Ondex

Documentation

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:
- Ondex tutorial and user guide in PDF format (Sept 2010)
- Ondex workflow manual (console-based alternative to the GUI)
Developer guides:
- Ondex workflow module development manual
- Ondex graph API manual
Translation of ondex.org:
- Belorussian provided by http://www.movavi.com/

Sample graphs

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
- AraCyc 6.0 (11/02/10)
- AtRegNet (26/09/09)
- Current KEGG
  - KEGG Arabidopsis (07/06/11)
  - KEGG Bacillus subtilis (07/06/11)
  - KEGG Human (07/06/11)
  - KEGG Mouse (07/06/11)
  - KEGG Rice (07/06/11)
  - KEGG Rat (07/06/11)
  - KEGG Yeast (07/06/11)
- Previous KEGG
  - KEGG Arabidopsis (11/02/10)
  - KEGG Arabidopsis, Rice, Sorghum, Wheat (15/09/09)
  - KEGG Yeast (11/02/10)
  - KEGG Human (11/02/10)
  - KEGG Mouse (11/02/10)
  - KEGG Yeast, Mouse, Human (11/02/10)
  - KEGG Plants (11/02/10)
  - KEGG Bacillus subtilis (24/02/10)
  - KEGG Arabidopsis (25/03/11)
  - KEGG Bacillus subtilis (25/03/11)
  - KEGG Human (25/03/11)
  - KEGG Mouse (25/03/11)
  - KEGG Rice (25/03/11)
  - KEGG Rat (25/03/11)
  - KEGG Yeast (25/03/11)
- Plant transcription factor database (PlnTFDB, 26/09/09)
- TAIR (23/09/09)
- TAIR interactome (17/08/09)
  TAIR protein-protein interactions.
- TIGR Rice (13/09/09)
- Current UniProt (swiss-prot)
  - UniProt Arabidopsis (12/04/11)
  - UniProt Bacillus subtilis (12/04/11)
  - UniProt Human (12/04/11)
  - UniProt Mouse (12/04/11)
  - UniProt Rat (12/04/11)
  - UniProt Rice (12/04/11)
  - UniProt Yeast (12/04/11)
  - Optional: Full Gene Ontology (12/04/11, for integration purpose)
- Previous UniProt
  - Uniprot Arabidopsis (13/09/09)
  - Uniprot All plants (13/09/09)
  - Uniprot All plants without publications (13/09/09)
  - Uniprot Human (07/07/09)
- Plant GO Slim (23/01/09)
- DRASTIC (17/02/09)
- Database of Arabidopsis Transcription Factors (DATF, 10/05/09)
- Gramene (26/09/09)
- EC (25/10/09)
- Human GOA (09/07/09)
- Intact Arabidopsis (09/11/09)
- Intact Ecoli (09/11/09)
- Intact Human (09/11/09)
- Intact Mouse (09/11/09)
- Intact Yeast (09/11/09)
- BioGRID Human (01/05/09)
- BioGRID Arabidopsis (17/08/09)
- BioGRID Yeast (version 2.0.54)
  The file contains genetic and physical interactions for yeast only from BioGRID 2.0.54. All Gene, RNA and Polypeptide concepts in it carry accessions of type MIPS Metadata representation of genetic interactions. All interaction concepts carry BioGRID evidence types and are linked to Publication concepts with relations of type pub_in.
- SGD yeast genome features (22/05/09)
  The graph is based on the file http://downloads.yeastgenome.org/chromosomal_feature/SGD_features.tab.
- Jamboree yeast metabolic network (version 2.0)
- Yeast regulatory network
  Based on the supplementary material file http://www.mrc-lmb.cam.ac.uk/genomes/madanm/tfcomb/tnet.txt of Balaji and Madan-Babu 2006.
- PlantCyc (version 3.0)
  Based on the BioPAX format file downloaded at http://www.plantcyc.org
- LycoCyc (version 1.0.1.1)
  Based on the BioPAX format file downloaded at http://pathway.gramene.org
Integrated datasets

Human GO and GOA (09/07/09)
Human Gene Ontology and human proteins annotated.
Arabidopsis GO and GOA (18/06/09)
Arabidopsis Gene Ontology and Arabidopsis proteins annotated.
Yeast Arabidopsis orthologs (21/03/09)
Orthologs of yeast proteins from SGD and Arabidopsis proteins from TAIR.
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.

Data integration and visualisation

Documentation

Sample graphs