USING ANNOTATORS IN GENOME RESEARCH

• US 20140012866A1
• Filed: 05/02/2013
• Published: 01/09/2014
• Est. Priority Date: 07/03/2012
• Status: Active Grant

• Current Assignee: International Business Machines Corporation
• Original Assignee: International Business Machines Corporation
• Inventors: Bowman, Stephen D., Reddy, Dandala V., Werts, David B.
• Granted Patent: US 9,104,657 B2
• Time in Patent Office: Days
• US Class Current: 707/755
• CPC Class Codes: G06F 16/33 Querying
• CPC Class Codes: G06F 40/205 Parsing
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided are techniques for locating one or more genome patterns. One or more lexical annotators that each identify a sequence of nucleotides are created. One or more parsing rule annotators are created using at least one of (1) one or more of the lexical annotators, (2) one or more dictionary entries, and (3) one or more previously-defined parsing rule annotators. The one or more parsing rule annotators are used to discover the one or more genome patterns comprising a combination of the lexical annotators and the parsing rule annotators.

Claims

1. A method for locating one or more genome patterns, comprising:

creating, using a processor of a computer, one or more lexical annotators that each identify a sequence of nucleotides;

creating one or more parsing rule annotators using at least one of (1) one or more of the lexical annotators, (2) one or more dictionary entries, and (3) one or more previously-defined parsing rule annotators; and

using the one or more parsing rule annotators to discover the one or more genome patterns comprising a combination of the lexical annotators and the parsing rule annotators.

2. The method of claim 1, wherein the combination of the lexical annotators and the parsing rule annotators comprises one or more lexical annotators and no parsing rule annotators.

3. The method of claim 1, wherein the combination of the lexical annotators and the parsing rule annotators comprises one or more parsing rule annotators and no lexical annotators.

4. The method of claim 1, wherein the parsing rule annotator indicates an order and a combination of lexical annotators, the one or more lexical annotators, the one or more dictionary entries, and other parsing rule annotators relative to each other.

5. The method of claim 1, wherein the parsing rule annotator creates a new annotation when finding a match on the combination of the lexical annotators and the parsing rule annotators.

6. The method of claim 1, further comprising:

creating an Unstructured Information Management Architecture (UIMA) pipeline to locate the one or more genome patterns.

7. The method of claim 1, wherein a Software as a Service (SaaS) is provided to perform the method.