Relevancy assessment and visualization of biological pathways

Patent metadata

Field	Value
Publication number	US-2016283608-A1
Application number	US-201514745616-A
Country	US
Kind code	A1
Filing date	Jun 22, 2015
Priority date	Mar 23, 2015
Publication date	Sep 29, 2016
Grant date	—

Abstract

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.

First claim

What is claimed is:

1 . A computer implemented method of assessing a relevancy of at least one pathway to a disease of interest, the at least one pathway having a source and a target, the method comprising:
developing, by a processor, an impact of the source on the at least one pathway; developing, by said processor, a value of targeting, based at least in part on an alteration of the at least one pathway, the at least one pathway with said drug of interest; identifying, by said processor, a relationship between the source and the target within the at least one pathway; and combining: said impact of the source on the at least one pathway; said value of targeting, based at least in part on an alteration of the at least one pathway, the at least one pathway with a drug of interest; and said relationship between the source and the target within the at least one pathway; wherein said combining results in an assessment of the relevancy of the at least one pathway to the disease of interest.

2 . The computer implemented method of claim 1 , wherein said impact of the target on the at least one pathway comprises a weighted value of the target.

3 . The computer implemented method of claim 1 , wherein said value of targeting, based at least in part on said alteration of the at least one pathway, the at least one pathway comprises a weighted value of the target.

4 . The computer implemented method of claim 1 , wherein said relationship between the source and the target within the at least one pathway comprises a topology of said at least one pathway from the source to the target.

5 . The computer implemented method of claim 1 , further comprising ranking, by said processor, said assessment in comparison with others of said assessment.

6 . The computer implemented method of claim 1 , further comprising based at least in part on said assessment, implementing, by said processor, a simplified visualization of said at least one pathway.

7 . The computer implemented method of claim 6 , wherein said simplified visualization comprises:
creating a graph of said at least one 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 implemented method of claim 7 , wherein said relative attributes comprise properties of said plurality of nodes or said plurality of edges of said second, simplified subgraph.

9 . A computer implemented method of simplifying a visualization of at least one pathway, the method comprising:
creating a graph of the at least one 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.

10 . The computer implemented method of claim 8 , wherein said relative attributes comprise properties of said plurality of nodes or said plurality of edges of said second, simplified subgraph.

11 . The computer implemented method of claim 8 , wherein said properties comprise:
a distance of synthetic links; or a superset complex.

Assignees

• IBM

Inventors

• Carmeli Boaz
• Erhan Bilal
• Koyama Takahiko
• Rhrissorrakrai Kahn
• Royyuru Ajay
• Utro Filippo
• Waks Zeev

Classifications

• G16H50/50

  for simulation or modelling of medical disorders · CPC title

• G16H50/20

  for computer-aided diagnosis, e.g. based on medical expert systems · CPC title

• G06F16/24578

  using ranking · CPC title

• G06F16/9024 Primary

  Graphs; Linked lists (G06F16/9027 takes precedence) · CPC title

• G16B45/00 Primary

  ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks · CPC title