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Reactome in a Tab-delimited file

Ewan Birney birney at
Sat Dec 4 03:16:21 PST 2004

Hi go'ers

I just wanted to bring your attention to a useful new download file for
Reactome, which is in the download section at:

It is a tab-delimited format of Reactome's protein accession numbers
projected into a pairwise-graph format. There are four types of edges:

  - direct complex   :- the two accession numbers are in the same complex
  - indirect complex :- ditto, but slightly different
  - reaction         :- the two accession numbers are in the same reaction
  - neighbouring_reaction :- the two accession numbers are in neighbouring reactions

each edge has the backing pubmed ids as well

This naive graph like structure excludes alot of knowledge of (for
example) phosphorylation state of the proteins and of course the precise
input/output/catalyst relationships in the reactions, which of course
Reactome has in its main data model. You can get some of this via SBML,
but SBML is not good at representing the precise accession numbers and the
components of multi-subunit complexes.

However, this naive tab-delimited format is very useful for bioinformatics

All of Reactome is completely downloadable and free for use, and you can
make a complete replication of the system on your own site. We are very
interested in encouraging other groups to annotate other pathways (in
particular in non-vertebrate organisms) so that we can potentially look at
pathway evolution in a sensible way.


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