NLP techniques, word stemming, and POS tagging (QTag) etc.
- import data from Pubmed. Import from other text sources will be added soon.
Sequence analysis
- use sequence similarity to identify elements in biological networks. Currently BLAST and Patternhunter are supported.
- cluster genes in orthologs and paraloguous groups, using an improved reimplementation of the INPARANOID method.
TAVERNA/GRID workflow support
- run data import, integration text mining process from TAVERNA (this functionality is currently been added)
- load integrated data from ONDEX via SOAP into TAVERNA (functionality will be added soon)
THE ONDEX FRONTEND
Data import/export
- import integrated networks from the ONDEX backend
- filter data from the ONDEX backend by species, etc
- import/export of networks in ONDEX XML
- import/export of networks in XGMML
- import and overlay tab delimited experimental data on biological networks (such as microarray data)
- export integrated networks as Petri Nets (Cell Illustrator format)
- export visible graphs as GML and GraphML (compatible to CytoScape, yEd)
Graph visualisation
- visualise large networks consisting of more than 100k elements
- support for a wide range of network layouts. Currently, own layouts that exploit the semantically rich data structure of ONDEX, as well as layouts from yFiles and JUNG are supported. Other graph libraries will be added soon.
Graph analysis
- Filters make irrelevant information invisible by blending out irrelevant nodes and edges. As a consequence of applying various filters, the size of graphs decreases significantly, allowing users to effectively separate important from unimportant information.
- Perform virtual knockout experiments to identify key elements in biological networks (knockout filter).
- Summarise and export graph analysis results in tabular format
- Export statistics on certain graph properties in tabular format
- Annotate sequence analysis results with information derived from the biological networks (i.e. metabolic pathways, signal transduction, Enzyme nomenclature etc)
- Automated analysis: it is possible to define, save and restore arbitrary combinations of filter, layout and export steps. This functionality allows the analysis of different datasets in one standardised pipeline.
Please send comments about this web site to sabr.technical at lists.ondex.org
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