Automated Link Path Generation for Chem2Bio2RDF



As its scope keeps expending for chem2bio2rdf, it becomes a pressing issue now for us to develop graph mining capabilities.


Linked.GIF

One intriguing example is to exam the relationship between side effect and pubchem bioassay (i.e. the tissue tested in a particular assay maybe related to the phenotypical manifestation of a certain side effect). A quick check on the above linked bubble tell you to link them through the big fat node in the middle. But wait a second...



[sider, chemogenomics_hub, bindingdb_ligand, bindingdb_protein, uniprot_hub, gi2uniprot, gi, pubchem_bioassay]
[sider, chemogenomics_hub, ctd, gene, gene2uniprot, uniprot_hub, gi2uniprot, gi, pubchem_bioassay]
[sider, chemogenomics_hub, drugbank_drug, drugbank_target, gene, gene2uniprot, uniprot_hub, gi2uniprot, gi, pubchem_bioassay]
[sider, chemogenomics_hub, matador, uniprot_hub, gi2uniprot, gi, pubchem_bioassay]
[sider, chemogenomics_hub, pubchem_bioassay]
[sider, chemogenomics_hub, qsar, gene, gene2uniprot, uniprot_hub, gi2uniprot, gi, pubchem_bioassay]
[sider, chemogenomics_hub, ttd_drug, ttd_target, uniprot_hub, gi2uniprot, gi, pubchem_bioassay]

The above outcome is return by the graph searching algorithm, and we found that there are actually more ways to relate a certain side effect to a certain bioassay, namely the second presents how these two maybe related from ligand binding perspective and the second has comparative toxicogenomics flavor.

More important, the above graph has been arranged a certain why that connection happens only across the close neighbors, Obviously this is not the case as there are plausible linkes can be made jumping over the nearby neighbors.


Another Example


is to exam the relationship between side effect and pubchem bioassay


[sider, chemogenomics_hub, bindingdb_ligand, bindingdb_protein, uniprot_hub, kegg]
[sider, chemogenomics_hub, ctd, gene, gene2uniprot, uniprot_hub, kegg]
[sider, chemogenomics_hub, drugbank_drug, drugbank_target, gene, gene2uniprot, uniprot_hub, kegg]
[sider, chemogenomics_hub, matador, uniprot_hub, kegg]
[sider, chemogenomics_hub, pubchem_bioassay, gi, gi2uniprot, uniprot_hub, kegg]
[sider, chemogenomics_hub, qsar, gene, gene2uniprot, uniprot_hub, kegg]
[sider, chemogenomics_hub, ttd_drug, ttd_target, uniprot_hub, kegg]