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Regulatory and signaling network assembly through linked open data

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Demonstration talk given by Marie Lefebvre at JOBIM 2017 (https://project.inria.fr/jobim2017) .

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Regulatory and signaling network assembly through linked open data

  1. 1. Regulatory and signaling network assembly through Linked Open Data Marie Lefebvre1 , Jérémie Bourdon2 , Carito Guziolowski2 , Alban Gaignard1 1 Nantes Academic Hospital, CHU de Nantes, France 2 LS2N - UMR 6004, University of Nantes, Ecole Centrale de Nantes, France DEMO - JOBIM 2017 - LILLE
  2. 2. Marie Lefebvre - JOBIM 2017 CONTEXT 2 Activation Inhibition Gene Complex Signaling network Gene Regulatory network Transcriptional factor Phosphorylation
  3. 3. Marie Lefebvre - JOBIM 2017 CONTEXT 3 COMPUTATIONAL PREDICTIONS Signaling networkGene regulatory network Directed graphs Precise semantics LOGIC AND PROBABILISTIC MODELS bayesian, boolean, constraints based, etc.
  4. 4. Marie Lefebvre - JOBIM 2017 CONTEXT 4 Signaling networkGene regulatory network Directed graphs Precise semantics COMPUTATIONAL PREDICTIONS LOGIC AND PROBABILISTIC MODELS bayesian, boolean, constraints based, etc.
  5. 5. Marie Lefebvre - JOBIM 2017 5 CHALLENGE : NETWORK RECONSTRUCTION 6 3 22 1 - Multiple data sources KEGG Pathways ✓ 514 pathways Reactome ✓ 2132 pathways ✓ 10754 reactions ● In 2014, more than 1552 databases that are publicly accessible online (1) ● More than 31 databases useful for network construction(2) (H. sapiens) (1) Fernandez-Suarez X.M., and al. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. Nucleic Acids Res. 2014;42:D1–D6 (2) i.e. StringDB, intAct, GeneMania, HipathDB, WikiPathway, MetaCyc, ConsensusPathDB, etc.
  6. 6. Marie Lefebvre - JOBIM 2017 6 CHALLENGE : NETWORK RECONSTRUCTION Different paths between TRAIL and FADD (apoptosis) 2 - Semantic heterogeneity KEGG Reactome
  7. 7. Marie Lefebvre - JOBIM 2017 7 CHALLENGE : NETWORK RECONSTRUCTION Different paths between TRAIL and FADD (apoptosis) 2 - Semantic heterogeneity KEGG Reactome
  8. 8. Marie Lefebvre - JOBIM 2017 Time for 200 biological entities input Logic oriented Upstream interactions PC Viz no result CyPath 2 < 1min Reactome online NA Reactome Cytoscape < 1min ChiBE < 1min 8 CHALLENGE : NETWORK RECONSTRUCTION 3 - State of the art approaches How to discover the upstream mechanisms that trigger a list of biological entities ?
  9. 9. Marie Lefebvre - JOBIM 2017 OBJECTIVES 9 ❖ Reconstruct a network from diverse biological entities ❖ Integrate diverse upstream regulators ❖ Large scale simulation-oriented networks (→ predictive models)
  10. 10. Marie Lefebvre - JOBIM 2017 10 APPROACH Linked Open Data Identify & Link Data Querying Reasoning Vocabularies Ontologies Information Knowledge
  11. 11. Marie Lefebvre - JOBIM 2017 11 OUR TOOL BRAvo Biological netwoRk Assembly
  12. 12. Marie Lefebvre - JOBIM 2017 12 IMPLEMENTATION Database ● Store and disseminate knowledge about biological pathways from 22 data sources ● BioPAX level 3 ● Freely available Graph SPARQL endpoint SPARQL query List of biological entities Workflow request results
  13. 13. Marie Lefebvre - JOBIM 2017 13 USE CASE /1
  14. 14. Marie Lefebvre - JOBIM 2017 14 USE CASE /1
  15. 15. Marie Lefebvre - JOBIM 2017 15 USE CASE /1
  16. 16. Marie Lefebvre - JOBIM 2017 16 USE CASE /1
  17. 17. Marie Lefebvre - JOBIM 2017 17 USE CASE /2
  18. 18. Marie Lefebvre - JOBIM 2017 18 USE CASE /2
  19. 19. Marie Lefebvre - JOBIM 2017 19 USE CASE /2
  20. 20. Marie Lefebvre - JOBIM 2017 20 USE CASE /2
  21. 21. Marie Lefebvre - JOBIM 2017 21 CONCLUSION BRAvo : Biological netwoRk Assembly ❖ Reconstruct gene regulatory network from diverse biological entities ■ From 210 entities → Time < 2min | 335 nodes & 4191 edges ❖ Integration of heterogeneous data from different data sources ❖ Designed for assembling models ❖ Available at https://github.com/symetric-group/bionets-demo GUI Interactive reconstruction Full reconstruction BATCH
  22. 22. Marie Lefebvre - JOBIM 2017 22 FUTURE WORKS ● Extend type of biological entities : complex, molecule ● Add type of interaction : catalysis, phosphorylation ● Add filters (receptor) Signaling network assembly Integrate drug information ● Integration of KEGG drug / DrugBank Simulation oriented controlled vocabulary ● Apply to several modeling frameworks Package ● Provide JAVA and Python API
  23. 23. Thank you for your attention

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