Method and system for automated inference of physico-chemical interaction knowledge via co-occurrence analysis of indexed literature databases

An automated inference system, comprising, in combination:

• an automated inference creator for extracting a database record from a structured literature database, parsing the database record to extract one or more individual information fields, wherein the one or more individual information fields include a set of chemical or biological molecule names, filtering the extracted set of chemical or biological molecule names to create a filtered set of chemical or biological molecules names, determining whether a chemical or biological molecule name from the filtered set has been stored in an inference database, and if not, storing the chemical or biological name in the inference database, and setting a co-occurrence count to a starting value for each pair of names including the chemical or biological name and another name from the filtered set that the chemical or biological name co-occurs with, and if so, incrementing co-occurrence counts for each pair of chemical or biological names including the chemical or biological name, optionally constructing a connection network using a plurality of database records from the inference database including co-occurrence counts, applying one or more analysis methods directly to database records in the inference database or to the optional connection network to determine possible inferences of physico-chemical relationships between chemical or biological molecules, and generating automatically a plurality of inferences regarding physico-chemical relationships between chemical or biological molecules using the results from the one or more analysis methods;
• an automated inference checker for creating a connection network from an inference database including inference knowledge, wherein the connection network includes a plurality of nodes representing a plurality of chemical or biological molecules names and a plurality of arcs connecting the plurality of nodes, wherein the plurality of arcs represent co-occurrences counts between chemical or biological molecules and wherein the inference database includes a plurality of inference database records including inference association information, applying one or more analysis methods to the connection network to determine any trivial inference associations, deleting automatically database records determined to include trivial inference associations from the inference database, thereby improving the inference knowledge stored in the inference database;
• one or more connection networks for creating inferences, wherein a connection network includes a plurality of nodes representing a plurality of chemical or biological molecules names and a plurality of arcs connecting the plurality of nodes, wherein the plurality of arcs represent co-occurrences between chemical or biological molecule names in indexed scientific literature database records;
• and
• an inference database for storing co-occurrence information, generating automatically inferences regarding known physico-chemical interactions regarding chemical or biological molecules using the co-occurrence counts stored in the inference database.