An apparatus for electronically identifying and compiling chemical structures found in a storage facility comprising one or more electronic files, the apparatus comprising: (a) a memory storing a code defining a set of instructions; and (b) a processor configured to execute the set of instructions, wherein the code comprises an optical structure recognition module configured to: (i) identify a plurality of candidate chemical structures in the one or more electronic files of the storage facility, wherein at least one of the electronic files comprises non-embedded images of chemical structures identifiable by the optical structure recognition module; (ii) for each identified candidate chemical structure, derive a chemical structure object with an associated set of properties including number of carbons; (iii) for each derived chemical structure object, apply one or more filters, including a filter to eliminate objects identified as having less than a selected number of carbons, wherein the selected number of carbons is configurable and set by a user based on an expected content of at least one of the electronic files; and (iv) store derived chemical structure objects not eliminated by the one or more filters in a searchable electronic compendium of identified objects. (a) a memory storing a code defining a set of instructions; and (b) a processor configured to execute the set of instructions, wherein the code comprises an optical structure recognition module configured to: (i) identify a plurality of candidate chemical structures in the one or more electronic files of the storage facility, wherein at least one of the electronic files comprises non-embedded images of chemical structures identifiable by the optical structure recognition module; (ii) for each identified candidate chemical structure, derive a chemical structure object with an associated set of properties including number of carbons; (iii) for each derived chemical structure object, apply one or more filters, including a filter to eliminate objects identified as having less than a selected number of carbons, wherein the selected number of carbons is configurable and set by a user based on an expected content of at least one of the electronic files; and (iv) store derived chemical structure objects not eliminated by the one or more filters in a searchable electronic compendium of identified objects. (i) identify a plurality of candidate chemical structures in the one or more electronic files of the storage facility, wherein at least one of the electronic files comprises non-embedded images of chemical structures identifiable by the optical structure recognition module; (ii) for each identified candidate chemical structure, derive a chemical structure object with an associated set of properties including number of carbons; (iii) for each derived chemical structure object, apply one or more filters, including a filter to eliminate objects identified as having less than a selected number of carbons, wherein the selected number of carbons is configurable and set by a user based on an expected content of at least one of the electronic files; and (iv) store derived chemical structure objects not eliminated by the one or more filters in a searchable electronic compendium of identified objects.