1. MINING FOR MEANING: Data mining & Knowledge extraction Laboratory of Parasitic Diseases, NIAID

2. Knowledge Experiment Results Data interpretation Conclusions

3. Experiment Results Knowledge Conclusions High publication rates Knowledge Data interpretation

5. Experiment Results Knowledge Conclusions High publication rates Knowledge High-throughput screening Results Data interpretation

6. Experiment Results Knowledge Conclusions Knowledge Results GENE EXPRESSION PROFILING Identify relevant genes Identify expression patterns Data interpretation

7. Experiment Results Knowledge Conclusions Knowledge GENE EXPRESSION PROFILING FUNCTIONAL PROFILING Identify relevant genes Identify expression patterns Identify functional implications Data interpretation

8. FUNCTIONAL PROFILING MINING FOR MEANING:

9. ProtozoanBacteriavs Leishmania Mycobacterium tuberculosis Leishmania majorLeishmania donovanivs Brugia malayi Toxoplasma gondii Elutriated Human Monocytes IntracellularExtracellular vs 7 donors Infection with 5 pathogens -overnight- DC IL-4 + GM-CSF Mac M-CSF RNA pools RNA pools U95

10. Dataset DC 12.000 genesExtraction  75 Gene expression profiling  Filter 1200 Dataset Mac

11. DC Pathogens Genes Fold Change (log2) Lm Ld Tg Bm 50 Bm 5 Mtb Fold Change (log2) Induced by intracellular pathogens Leishmania & TB Toxoplasma & TB Toxoplasma

13. FUNCTIONAL PROFILING MINING FOR MEANING: WITH GENE ONTOLOGIES - GO

14. http://www.geneontology.org/

15. http://apps1.niaid.nih.gov/david/

19. FUNCTIONAL PROFILING MINING FOR MEANING: WITH GENE ONTOLOGIES - GO WITH LITERATURE ONTOLOGIES - MESH

20. http://www.nlm.nih.gov/mesh/MBrowser.html

21. http://132.239.155.52/HAPI/TEST_377.HTML http://array.ucsd.edu/hapi/

23. FUNCTIONAL PROFILING MINING FOR MEANING: WITH GENE ONTOLOGIES - GO WITH LITERATURE ONTOLOGIES - MESH WITH LITERATURE ABSTRACTS

24. Experiment Results Knowledge Conclusions Knowledge Data interpretation 12 million references

25. Experiment Results Knowledge Conclusions Knowledge Results Data interpretation 12 million references

26. FUNCTIONAL PROFILING MINING FOR MEANING: WITH LITERATURE ABSTRACTS  Co-citation Network

27. http://www.pubgene.com/

28. FUNCTIONAL PROFILING MINING FOR MEANING: WITH LITERATURE ABSTRACTS  Co-citation Network  Natural Language Processing

30. FUNCTIONAL PROFILING MINING FOR MEANING: WITH LITERATURE ABSTRACTS  Co-citation Network  Natural Language Processing  L LL Literature Profiling

32. Select relevant terms Determine term occurrence in abstracts Retrieve relevant literature for each gene Gene A Gene B Gene C… Gene X 1.Gene - Literature indexation 3.Term filtering DiscriminationCo-occurrence Analyze functional relationships 2. Analysis of abstract contents Abstracts Term occurrences in abstracts

33. KNOWLEDGE 12 million references Experimental system Gene List - Translate genelists into keywords - Interpret data - Identify functional relationships

36. FUNCTIONAL PROFILING MINING FOR MEANING: LITERATURE MINING

37. Experiment Results Knowledge Conclusions High publication rates Knowledge Data interpretation

38. DATA MINING LITERATURE MINING MINING FOR MEANING: DOCUMENT CLUSTERING

40. DATA MINING LITERATURE MINING MINING FOR MEANING: DOCUMENT CLUSTERING NLP

42. DATA MINING LITERATURE MINING MINING FOR MEANING: DOCUMENT CLUSTERING NLP LITERATURE PROFILING

43. Experiment Results Knowledge Conclusions Knowledge Results GENE EXPRESSION PROFILING Identify relevant genes Identify expression patterns Data interpretation