Simplified visualization and relevancy assessment of biological pathways
Embodiments are directed to computer implemented method of assessing a relevancy of a pathway to a disease of interest, the pathway having a source and a target. The method includes developing an impact of the source on the pathway. The method further includes developing a value of targeting, based at least in part on an alteration of the pathway, the pathway with a drug of interest. The method further includes identifying a relationship between the source and the target within the pathway. The method further includes combining: the impact of the source on the pathway; the value of targeting, based at least in part on the alteration of the pathway, the pathway with a drug of interest; and the relationship between the source and the target within the pathway, wherein the combining results in an assessment that represents the relevancy of the pathway to the disease of interest.
1. A computer system for generating a simplified visualization of a plurality of biological pathways, the system comprising:
a processor and stored program instructions configured to assess relevancy of each of the plurality of biological pathways to a disease of interest, wherein the plurality of biological pathways corresponds to a plurality of source genes and a plurality of target druggable molecular entities;
wherein the processor and stored program instruction are configured to assess the relevancy of each of the plurality of biological pathways to the disease of interest by performing, for each of the plurality of biological pathways, each of the plurality of source genes, and each of the plurality of target druggable molecular entities, a method comprising:
developing an assessment of an impact of a source gene that is one of the plurality of source genes on at least one of the plurality of biological pathways;
developing a value of targeting the at least one of the plurality of biological pathways with a drug of interest, wherein the targeting is based at least in part on an alteration of the at least one of the plurality of biological pathways;
identifying a relationship between the source gene and a target druggable molecular entity that is one of the plurality of target druggable molecular entities, wherein the target druggable molecular entity is within the at least one of the plurality of biological pathways;
combining:
said assessment of said impact of the source gene on the at least one of the plurality of biological pathways;
said value of the targeting of the at least one of the plurality of biological pathways with said drug of interest; and
said relationship between the source gene and the target druggable molecular entity within the at least one of the plurality of pathways;
wherein said combining results in an assessment of the relevancy of the at least one of the plurality of biological pathways to the disease of interest; and
generating the simplified visualization of the plurality of biological pathways based at least in part on said assessments of the relevancies of each of the plurality of biological pathways;
wherein generating the simplified visualization comprises:
creating a graph of said at least one of the plurality of biological pathways, wherein said graph comprises a plurality of nodes connected by edges;
identifying relevant paths of said graph;
removing from said relevant paths non-informative or non-significant nodes to create a first subgraph; and
simplifying relations and relative attributes of said first subgraph to create a second, simplified subgraph.
2. The computer system of claim 1 , wherein said assessment of said impact of the source gene on the at least one of a plurality of biological pathways comprises a weighted value of the source gene.
3. The computer system of claim 1 , wherein said value of the targeting of the at least one of the plurality of biological pathways comprises a weighted value of the target druggable molecular entity.
4. The computer system of claim 1 , wherein said relationship between the source gene and the target druggable molecular entity within the at least one of the plurality of biological pathways comprises a topology of said at least one of the plurality of biological pathways from the source gene to the target druggable molecular entity.
5. The computer system of claim 1 , further comprising said processor and stored program instructions configured to rank said assessment of the relevancy of the at least one of the plurality of biological pathways to the disease of interest in comparison with others of said assessment of the relevancy of the at least one of the plurality of biological pathways to the disease of interest, wherein the simplified visualization is implemented based at least in part on the rank of said assessment of the relevancy of the at least one of the plurality of biological pathways.
6. The computer system of claim 1 , wherein said relative attributes of said first graph are used to provide properties of said plurality of nodes or said plurality of edges of said second, simplified subgraph.
7. A computer program product configured to generate a simplified visualization of a relevancy of at least one biological pathway to a disease of interest, the at least one biological pathway having a source gene and a target druggable molecular entity, the computer program product comprising:
a computer readable storage medium having program instructions embodied therewith, wherein the computer readable storage medium is not a transitory signal, the program instructions readable by a processor circuit to cause the processor circuit to perform multiple iterations of a method, one iteration of the multiple iterations of the method comprising:
developing an assessment of an impact of the source gene on the at least one biological pathway;
developing a value of targeting the at least one biological pathway with a drug of interest, wherein the targeting is based at least in part on an alteration of the at least one biological pathway;
identifying a relationship between the source gene and the target druggable molecular entity within the at least one pathway; and
combining:
said assessment of said impact of the source gene on the at least one biological pathway;
said value of the targeting of the at least one biological pathway with said drug of interest; and
said relationship between the source gene and the target druggable molecular entity within the at least one biological pathway;
wherein said combining results in an assessment of the relevancy of the at least one biological pathway to the disease of interest;
ranking said assessment of the relevancy of the at least one biological pathway to the disease of interest in comparison with assessments of a relevancy of the at least one biological pathway to the disease of interest that result from others of the multiple iterations of the method; and
generating the simplified visualization of said at least one biological pathway, wherein the simplified visualization is implemented based at least in part on said ranking of said assessment of the relevancy of the at least one biological pathway to the disease of interest;
wherein generating the simplified visualization comprises:
creating a graph of said at least one biological pathway, wherein said graph comprises a plurality of nodes connected by edges;
identifying relevant paths of said graph;
removing from said relevant paths non-informative or non-significant nodes to create a first subgraph; and
simplifying relations and relative attributes of said first subgraph to create a second, simplified subgraph.
8. The computer program product of claim 7 , wherein:
said assessment of said impact of the target druggable molecular entity on the at least one biological pathway comprises a weighted value of the target druggable molecular entity;
said value of the targeting of the at least one biological pathway comprises a weighted value of the target druggable molecular entity; and
said relationship between the source gene and the target druggable molecular entity within the at least one biological pathway comprises a topology of said at least one biological pathway from the source gene to the target druggable molecular entity.