Graphs for Data Science in Public Health Research
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Speaker: Dr. Alexander Jarasch, Head of Data & Knowledge Management, German Center for Diabetes Research (DZD)
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Graphs for Data Science in Public Health Research
- 1. The Covid Graph How the neo4j community joins forces against Covid19 https://covidgraph.org/
- 2. Who we are We are a diverse team of scientists, developers and data people from academia and industry
- 3. Overall goal We build a knowledge graph on COVID-19 that integrates various public datasets. We structure data - connect data We connect entities from biomedical field such as genes, proteins, molecular pathways https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge
- 5. Let’s assume the following scenario
- 6. Our super heros - researchers and medical doctors Did you read this interesting paper about Covid19 and Gen X? No not yet…!
- 7. … have expert knowledge Did you read this interesting paper about Covid19 and Gen X? No not yet…! … oh, and this publication reveals that ‚XYZ‘ is a marker for diabetes… oh yeah I knew that…!
- 8. … have expert knowledge Did you read this interesting paper about Covid19 and Gen X? No not yet…! … oh, and this publication reveals that ‚XYZ‘ is a marker for diabetes… oh yeah I knew that…! Did you know that protein Y is mentioned to cause lung disease? No but sounds interesting…!
- 9. Challenge today: cope with literature Did you read this interesting paper about Covid19 and Gen X? No not yet…! … oh, and this publication reveals that ‚XYZ‘ is a marker for diabetes… oh yeah I knew that…! Did you know that protein Y is mentioned to cause lung disease? No but sounds interesting…! 44k
- 10. Cope with literature, genes, proteins, … Covid19 and Diabetes? 100k genomes - cool tell me about the results AD? Didn’t know about this study… P881208…? cryo-EM structure of the complete and ligand- saturated receptor ectodomain
- 11. Where we might help
- 12. mentioned mentioned is Keyword is is Lung Protein Y Gene X Covid19 Disease Disease Publication A Study Did you read this interesting paper about Covid19 and Gen X? … oh, and this publication reveals that ‚XYZ‘ is a marker for diabetes…Did you know that protein Y is mentioned to cause lung disease?
- 13. mentioned mentioned is Keyword is is Lung Protein Y Gene X Covid19 Disease Disease Publication A Study encodes Extend our knowledge
- 14. mentioned mentioned is Keyword is hasclinicalstudy is Covid19 Protein Y Gene X Covid19 Disease Disease Publication A Study encodes Millions of connections
- 16. has synonyms has synonyms transcribed translated mentioned mentioned is Keyword is isbiomarker is Covid19 Protein Y Gene X Diabetes Disease Disease Pub A HbA1c encodes Metabolite M Transcript Z SNP K
- 17. has synonyms has synonyms transcribed translated mentioned mentioned is Keyword is isbiomarker is Covid19 Protein Y Gene X Diabetes Disease Disease Pub A HbA1c encodes Metabolite M Transcript Z SNP K Publication 1 Publication 2 Publication 31 Publication 5430 Patent WOxxxPatent WOxxx Patent WOxxx
- 18. Covid19 and other diseases, risks,… Find hidden connections Diabetes Corona virus ? people with diabetes = increased risk of infection = increased risk to die
- 19. What connects us all
- 21. Data model
- 22. Example synonyms for gene „FOXA2“ obviously the synonyms of FOXA2 are not that obvious in our graph database query include all synonyms on gene, transcript and on protein level
- 23. Lung genes mentioned in papers
- 24. Lung genes mentioned in papers
- 25. How we visualize
- 27. Browsing patents
- 28. Our appeal data loader know-how user application Developer Researcher try out tool define use cases end user application support Content Provider provide access data Contact us via: https://covidgraph.org