Grand Challenges in Computational Biology - Project web sites - Inria
Grand Challenges in Computational Biology - Project web sites - Inria
Grand Challenges in Computational Biology - Project web sites - Inria
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Hyperdimensional <strong>in</strong>formation networkfor data <strong>in</strong>tegration, navigation & community annotationNodes: Genes/prote<strong>in</strong>sEdges: different types of connection between genes (e.g., orthology, similarstructure, <strong>in</strong>teraction, disease association, regulated by, adjacent <strong>in</strong> metabolicnetwork, genome neighbor, etc.).Edges have weights proportional to confidenceExperimental data can enter at any po<strong>in</strong>t <strong>in</strong> the graph, and be propagated toneighbor<strong>in</strong>g nodes based on learned rules:• Biological process for one gene can be made available to genome neighbors• A prote<strong>in</strong>-prote<strong>in</strong> <strong>in</strong>teraction between two genes <strong>in</strong> one species can be used to <strong>in</strong>fer correspond<strong>in</strong>g<strong>in</strong>teraction between their orthologs <strong>in</strong> another• Roles <strong>in</strong> a pathway (e.g., EC number) known for one gene can be assigned to an ortholog• Participation <strong>in</strong> a biological process can be <strong>in</strong>ferred based on genome neighbors• 3D structure <strong>in</strong>formation can be propagated to all homologs• Prote<strong>in</strong> structure <strong>in</strong>formation can be propagated to all homologsBiologists can: subscribe to news feeds arriv<strong>in</strong>g at their selected nodes, upload data, attach l<strong>in</strong>ks totheir papers, manually curate biological functionsManual annotations from biologists will need to be weighted accord<strong>in</strong>g to estimated confidence