SYSTEMS, METHODS, AND APPARATUS FOR PROCESSING DOCUMENTS TO IDENTIFY STRUCTURES

• US 20110276589A1
• Filed: 05/03/2011
• Published: 11/10/2011
• Est. Priority Date: 05/03/2010
• Status: Active Grant

• Current Assignee: Revvity Signals Software Incorporated
• Original Assignee: ArtusLabs, Inc. (Revvity, Inc.)
• Inventors: Ballard, William B., Smith, Robin Y., Flicker, Scott G., Greenhow, Sean G.
• Granted Patent: US 8,433,723 B2
• Time in Patent Office: Days
• US Class Current: 707/769
• CPC Class Codes: G06F 16/248 Presentation of query results
• CPC Class Codes: G06V 30/422 Technical drawings; Geographical maps
• CPC Class Codes: G16C 20/40 Searching chemical structures or physicochemical data
• CPC Class Codes: G16C 20/80 Data visualisation
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing

Abstract

In various embodiments, multiple heterogeneous documents are processed to identify structures, such as chemical structures, contained therein, including non-embedded structures. Also described is a graphical user interface that permits a user to search for a structure or substructure within a set of electronic documents, then displays the matching structures as well as the actual pages of the documents on which the matching structures are found. Display of the actual pages allows the user to verify the matches and provides helpful context for the user.

Claims

1. 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 for storing a code defining a set of instructions; and

(b) a processor for executing 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, 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; and

(iv) store objects not eliminated by the one or more filters in a searchable electronic compendium of identified objects.

2. The apparatus of claim 1, wherein the storage facility comprises a plurality of electronic files of two or more different file types.

3. The apparatus of claim 2, wherein the two or more different file types comprise at least two members selected from the group consisting of PDF, Word, Tiff, Excel, Mol File, RXN File, RTF, PowerPoint, cdx, BMP, JPEG, Plain Text, and SDF.

4. The apparatus of any one of the preceding claims, wherein the optical structure recognition module is configured to, for each identified candidate, derive a chemical structure object with an associated set of properties including two or more of the following:

(A) number of carbons, (B) number of hetero atoms, (C) number of bonds, (D) number of bonds of a selected bond order, (E) number of rings, and (F) formula weight.

5. The apparatus of claim 4, wherein the optical structure recognition module is configured to, for each derived chemical structure object, compute a value of a confidence factor based on two or more properties associated with the derived chemical structure object and eliminate objects based on confidence factor values in order to reduce false positives.

6. The apparatus of any one of the preceding claims, wherein the optical structure recognition module is configured to, for each derived chemical structure object not eliminated by the one or more filters, associate therewith identification of an electronic document in which the chemical structure is located, and a page or portion thereof on which the chemical structure is located, thereby facilitating identification of the origin of a particular chemical structure or substructure in the one or more electronic files during a search of the electronic compendium for the particular chemical structure or substructure.

15. The apparatus of any one of claims 1-6, wherein the optical structure recognition module is configured to, for at least one identified candidate chemical structure, derive a chemical structure object with an associated set of properties including stereochemistry.

7. An apparatus for displaying one or more chemical structures found in an electronic search of a storage facility comprising one or more electronic files, the apparatus comprising:

(a) a memory for storing a code defining a set of instructions; and

(b) a processor for executing the set of instructions, wherein the code comprises a graphical user interface module configured to;

(i) in a first designated location of a graphical user interface (GUI) display, display one or more chemical structures or substructures derived from an electronic search of a storage facility comprising one or more electronic files, wherein each of the displayed structures or substructures matches or contains a user-identified chemical structure or substructure;

(ii) in a second designated location of the GUI display, display a list of, and/or icon(s) representing, one or more electronic files from the storage facility, each file containing one or more of the structures or substructures displayed in the first designated location of the GUI display; and

(iii) in a third designated location of the GUI display, display a page, or portion thereof, of a selected one of the electronic files listed and/or represented in the second designated location of the GUI display, wherein the displayed page contains a selected one of the chemical structures or substructures displayed in the first designated location of the GUI display.

8. The apparatus of claim 7, wherein at least one of the chemical structures or substructures derived from the electronic search of the storage facility corresponds to a non-embedded image of the chemical structure or substructure in the one or more electronic files.

9. The apparatus of claim 7 or 8, wherein the storage facility comprises a plurality of file types.

10. The apparatus of claim 9, wherein the plurality of file types comprises at least two members selected from the group consisting of PDF, Word, Tiff, Excel, Mol File, RXN File, RTF, PowerPoint, cdx, BMP, JPEG, Plain Text, and SDF.

11. A method for electronically identifying and compiling chemical structures found in a storage facility comprising one or more electronic files, the method comprising:

creating and/or downloading electronic files for storage in a storage facility, wherein creating electronic files optionally comprises electronically scanning paper documents;

identifying a plurality of candidate chemical structures in the electronic files of the storage facility using an optical structure recognition module, wherein at least one of the electronic files comprises non-embedded images of chemical structures identifiable by the optical structure recognition module;

for each identified candidate, deriving a chemical structure object with an associated set of properties including number of carbons;

for each derived chemical structure object, applying one or more filters, including a filter to eliminate objects identified as having less than a selected number of carbons;

storing objects not eliminated by the one or more filters in a searchable electronic compendium of identified objects; and

displaying results of a user-initiated search of the electronic compendium of identified objects on an electronic display.

12. The method of claim 11, wherein the displaying step comprises:

in a first designated location of a graphical user interface (GUI) display, displaying one or more of the derived chemical structure objects, wherein each of the displayed objects matches or contains a user-identified chemical structure or substructure;

in a second designated location of the GUI display, displaying a list of and/or icon(s) representing, one or more of the electronic files of the storage facility, each file containing one or more of the derived chemical structure objects displayed in the first designated location of the GUI display; and

in a third designated location of the GUI display, displaying a page, or portion thereof, of a selected one of the electronic files listed and/or represented in the second designated location of the GUI display, wherein the displayed page contains a selected one of the chemical structure objects displayed in the first designated location of the GUI display.

13. The method of claim 11 or 12, wherein the storage facility comprises a plurality of file types.

14. The method of claim 13, wherein the plurality of file types comprises at least two members selected from the group consisting of PDF, Word, Tiff, Excel, Mol File, RXN File, RTF, PowerPoint, cdx, BMP, JPEG, Plain Text, and SDF.