Methods and apparatus for assessing pathways for bio-chemical synthesis

Patent metadata

Field	Value
Publication number	US-2016196323-A1
Application number	US-201514984190-A
Country	US
Kind code	A1
Filing date	Dec 30, 2015
Priority date	Jan 5, 2015
Publication date	Jul 7, 2016
Grant date	—

Abstract

In a method of assessing a bio-chemical synthesis pathway, input data (that is, data representing a chemical pathway, a reaction, and/or a molecule) is processed to extract a feature of at least one selected from an association of a molecular substructure, an association of at least one molecular substructure classified according to a molecular transformation type, and an association of a reaction transformation type. The input data may be ranked or filtered based on an association measure extracted from a chemical knowledgebase (e.g., database storing chemical data), thereby enabling a prediction or selection of an appropriate chemical pathway, reaction, and/or molecule.

First claim

What is claimed is:

1 . A method of assessing a chemical pathway, reaction, and molecule, the method comprising the steps, implemented in a processor of a data processing apparatus, of:
processing input data; extracting a feature from the processed input data; obtaining an association measure coefficient based on data from a chemical knowledgebase; and assessing the processed input data based on the obtained association measure coefficient, wherein the input data and the chemical knowledgebase each comprise at least one chemical pathway, at least one reaction, and at least one molecule.

2 . The method of claim 1 , wherein the processing of input data comprises at least one of:
identifying a reaction transformation for the at least one reaction included in the input data, and classifying the at least one reaction included in the input data based on an at least one reaction transformation type; identifying a molecular transformation for the at least one molecule included in the input data, and classifying the at least one molecule included in the input data based on an at least one molecular transformation type; and identifying a molecular substructure contained in the at least one molecule included in the input data.

3 . The method of claim 1 , wherein the extracted feature comprises an association of a molecular substructure, an association of a molecular substructure classified according to a molecular transformation type, and an association of a reaction transformation type.

4 . The method of claim 1 , wherein the obtaining of an association measure coefficient based on data from a chemical knowledgebase comprises:
processing the chemical knowledgebase; extracting a feature from the processed chemical knowledgebase, wherein the feature contains at least one of an association of a molecular substructure, an association of a molecular substructure classified according to a molecular transformation type, and an association of a reaction transformation type; and obtaining the association measure coefficient based on a feature extracted from the processed chemical knowledgebase and a feature extracted from the processed input data.

5 . The method of claim 4 , wherein the processing of the chemical knowledgebase comprises at least one of:
identifying a reaction transformation for at least one reaction included in the chemical knowledgebase and classifying the at least one reaction based on at least one reaction transformation type; identifying a molecular transformation for at least one molecule included in the chemical knowledgebase and classifying the at least one molecule based on at least one molecular transformation type; and identifying a molecular substructure contained in the at least one molecule included in the chemical knowledgebase.

6 . The method of claim 2 , wherein the molecular transformation, for the at least one molecule included in the input data, comprises at least one molecule substructure residing on the at least one molecule included in the input data and at least one of a bond change, a bond rearrangement, and a chemical state change that occurs during a reaction process on the at least one molecule included in the input data.

7 . The method of claim 2 , wherein the reaction transformation, for the at least one reaction included in the input data, comprises a set of molecular transformations of the at least one molecule participating in a reaction included in the input data.

8 . The method of claim 5 , wherein the molecular transformation, for the at least one molecule included in the chemical knowledgebase, comprises at least one molecule substructure residing on the at least one molecule included in the chemical knowledgebase and at least one of a bond change, a bond rearrangement, and a chemical state change that occurs during a reaction process on the at least one molecule included in the chemical knowledgebase.

9 . The method of claim 5 , wherein the reaction transformation, for the at least one reaction included in the chemical knowledgebase, comprises a set of molecular transformations of the at least one molecule participating in a reaction included in the chemical knowledgebase.

10 . The method of claim 3 , wherein the association of a molecular substructure, in the feature extracted from the input data, is derived from at least one of an occurrence of at least one molecular substructure and a co-occurrence of the at least one molecular substructure, wherein the co-occurrence is recorded with a relative distance between the molecular substructures.

11 . The method of claim 3 , wherein the association of a reaction transformation type, in the feature extracted from the input data, is derived from at least one of an occurrence of at least one reaction transformation type and a co-occurrence of the at least one reaction transformation type.

12 . The method of claim 4 , wherein the association of a molecular substructure, in the feature extracted from the chemical knowledgebase, is derived from at least one of an occurrence of at least one molecular substructure and a co-occurrence of the at least one molecular substructure,
wherein the co-occurrence is recorded with a relative distance between the molecular substructures.

13 . The method of claim 4 , wherein the association of a reaction transformation type, in the feature extracted from the chemical knowledgebase, is derived from at least one of an occurrence of at least one reaction transformation type and a co-occurrence of the at least one reaction transformation type.

14 . The method claim 1 , wherein the assessing of the input data comprises:
assigning a score to at least one feature extracted from the input data based on the obtained association measure coefficient; and computing a composite score, based on the assigned score, for at least one of the at least one chemical pathway, the at least one reaction, and the at least one molecule included in the input data.

15 . The method of claim 14 , wherein the assessing of the input data comprises assigning a rank, according to the computed composite score, to at least one of the at least one chemical pathway, the at least one reaction, and the at least one molecule included in the input data.

16 . The method of claim 14 , wherein the assessing of the input data comprises selecting at least one of the chemical pathway, the reaction, and the molecule, of which the composite score is greater than a threshold value included in the input data.

17 . An apparatus comprising:
a memory and at least one processor operatively coupled to the memory, wherein the processor comprises: a processing module configured to process input data; a feature extracting module configured to extract a feature from the processed input data; a module configured to obtain an association measure coefficient an association measure coefficient from chemical knowledgebase; and an analyzing assessment module configured to analyze the input data based on the association measure coefficient to assess the input data.

18 . A non-transitory computer-readable recording medium having recorded thereon a program for causing a processor to execute a method of assessing a chemical pathway, reaction, and molecule, by:
processing input data; extracting a feature from the processed input data; obtaining an association measure coefficient based on data from a chemical knowledgebase; and assessing the processed input data based on the obtained association measure coefficient, wherein the input data and the chemical

Assignees

• Samsung Electronics Co Ltd

Inventors

• Kim Taeyong
• Siva Kumar Venkata Tadi
• Giri Varun
• Bhaduri Anirban

Classifications

• G16C20/10 Primary

  Analysis or design of chemical reactions, syntheses or processes · CPC title

• G06F17/30598 Primary

  Physics · mapped topic

• G06F17/3053

  Physics · mapped topic