System and method for scientific information knowledge management

• US 20070162411A1
• Filed: 12/18/2006
• Published: 07/12/2007
• Est. Priority Date: 12/16/2005
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: NextBio
• Inventors: Su, Qiaojuan, Kupershmidt, Ilya, Andry, Francois
• Granted Patent: US 8,275,737 B2
• Time in Patent Office: Days
• US Class Current: 706/60
• CPC Class Codes: G06F 16/21 Design, administration or maintenance of databases
• CPC Class Codes: G06N 5/02 Knowledge representation; Symbolic representation

Abstract

The present invention relates to methods, systems and apparatus for capturing, integrating, organizing, navigating and querying large-scale data from high-throughput biological and chemical assay platforms. It provides a highly efficient meta-analysis infrastructure for performing research queries across a large number of studies and experiments from different biological and chemical assays, data types and organisms, as well as systems to build and add to such an infrastructure.

Claims

1. A knowledge base for storing, managing, organizing and querying data comprising scientific experiment information, said knowledge base comprising:

a plurality of feature sets, each feature set comprising at least one feature and associated statistical information;

an index set comprising mapping identifiers, wherein each mapping identifier represents a unique feature;

a taxonomy comprising a list of tags that may be associated with features in the plurality of feature sets; and

a scoring table comprising information about the correlation between each feature set and all other feature sets.

2. A method of providing data to a knowledge base of scientific information;

the method comprising;

(a) receiving raw data from one or more samples, wherein the raw data includes information on one or more features with indications of responses of said features to a treatment or stimulus;

(b) producing an input feature set from the raw data by removing or reorganizing information about at least some less relevant features;

(c) correlating the input feature set against a plurality or all of the pre-existing feature sets in the knowledge base;

(d) correlating the input feature set against one or more feature groups in the knowledge base, wherein the feature groups provide collections of features having structural and/or functional characteristics in common; and

(e) storing correlation information generated in (c) and (d) for use in responding to queries involving feature groups or feature sets.

3. The method of claim 2, wherein the features comprise genes of an organism.

4. The method of claim 2, wherein the features comprise chemical compounds and indications of responses are effect(s) of chemical compounds on biological systems.

5. The method of claim 2, wherein the correlating in (c) comprise performing a rank-based statistical algorithm.