Methods and systems for analyzing complex biological systems

• US 6,873,914 B2
• Filed: 11/20/2002
• Issued: 03/29/2005
• Est. Priority Date: 11/21/2001
• Status: Expired due to Term

• Current Assignee: Metabolon Incorporated
• Original Assignee: Icoria, Inc. (Abbvie Incorporated)
• Inventors: Winfield, Stephanie, Beecher, Christopher, Glassbrook, Norman, Nye, Gordon James, Ranasinghe, Yasmin, Broadwell, David, Popa-Burke, Ioana
• Primary Examiner(s): Hoff, Marc S.
• Assistant Examiner(s): Raymond, Edward
• Application Number:
  US10/300,360
• Publication Number:
  US 20040019435A1
• Time in Patent Office: 860 Days
• Field of Search: 702/19, 702/32, 702/90, 702/182, 702/183, 702/104, 700 26- 30, 700/266, 707100-102, 707/103.R, 707/103.Y, 707/103.Z
• US Class Current: 702/19
• CPC Class Codes: G01N 30/72 Mass spectrometers mass spectrometers per se H01J49/00
• CPC Class Codes: G01N 30/8655 Details of data formats
• CPC Class Codes: G01N 30/8658 Optimising operation parameters
• CPC Class Codes: G01N 30/8662 Expert systems; optimising a large number of parameters
• CPC Class Codes: G01N 30/8679 Target compound analysis, i.e. whereby a limited number of peaks is analysed
• CPC Class Codes: G01N 30/8693 Models, e.g. prediction of retention times, method development and validation
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface

Abstract

The present invention provides methods and systems for organizing complex and disparate data. More specifically, the present invention provides methods and systems for organizing complex and disparate data into coherent data sets. Coherent data sets resulting from the methods and systems of the present invention serve as models for biological systems. Methods and systems for integrating data and creating coherent data sets are useful for numerous biological applications, such as, for example, determining gene function, identifying and validating drug and pesticide targets, identifying and validating drug and pesticide candidate compounds, profiling drug and pesticide compounds, producing a compilation of health or wellness profiles, determining compound site(s) of action, identifying unknown samples, and numerous other applications in the agricultural, pharmaceutical, forensic, and biotechnology industries.

Claims

1. A system for examining metabolites in a biological sample, comprising:

a) means for entering a unique identifier of at least one biological sample into a computer tracking system;

b) means for simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least LC-MS, GC-MS, and NMR;

c) means for storing in said computer tracking system said chemical component data, wherein said data are linked to said unique identifier;

d) means for characterizing and/or identifying said chemical components; and

e) means for linking said characerized and/or identified chemical components to metabolites in biochemical pathways.

2. A system for examining metabolites in a biological sample, comprising:

a) means for entering a unique identifier of at least one biological sample into a computer tracking system;

b) means for simultaneously collecting data from said sample, for a plurality of peaks, each peak comprising at least one chemical component, wherein said data comprise data from at least LC-MS, GC-MS, and ICP-MS;

c) means for storing in said computer tracking system said chemical component data, wherein said data are linked to said unique identifier;

d) means for characterizing and/or identifying said chemical components; and

e) means for linking said characerized and/or identified chemical components to metabolites in biochemical pathways.