US 2005/0165594 A1 · System, method and apparatus for causal implication analysis in biological networks

Abstract

Described are methods, systems and apparatus for hypothesizing a biological relationship in a biological system. A database of biological assertions is provided consisting of biological elements, relationships among the biological elements, and relationship descriptors characterizing the properties of the elements and relationships. A biological element may be selected from the database and a logical simulation may be performed within the biological database, from the selected biological element, through relationship descriptors, along a path defined by potentially causative biological elements to discern a biological element hypothetically responsible for the change in the selected biological element. The logical simulation may be either a backward logical simulation, performed upstream through the relationship descriptors to discern a hypothetical responsible biological element, or a forward logical simulation, performed downstream through the relationship descriptors to discern the extent to which the perturbation generates the observed change in the selected biological element.

Claims48

Dependent claims

A software implemented method for hypothesizing a biological relationship in a biological system, the method comprising:

(a) providing a database of biological assertions comprising a multiplicity of nodes representative of biological elements, relationship descriptors describing relationships between nodes, and characterizing properties of said nodes and relationships;
(b) selecting a target node in the database known from experimental observation to correspond to a biological element which increases in number or concentration, decreases in number or concentration, appears within, or disappears from a real biological system when it is perturbed;
and
(c) performing a backward logical simulation within said database from said target node through said relationship descriptors upstream along a path defined by potentially causative nodes to discern a node hypothetically responsible for the experimentally observed change in said target node.

1 more element

A software implemented method for hypothesizing a biological relationship in a biological system, the method comprising:

(a) providing a database of biological assertions comprising a multiplicity of nodes representative of biological elements, relationship descriptors describing relationships between nodes, and characterizing properties of said nodes and relationships;
(b) selecting for investigation a target node in the database;
(c) specifying a perturbation of said target node comprising an effective increase in concentration or number, stimulation of activity, an effective decrease in concentration or number, inhibition of activity, or the appearance or disappearance thereof;
and
(d) performing a logical simulation within said database from said target node, through said relationship descriptors:
(i) upstream along a path defined by nodes affecting the state of said target node directly or indirectly to discern a hypothesis potentially explanatory of a cause of the specified change in said target node within the system or a node hypothetically responsible for said specified change in said target node, or;
(ii) downstream along a path defined by nodes affected by said target node directly or indirectly to discern a hypothesis potentially explanatory of an effect of the specified change in said target node within the system or a node hypothetically affected by said specified change in said target node.

4 more elements

Dependencies are inferred from the claim text.

System, method and apparatus for causal implication analysis in biological networks

Life of this patent

System, method and apparatus for causal implication analysis in biological networks

Life of this patent

Abstract

Claims48