Patent Document ID: 8594941
Application ID: 10992973
Patent Flag: 1

Claim One:
1. Apparatus for hypothesizing a biological relationship, comprising: a processor; an electronic data store holding a database comprising a multiplicity of nodes representative of biological elements, and relationship descriptors describing causal relationships between nodes, the causal relationships defining how an increase or decrease in activity or abundance of one node has been shown, or is suspected, to cause an increase or decrease in the activity or abundance of another node, the database being non-specific in that at least some relationship descriptors define casual relationships that are not known or suspected to be relevant to any particular biological context of interest; and computer memory holding computer program instructions which, when executed by the processor, hypothesize the biological relationship from the collection of non-specific relationship descriptors by executing one of: a reverse logical simulation, and a forward logical simulation, the computer program instructions executable: (a) for a reverse logical simulation: (i) to select a set of target nodes; (ii) to associate to the set of target nodes a set of perturbations, wherein each target node of the set of target nodes has an associated perturbation, and wherein the set of perturbations represent one of: experimentally-observed perturbations and theoretical perturbations; (iii) with respect to at least one particular source node that is hypothetically responsible for the set of perturbations, to traverse causal relationships in the database in a reverse direction, from an effect to a cause of each causal relationship, to identify a set of one or more paths from each of the target nodes back to the particular source node, the set of paths comprised of casual relationships of which at least one such causal relationship is not known or suspected to be relevant to the particular biological context of interest; (iv) based on results obtained from the traversing step, to define, as a hypothesized biological relationship, the particular source node, together with the one or more casual relationships that comprise the set of paths that link the particular source node to the set of target nodes; and (v) to compute one or more scores associated with the hypothesized biological relationship based on the set of perturbations and the set of paths; (b) for a forward logical simulation: (i) to select a set of source nodes; (ii) to associate to the set of source nodes a set of perturbations, wherein each source node of the set of source nodes has an associated perturbation, and wherein the set of perturbations represent one of: experimentally-observed perturbations and theoretical perturbations; (iii) with respect to at least one particular target node, to traverse causal relationships in the database in a forward direction, from a cause to an effect of each causal relationship, to identify a set of one or more paths from each of the source nodes forward to the particular target node, the set of paths comprised of casual relationships of which at least one such causal relationship is not known or suspected to be relevant to the particular biological context of interest; (iv) based on results obtained from the traversing step, to define, as the hypothesized biological relationship, the particular target node, together with the one or more casual relationships that comprise the set of paths that link the particular target node to the set of source nodes; and (v) to compute one or more scores associated with the hypothesized biological relationship based on the set of perturbations and the set of paths.