Please have a seat. Our program will commence shortly. B iomarker A utomated R etrieval T ool. K N. R C. Ronny Chan, Kim Ngo Earth Science Data Systems Dept. Bioinformatics Relationship. Science produces massive amounts of data Data needs to be analyzed, stored, & retrieved
Ronny Chan, Kim Ngo
Earth Science Data Systems Dept.
This is data-mining
Where are the Biomarkers?
An indicator of cancerous growth.
Create a program that allows people to quickly scan literature for the most relevant keywords/biomarkers
Introduced by Gerald Salton in the 60’s.
Used widely in different search enginesVector Space Model
PubMed Query Agent
Data Retrieval and Output
5 ARTICLES = 160 sec
20 ARTICLES = 1904 sec
100 ARTICLES = 8^38 years
UPDATE: AUGUST 18, 2004
100 ARTICLES = 8^19 years
Biomarkers and surrogate endoints: preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 69(3), 89-95 (2001).
National Science Foundation (NSF)
National Institute of Health (NIH)
Earth Science Data System, JPL
Southern California Bioinformatics Summer Institute (So Cal BSI)
ALL SoCalBSI Colleagues
Q : malignant breast cancer
D 1: detection of malignant level in the cell
D 2: sighting of breast stage in the breast cancer
D 3: detection of malignant stage in the cancer
Keyword tf * idf