Doctoral Consortium@RuleML2015: GROOLS: Reactive Graph Reasoning for Genome Annotation

GROOLS

Reactive Graph Reasoning forGenome Annotation

Jonathan MERCIER

CEA - LABGeM France

August 4, 2015 / RuleML 2015, Berlin

Genoscope

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

BiologyAsserted bio-fact from bio experiment

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

BiologyGenome sequencing and annotation

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

BiologyGenome sequencing and annotation

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

BiologyGenome sequencing and annotation

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

BiologyGenome sequencing and annotation

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

BiologyGenome sequencing and annotation

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BiologyPredicted bio-fact by bio-annotator

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

BioinformaticsGROOLS Object model

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

BioinformaticsPrior knowledge DAG

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

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

BioinformaticsObject-Oriented Expert System

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

BioinformaticsDAG Reasoning

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

BioinformaticsDAG Reasoning

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

BioinformaticsDAG Reasoning

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

BioinformaticsDAG Reasoning

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

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

Perspective

▶ Applying to real data

▶ Data mining

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

Perspective

▶ Applying to real data

▶ Data mining

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

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