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.

1 - 35 . (canceled) 
     
     
         36 . 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 at least a pair of target nodes in the database; and   (c) performing a logical simulation within said database between said target nodes through said relationship descriptors along a path defined by at least one potentially causative node or at least one potential effector node to discern one or a group of pathways hypothetically linking said target nodes.   
     
     
         37 . The method of  claim 36  comprising the additional steps of:
 (a) simulating perturbation of one of said pair of nodes; and 
 (b) performing a forward logical simulation within said database through said relationship descriptors from said virtually perturbed node downstream along a path defined by potentially affected nodes to discern the extent to which said simulated perturbation generates a predicted effect on the other of said pair of nodes. 
 
     
     
         38 . The method of  claim 36  wherein the database comprises noisy data, erroneous data, or omits nodes representing structures, processes, or networks present in the biological system. 
     
     
         39 . The method of  claim 38  further comprising applying a probability algorithm to plural hypothetical pathways to assess which pathway has the highest probability of representing real biology. 
     
     
         40 . The method of  claim 36  comprising the additional step of conducting an experiment on a specimen of said biological system to determine the existence or operability of said hypothetical pathway. 
     
     
         41 . The method of  claim 36 , wherein said relationship descriptors comprise descriptors of the condition, location, source, amount, or substructure of a molecule, biological structure, physiological condition, trait, phenotype, biological process, clinical data, medical data, or disease data and chemistry. 
     
     
         42 . The method of  claim 36 , wherein one or more relationship descriptors correspond to an epistemological relationship between a pair of nodes. 
     
     
         43 . The method of  claim 36 , wherein one or more of the relationship descriptors comprise a case frame. 
     
     
         44 - 48 . (canceled)