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Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

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Mining patents using molecular similarity search.

James Rhodes¹, Stephen Boyer, Jeffrey Kreulen

¹IBM, Almaden Services Research, San Jose, CA 95120, USA. jjrhodes@us.ibm.com

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

|November 10, 2007

Summary

This study introduces a novel system for exploring US patents using molecular information. It enhances intellectual property (IP) searches by identifying chemical structures, outperforming traditional keyword methods.

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Area of Science:

Biomedical research
Cheminformatics
Intellectual Property (IP) analysis

Background:

Text analytics is crucial in biomedical research.
Core algorithms for entity identification and relation extraction are advancing.
Practical applications for text analytics in this field are needed.

Purpose of the Study:

To develop a system for exploring the US Patent corpus using molecular information.
To provide a practical application for text analytics in biomedical research and IP discovery.
To improve the identification of intellectual property compared to traditional methods.

Main Methods:

Developed a system integrating a chemical annotator, a similarity search engine using the International Chemical Identifier (InChI) standard, and data mining tools.
Indexed 3,623,248 unique chemical structures from 4,375,036 US Patents and Patent Applications.
Enabled users to draw molecules, search for related IP, and analyze results via a web interface.

Main Results:

Successfully identified and indexed a large number of unique chemical structures from the US patent corpus.
Demonstrated the system's capability to facilitate IP exploration based on molecular information.
Showcased a more effective approach to IP identification than conventional keyword-based searches.

Conclusions:

The developed system offers a powerful new method for exploring the US Patent corpus using molecular data.
This approach significantly enhances the discovery and analysis of intellectual property.
Leveraging chemical information in patent searches provides superior results compared to keyword-based strategies.