MINING FOR MEANING: Data mining

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MINING FOR MEANINGData mining Knowledge
extraction
Laboratory of Parasitic Diseases, NIAID
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Data interpretation


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Data interpretation
Experiment
Results
Knowledge
Knowledge

• High publication rates

Conclusions
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Data interpretation
Experiment
Results
Knowledge
Knowledge

• High publication rates

Conclusions
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Data interpretation
Experiment
GENE EXPRESSION PROFILING
Results
Results
Identify relevant genes
Identify expression patterns
Knowledge
Knowledge
Conclusions
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Data interpretation
Experiment
GENE EXPRESSION PROFILING
Results
Identify relevant genes
Identify expression patterns
Knowledge
Knowledge
FUNCTIONAL PROFILING
Identify functional implications
Conclusions
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MINING FOR MEANING
FUNCTIONAL PROFILING
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12.000 genes
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Induced by
Bm 50
DC
Bm 5
Mtb
Lm
Ld
Tg
Pathogens
intracellular pathogens
Fold Change (log2)
Fold Change (log2)
Leishmania TB
Genes
Toxoplasma TB
Fold Change (log2)
Fold Change (log2)
Toxoplasma
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MINING FOR MEANING
FUNCTIONAL PROFILING
WITH GENE ONTOLOGIES - GO
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http//www.geneontology.org/
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http//apps1.niaid.nih.gov/david/
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MINING FOR MEANING
FUNCTIONAL PROFILING
WITH GENE ONTOLOGIES - GO
WITH LITERATURE ONTOLOGIES - MESH
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http//www.nlm.nih.gov/mesh/MBrowser.html
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http//array.ucsd.edu/hapi/
http//132.239.155.52/HAPI/TEST_377.HTML
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MINING FOR MEANING
FUNCTIONAL PROFILING
WITH GENE ONTOLOGIES - GO
WITH LITERATURE ONTOLOGIES - MESH
WITH LITERATURE ABSTRACTS
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Data interpretation
Experiment
Results
Knowledge
Knowledge
12 million references
Conclusions
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Data interpretation
Experiment
Results
Results
Knowledge
Knowledge

Conclusions
12 million references
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MINING FOR MEANING
FUNCTIONAL PROFILING
WITH LITERATURE ABSTRACTS
? Co-citation Network
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http//www.pubgene.com/
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MINING FOR MEANING
FUNCTIONAL PROFILING
WITH LITERATURE ABSTRACTS
? Co-citation Network
? Natural Language Processing
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MINING FOR MEANING
FUNCTIONAL PROFILING
WITH LITERATURE ABSTRACTS
? Co-citation Network
? Natural Language Processing
? Literature Profiling
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Retrieve relevant literature for each gene
Determine term occurrence in abstracts
Select relevant terms
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- Identify functional relationships
- Translate genelists into keywords
- Interpret data
Experimental system
Gene List
12 million references
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MINING FOR MEANING
FUNCTIONAL PROFILING
LITERATURE MINING
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Data interpretation
Experiment
Results
Knowledge
Knowledge

• High publication rates

Conclusions
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MINING FOR MEANING
DATA MINING
LITERATURE MINING
DOCUMENT CLUSTERING
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MINING FOR MEANING
DATA MINING
LITERATURE MINING
DOCUMENT CLUSTERING
NLP
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MINING FOR MEANING
DATA MINING
LITERATURE MINING
DOCUMENT CLUSTERING
NLP
LITERATURE PROFILING
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Data interpretation
Experiment
GENE EXPRESSION PROFILING
Results
Results
Identify relevant genes
Identify expression patterns
Knowledge
Knowledge
Conclusions