LINK is a tool to infer and analyze networks reprensenting signaling pathways. LINK is based on
- a background interactome (a network of all known PPIs)
- a corpus: the textual content of published documents annotating the PPIs of the interactome
To infer networks, LINK receives as input a seed, conisting of a starting seed of proteins and/or description of interactions between them. Interactions can be provided either as
- Edges from the backgroun interactome
- PMIDs corresponding to documents annotating PPI
- Free text
An overview of LINK is given in the next figure :
Two example reconstructions are provided in the experiments folder:
- Cisplatin network
- IL-2 reconstruction (compared to the NetPath reference pathway)
Results for the example Il-2 reconstruction provided with the code are :
| Tag | Edges | TP Edges | REF Edges | Edges Prec | Edges Recall | Nodes | TP Nodes | REF Nodes | Nodes Prec | Nodes Recall |
|---|
MST | 9 | 7 | 96 | 0.777777777778 | 0.0729166666667 | 10 | 10 | 43 | 1.0 | 0.232558139535
Expanded 20 | 20 | 16 | 96 | 0.8 | 0.166666666667 | 15 | 15 | 43 | 1.0 | 0.348837209302 Expanded 20 | 20 | 16 | 96 | 0.8 | 0.166666666667 | 15 | 15 | 43 | 1.0 | 0.348837209302 Expanded 50 | 50 | 38 | 96 | 0.76 | 0.395833333333 | 31 | 27 | 43 | 0.870967741935 | 0.627906976744 Expanded 70 | 70 | 47 | 96 | 0.671428571429 | 0.489583333333 | 37 | 28 | 43 | 0.756756756757 | 0.651162790698 Expanded 100 | 100 | 54 | 96 | 0.54 | 0.5625 | 51 | 33 | 43 | 0.647058823529 | 0.767441860465