What is network reconstruction in CutDB?

[ksd]

Here is an explanation of network reconstruction in CutDB from Alexey
http://cutdb.burnham.org/

Users can define three parameters to show the network diagrams:

(i) ID display mode (accession number or UniRef90 IDs (http://
www.ebi.ac.uk/uniref/);

(ii) flexibility of connection: all nodes are unique (accession mode)
or the nodes are connected within given threshold of sequence
similarity (90% identity);

(iii) steps of expanding the edges are extended by given extension
level (by protein-protein interaction data and proteolytic events
data).

This is also covered in the PMAP database publication:
http://www.ncbi.nlm.nih.gov/pubmed/18842634

A diagram showing automatic pathway reconstruction (in PathwayDB) is
also within the paper:
http://nar.oxfordjournals.org/cgi/content/full/37/suppl_1/D611#F3