Grools talk at ruleML

1. GROOLS
Reactive Graph Reasoning for
Genome Annotation
Jonathan MERCIER
CEA - LABGeM France
August 4, 2015 / RuleML 2015, Berlin

2. Genoscope
source code: https://github.com/Grools GROOLS 1 / 13

3. Biology
Asserted bio-fact from bio experiment
source code: https://github.com/Grools GROOLS 2 / 13

4. Biology
Genome sequencing and annotation
source code: https://github.com/Grools GROOLS 3 / 13

5. Biology
Genome sequencing and annotation
source code: https://github.com/Grools GROOLS 3 / 13

6. Biology
Genome sequencing and annotation
source code: https://github.com/Grools GROOLS 3 / 13

7. Biology
Genome sequencing and annotation
source code: https://github.com/Grools GROOLS 3 / 13

8. Biology
Genome sequencing and annotation
source code: https://github.com/Grools GROOLS 3 / 13

9. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

10. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

11. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

12. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

13. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

14. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

15. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

16. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

17. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

18. Biology
Predicted bio-fact by bio-annotator
source code: https://github.com/Grools GROOLS 4 / 13

19. Bioinformatics
GROOLS Object model
source code: https://github.com/Grools GROOLS 5 / 13

20. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

21. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

22. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

23. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

24. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

25. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

26. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

27. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

28. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

29. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

30. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

31. Bioinformatics
Prior knowledge DAG
source code: https://github.com/Grools GROOLS 6 / 13

32. Belnap’s logic
Truth tables
Table: Four-valued logic truth tables. T: true, F: false, B: both, N: none.
F(¬α)
T F
B B
N N
F T
F(∧α) T B N F
T T B N F
B B B F F
N N F N F
F F F F F
F(∨α) T B N F
T T T T T
B T B T B
N T T N N
F T B N F
source code: https://github.com/Grools GROOLS 7 / 13

33. Bioinformatics
Object-Oriented Expert System
source code: https://github.com/Grools GROOLS 8 / 13

34. Bioinformatics
DAG Reasoning
source code: https://github.com/Grools GROOLS 9 / 13

35. Bioinformatics
DAG Reasoning
source code: https://github.com/Grools GROOLS 9 / 13

36. Bioinformatics
DAG Reasoning
source code: https://github.com/Grools GROOLS 10 / 13

37. Bioinformatics
DAG Reasoning
source code: https://github.com/Grools GROOLS 10 / 13

38. Conclusion truth table
Table: Sixteen-valued logic truth table
hhhhhhhhhAssertion
Prediction
PRESENT ABSENT BOTH UNKNOWN
REQUIRED Confirmed P. Unexpected A. Contradictory A. Missing
AVOIDED Unexpected P. Confirmed A. Contradictory P. Absent
BOTH Ambiguous P. Ambiguous A. Ambiguous C. Ambiguous
UNKNOWN Unconfirmed P. Unconfirmed A. Unconfirmed C. Unknown
Legend
A. Absence
P. Presence
C. Contradiction
source code: https://github.com/Grools GROOLS 11 / 13

39. Perspective
▶ Applying to real data
▶ Data mining
source code: https://github.com/Grools GROOLS 12 / 13

40. Perspective
▶ Applying to real data
▶ Data mining
source code: https://github.com/Grools GROOLS 12 / 13

41. Acknowledgements
LABGeM systems biology team:
David Vallenet
Claudine Medigue
Karine Bastard
Mark Stam
Special thanks to:
Alain Viari (INRIA)
Anne Morgat (SIB)
UniProt team (EBI-SIB)
source code: https://github.com/Grools GROOLS 13 / 13