- Ondex embeds online documentation. This can be launched by selecting 'documentation' in the Help menu, by
pressing the F1 key, or by clicking on tooltips in the various menus.
- User guides:
- Developer guides:
The following Ondex data graphs, downloadable in OXL format, are provided for users who wish to experiment with Ondex
with larger datasets than those provided with the tutorial. They are provided for testing and evaluation purposes and we
do not recommend that they are used for research purposes. Most of the sets provide Ondex views on partial or complete
views of individual public databases. A number of pre-integrated datasets from multiple databases are also available. We
gratefully acknowledge Artem Lysenko, Matthew Hindle and Jochen Weile for making these available.
If you are experiencing problems downloading these datasets, please contact us.
- Single databases
- Integrated datasets
GO and GOA (09/07/09)
Human Gene Ontology and human proteins annotated.
GO and GOA (18/06/09)
Arabidopsis Gene Ontology and Arabidopsis proteins annotated.
Arabidopsis orthologs (21/03/09)
Orthologs of yeast proteins from SGD and Arabidopsis proteins from TAIR.
interactome, Intact, BioGRID (17/08/09)
Protein-protein interactions from TAIR, Intact and BioGRID.
Poplar KB 2.0 (06/09/10)
Poplar knowledge base integrating Poplar predicted genes, PoplarCyc, Poplar TFDB, Gene Ontology, Plant Ontology,
Trait Ontology, UniProt Plants, PFam and relevant abstracts from Medline.
Human KEGG, UniProt, GO (12/04/11)
KEGG pathways for human integrated with all human proteins from UniProt-SwissProt and overlayed with the full
Gene Ontology. No further clean-up has been applied. Warning: huge dataset.
Chemogenomics using Ondex - slides, tutorial scripts and sample graphs (2012)
Complete set of materials for Ondex session from the EMBO Practical Course on Plant Bioinformatics 2012, EBI,
prediction in pathogenic fungi (2012)
Whole-genome orthology prediction for Mycosphaerella graminicola and Fusarium graminearum using
F. graminearum dataset - coexpression, PPI, sequence similarity and PHI-Base annotations (2013)
A companion Ondex dataset for the
Lysenko et al. (2013) paper.