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

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Page 1: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

GROOLS

Reactive Graph Reasoning forGenome Annotation

Jonathan MERCIER

CEA - LABGeM France

August 4, 2015 / RuleML 2015, Berlin

Page 2: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

Genoscope

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

https://github.com/Grools
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BiologyAsserted bio-fact from bio experiment

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

https://github.com/Grools
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BiologyGenome sequencing and annotation

source code: https://github.com/Grools GROOLS 3 / 13

https://github.com/Grools
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BiologyGenome sequencing and annotation

source code: https://github.com/Grools GROOLS 3 / 13

https://github.com/Grools
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BiologyGenome sequencing and annotation

source code: https://github.com/Grools GROOLS 3 / 13

https://github.com/Grools
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BiologyGenome sequencing and annotation

source code: https://github.com/Grools GROOLS 3 / 13

https://github.com/Grools
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BiologyGenome sequencing and annotation

source code: https://github.com/Grools GROOLS 3 / 13

https://github.com/Grools
Page 9: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
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BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
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BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
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BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 13: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 14: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 15: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 16: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 17: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 18: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BiologyPredicted bio-fact by bio-annotator

source code: https://github.com/Grools GROOLS 4 / 13

https://github.com/Grools
Page 19: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BioinformaticsGROOLS Object model

source code: https://github.com/Grools GROOLS 5 / 13

https://github.com/Grools
Page 20: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
Page 22: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
Page 23: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
Page 24: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
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BioinformaticsPrior knowledge DAG

source code: https://github.com/Grools GROOLS 6 / 13

https://github.com/Grools
Page 32: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

Belnap’s logicTruth 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

https://github.com/Grools
Page 33: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

BioinformaticsObject-Oriented Expert System

source code: https://github.com/Grools GROOLS 8 / 13

https://github.com/Grools
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BioinformaticsDAG Reasoning

source code: https://github.com/Grools GROOLS 9 / 13

https://github.com/Grools
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BioinformaticsDAG Reasoning

source code: https://github.com/Grools GROOLS 9 / 13

https://github.com/Grools
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BioinformaticsDAG Reasoning

source code: https://github.com/Grools GROOLS 10 / 13

https://github.com/Grools
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BioinformaticsDAG Reasoning

source code: https://github.com/Grools GROOLS 10 / 13

https://github.com/Grools
Page 38: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

Conclusion truth table

Table: Sixteen-valued logic truth tablehhhhhhhhhAssertion

PredictionPRESENT ABSENT BOTH UNKNOWN

REQUIRED Confirmed P. Unexpected A. Contradictory A. MissingAVOIDED Unexpected P. Confirmed A. Contradictory P. AbsentBOTH Ambiguous P. Ambiguous A. Ambiguous C. AmbiguousUNKNOWN Unconfirmed P. Unconfirmed A. Unconfirmed C. Unknown

LegendA. AbsenceP. PresenceC. Contradiction

source code: https://github.com/Grools GROOLS 11 / 13

https://github.com/Grools
Page 39: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

Perspective

▶ Applying to real data

▶ Data mining

source code: https://github.com/Grools GROOLS 12 / 13

https://github.com/Grools
Page 40: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

Perspective

▶ Applying to real data

▶ Data mining

source code: https://github.com/Grools GROOLS 12 / 13

https://github.com/Grools
Page 41: Doctoral consortium@rule ml2015 grools reactive graph reasoning for genome annotation

Acknowledgements

LABGeM systems biology team:David VallenetClaudine MedigueKarine BastardMark Stam

Special thanks to:Alain Viari (INRIA)Anne Morgat (SIB)UniProt team (EBI-SIB)

source code: https://github.com/Grools GROOLS 13 / 13

https://github.com/Grools

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