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HealthECCO: Bringing the world’s health knowledge to research and medical decision makers

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HealthECCO: Bringing the world’s health knowledge to research and medical decision makers

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Martin Preusse, Kaiser&Preusse
Neo4j Health Care & Life Sciences Workshop 2021

Transcript

  1. 1. Bringing the world’s health knowledge to research and medical decision makers.
  2. 2. The beginning of CovidGraph in March2020 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
  3. 3. Who we are
  4. 4. Bring knowledge to…
  5. 5. Cope not only with literature, but also genes, proteins, diseases,… 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 128’000 texts on only Covid-19 in the 6 month
  6. 6. 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? Humans think in graphs
  7. 7. mentioned mentioned is Keyword is is Lung Protein
 Y Gene
 X Covid19 Disease Disease Publication A Study encodes Extend our knowledge And we help by bringing the pieces together
  8. 8. mentioned mentioned is Keyword is h a s c l i n i c a l s t u d y is Covid19 Protein
 Y Gene
 X Covid19 Disease Disease Publication A Study encodes Millions of connections
  9. 9. has synonyms has synonyms t r a n s c r i b e d t r a n s l a t e d mentioned Protein
 Y Gene
 X encodes Metabolite
 M Transcript
 Z SNP
 K
  10. 10. has synonyms has synonyms t r a n s c r i b e d t r a n s l a t e d mentioned mentioned m entioned in is i s b i o m a r k e r is Covid19 Protein
 Y Gene
 X Diabetes Disease Disease HbA1c encodes Metabolite
 M Transcript
 Z SNP
 K Publication
 1 Publication
 2 Publication
 31 Publication
 5430 Patent
 WOxxx Patent
 WOxxx Patent
 WOxxx
  11. 11. Data sources and numbers A U T H O R _ H A S _ A F F I L I A T I O N AUTHORCOLLECTION_HAS_AUT… B O D Y T E X T C O L L E C T I O N _ H A S … ABSTRACTCOLLECTION_HAS_ABSTRA… R E F E R E N C E C O L L E C T IO N _ H A S _ R E … BODYTEXT_HAS_CITATION PAPER_HAS_REFERENCECOLLECTI… C I T A T I O N _ H A S _ R E F E R E N … ABSTRACT_HAS_CITATION AFFILIAT ION_HAS _LOCAT ION Abstract Affiliation Author BodyText Citation Location Paper Reference HAS_FRAGMENT HAS_FRAGMENT H A S _ F R A G M E N T MENTIONS HAS_FRAGMENT HAS_FRAGMENT H A S _ F R A G M E N T Sentence PATENT_HAS_PATENTABSTRACT APPLICANT PAT ENT _HA S_P ATE NTN UMB ER PATENT_HAS_PATENTTITLE PATENT_HAS_PATENTDE… P A T E N T _ H A S _ P A T E N T C L A I M Entity Patent PatentAbstract PatentClaim PatentDescripti… PatentNumber PatentTitle SYNONYM M A P S MAPS MAPS MAPS CODES CODES Gene GeneSymbol Protein Transcript ASSOCIAT ION PART_OF M E M B E R GOTerm Pathway E X P R E S S E D GtexTissue CURRENT_TOTAL REPORTED LOCATED_IN LOCATED_IN P A R T _ O F AgeGroup City Country DailyReport Province HAS_EXCLUSION_CRITERIA IS_PHASE CONDUCTED_AT P U B L I S H E D HAS_INCLUSION_CRITERIA ClinicalTrial ExclusionCriteria Facility InclusionCriteria Phase 144’000 32’000 125’000 128’000 410’000 484’000 1700 55 21’000 47’000 30’000’000
  12. 12. Angiotensin-converting enzyme 2 GENE_OR_GENOME ( ACE2 GENE_OR_GENOME ) as a SARS-CoV-2 CORONAVIRUS receptor: molecular mechanisms and potential therapeutic target. SARS-CoV-2 CORONAVIRUS has been sequenced [3 CARDINAL]. A phylogenetic analysis [3 CARDINAL, 4 CARDINAL] found a bat WILDLIFE origin for the SARS-CoV-2 CORONAVIRUS. There is a diversity of possible intermediate hosts for SARS-CoV-2 CORONAVIRUS, including pangolins WILDLIFE, but not mice EUKARYOTE and rats EUKARYOTE [5 CARDINAL]. There are many similarities of SARS-CoV-2 CORONAVIRUS with the original SARS-CoV CORONAVIRUS. Using computer modeling, Xu et al. [6 CARDINAL] found that the spike proteins GENE_OR_GENOME of SARS-CoV-2 CORONAVIRUS and SARS-CoV CORONAVIRUS have almost identical 3-D structures in the receptor-binding domain that maintains van der Waals forces PHYSICAL_SCIENCE. SARS-CoV CORONAVIRUS spike protein has a strong binding affinity to human ACE2 GENE_OR_GENOME, based on biochemical interaction studies and crystal structure analysis [7 CARDINAL]. SARS-CoV-2 CORONAVIRUS and SARS-CoV spike proteins GENE_OR_GENOME share 76.5% identity in amino acid sequences NLP - we transform text into knowledge
  13. 13. How you can access it https://db.covidgraph.org/semspect https://db.covidgraph.org/browser https://db.covidgraph.org/browser/bloom https://live.yworks.com/covidgraph
  14. 14. use case 1 ”Find the most relevant gene”
  15. 15. GDS library - page rank - find the most relevant gene finding ACE2 - the receptor the SARS-Cov2 virus uses to enter the cell Interactive Scalable Semi-natural language query Especially for
 non-computer scientists
  16. 16. Who’s this ACE2-guy? source: https://www.benaroyaresearch.org/blog/post/11-things-know-about-mrna-vaccines-covid-19
  17. 17. SysBio model for “ACE2”?
  18. 18. use case 2 ”Freedom-to-operate on hemostasis”
  19. 19. Browse patent landscape for 'hemostasis' and Covid-19
  20. 20. From pathway to patents to sysbio-model in 30s clicking or 0.2s by query
  21. 21. use case 3 ”Sentiment analysis of press releases can yield information on how drugs / vaccines work”
  22. 22. Sentiment of press release positive negative neutral Publisher Drug
  23. 23. Remdesivir Hydroxy-chloroquine drugs press texts with sen9ment (posi9ve/neutral/nega9ve) Meltwater's sentiment analysis to analyze press releases on clinical trials

Description

Martin Preusse, Kaiser&Preusse
Neo4j Health Care & Life Sciences Workshop 2021

Transcript

  1. 1. Bringing the world’s health knowledge to research and medical decision makers.
  2. 2. The beginning of CovidGraph in March2020 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
  3. 3. Who we are
  4. 4. Bring knowledge to…
  5. 5. Cope not only with literature, but also genes, proteins, diseases,… 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 128’000 texts on only Covid-19 in the 6 month
  6. 6. 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? Humans think in graphs
  7. 7. mentioned mentioned is Keyword is is Lung Protein
 Y Gene
 X Covid19 Disease Disease Publication A Study encodes Extend our knowledge And we help by bringing the pieces together
  8. 8. mentioned mentioned is Keyword is h a s c l i n i c a l s t u d y is Covid19 Protein
 Y Gene
 X Covid19 Disease Disease Publication A Study encodes Millions of connections
  9. 9. has synonyms has synonyms t r a n s c r i b e d t r a n s l a t e d mentioned Protein
 Y Gene
 X encodes Metabolite
 M Transcript
 Z SNP
 K
  10. 10. has synonyms has synonyms t r a n s c r i b e d t r a n s l a t e d mentioned mentioned m entioned in is i s b i o m a r k e r is Covid19 Protein
 Y Gene
 X Diabetes Disease Disease HbA1c encodes Metabolite
 M Transcript
 Z SNP
 K Publication
 1 Publication
 2 Publication
 31 Publication
 5430 Patent
 WOxxx Patent
 WOxxx Patent
 WOxxx
  11. 11. Data sources and numbers A U T H O R _ H A S _ A F F I L I A T I O N AUTHORCOLLECTION_HAS_AUT… B O D Y T E X T C O L L E C T I O N _ H A S … ABSTRACTCOLLECTION_HAS_ABSTRA… R E F E R E N C E C O L L E C T IO N _ H A S _ R E … BODYTEXT_HAS_CITATION PAPER_HAS_REFERENCECOLLECTI… C I T A T I O N _ H A S _ R E F E R E N … ABSTRACT_HAS_CITATION AFFILIAT ION_HAS _LOCAT ION Abstract Affiliation Author BodyText Citation Location Paper Reference HAS_FRAGMENT HAS_FRAGMENT H A S _ F R A G M E N T MENTIONS HAS_FRAGMENT HAS_FRAGMENT H A S _ F R A G M E N T Sentence PATENT_HAS_PATENTABSTRACT APPLICANT PAT ENT _HA S_P ATE NTN UMB ER PATENT_HAS_PATENTTITLE PATENT_HAS_PATENTDE… P A T E N T _ H A S _ P A T E N T C L A I M Entity Patent PatentAbstract PatentClaim PatentDescripti… PatentNumber PatentTitle SYNONYM M A P S MAPS MAPS MAPS CODES CODES Gene GeneSymbol Protein Transcript ASSOCIAT ION PART_OF M E M B E R GOTerm Pathway E X P R E S S E D GtexTissue CURRENT_TOTAL REPORTED LOCATED_IN LOCATED_IN P A R T _ O F AgeGroup City Country DailyReport Province HAS_EXCLUSION_CRITERIA IS_PHASE CONDUCTED_AT P U B L I S H E D HAS_INCLUSION_CRITERIA ClinicalTrial ExclusionCriteria Facility InclusionCriteria Phase 144’000 32’000 125’000 128’000 410’000 484’000 1700 55 21’000 47’000 30’000’000
  12. 12. Angiotensin-converting enzyme 2 GENE_OR_GENOME ( ACE2 GENE_OR_GENOME ) as a SARS-CoV-2 CORONAVIRUS receptor: molecular mechanisms and potential therapeutic target. SARS-CoV-2 CORONAVIRUS has been sequenced [3 CARDINAL]. A phylogenetic analysis [3 CARDINAL, 4 CARDINAL] found a bat WILDLIFE origin for the SARS-CoV-2 CORONAVIRUS. There is a diversity of possible intermediate hosts for SARS-CoV-2 CORONAVIRUS, including pangolins WILDLIFE, but not mice EUKARYOTE and rats EUKARYOTE [5 CARDINAL]. There are many similarities of SARS-CoV-2 CORONAVIRUS with the original SARS-CoV CORONAVIRUS. Using computer modeling, Xu et al. [6 CARDINAL] found that the spike proteins GENE_OR_GENOME of SARS-CoV-2 CORONAVIRUS and SARS-CoV CORONAVIRUS have almost identical 3-D structures in the receptor-binding domain that maintains van der Waals forces PHYSICAL_SCIENCE. SARS-CoV CORONAVIRUS spike protein has a strong binding affinity to human ACE2 GENE_OR_GENOME, based on biochemical interaction studies and crystal structure analysis [7 CARDINAL]. SARS-CoV-2 CORONAVIRUS and SARS-CoV spike proteins GENE_OR_GENOME share 76.5% identity in amino acid sequences NLP - we transform text into knowledge
  13. 13. How you can access it https://db.covidgraph.org/semspect https://db.covidgraph.org/browser https://db.covidgraph.org/browser/bloom https://live.yworks.com/covidgraph
  14. 14. use case 1 ”Find the most relevant gene”
  15. 15. GDS library - page rank - find the most relevant gene finding ACE2 - the receptor the SARS-Cov2 virus uses to enter the cell Interactive Scalable Semi-natural language query Especially for
 non-computer scientists
  16. 16. Who’s this ACE2-guy? source: https://www.benaroyaresearch.org/blog/post/11-things-know-about-mrna-vaccines-covid-19
  17. 17. SysBio model for “ACE2”?
  18. 18. use case 2 ”Freedom-to-operate on hemostasis”
  19. 19. Browse patent landscape for 'hemostasis' and Covid-19
  20. 20. From pathway to patents to sysbio-model in 30s clicking or 0.2s by query
  21. 21. use case 3 ”Sentiment analysis of press releases can yield information on how drugs / vaccines work”
  22. 22. Sentiment of press release positive negative neutral Publisher Drug
  23. 23. Remdesivir Hydroxy-chloroquine drugs press texts with sen9ment (posi9ve/neutral/nega9ve) Meltwater's sentiment analysis to analyze press releases on clinical trials

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