The case for an open biomedical knowledgebase
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2017-02-27 TOKeN meeting @ Amazon Labs
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The case for an open biomedical knowledgebase
- 1. The case for an open biomedical knowledgebase Andrew Su, Ph.D. @andrewsu asu@scripps.edu http://sulab.org February 27, 2017 Slides: slideshare.net/andrewsu
- 2. Take-home #1 TOKeN is critical for biomedical research 2
- 3. The biomedical literature is massive… 3 0 200,000 400,000 600,000 800,000 1,000,000 1,200,000 1,400,000 1985 1990 1995 2000 2005 2010 2015 Number of new PubMed-indexed articles
- 4. … but it is very hard to query and compute 4
- 5. … but it is very hard to query and compute 5 Imatinib Crizotinib Erlotinib Gefitinib Sorafenib Lapatinib Dasatinib … Acute myeloid leukemia Acute lymphoblastic leukemia Chronic myelogenous leukemia Chronic lymphocytic leukemia Hodgkin lymphoma Non-Hodgkin lymphoma Myeloma … AND Gleevec Glivec STI-571 STI 571 STI571 ST1571 ST 1571 CGP-57148 CGP 57148 CGP57148 CGP57148B …
- 6. 6 Identified 517 operons and 103 small regulatory RNAs...
- 7. 7 A 35 page PDF!
- 8. Hyper-specialization… … and decreased synergies at the interfaces
- 9. Take-home #2 Wikidata is an outstanding community platform 9 #1: TOKeN is critical for biomedical research
- 10. Seeding Wikidata with biomedical data • All human, mouse genes and proteins (~175k items) • All FDA approved drugs (~2k items) • All human diseases from Disease Ontology (~7k items) • 120 reference microbial genomes Mitraka et al (2015) Semantic Web Applications for the Life Sciences Burgstaller-Muelbacher et al (2016) Database Putman et al (2016) Database
- 11. 11 “Show all operons present in Listeria monocytogenes.”
- 12. 12 The Stone Soup of Knowledge… HT: Jamie Taylor, The Stone Soup of Data, WWW2007
- 13. “Show all tyrosine kinase inhibitors that are used to treat hematologic cancers.”
- 14. “Show all monoclonal antibodies used to treat melanoma.”
- 15. “Show all human membrane proteins associated with colorectal cancer.”
- 16. Appealing to domain experts’ selfish motives 16
- 17. 17
- 18. Take-home #3 Drug repurposing is a promising application 18 #2: Wikidata is an outstanding community platform #1: TOKeN is critical for biomedical research
- 19. 19 “Repurposing generally refers to studying drugs that are already approved to treat one disease or condition to see if they are safe and effective for treating other diseases”.
- 20. Raynaud disease and fish oil 20 Raynaud disease
- 21. Raynaud disease and fish oil 21 Raynaud disease Fish oil / EPA Abnormal platelet activity Abnormal blood viscosity High blood viscosity Elevated RBC rigidity Vasodilation Low blood triglycerides Increased prostacyclins
- 22. Raynaud disease and fish oil 22
- 23. “Undiscovered public knowledge” 23 Raynaud disease Fish oil / EPA Abnormal platelet activity Abnormal blood viscosity High blood viscosity Elevated RBC rigidity Vasodilation Low blood triglycerides Increased prostacyclins A C B B B B B B B
- 24. Take-home #4 (Bonus) Data licensing is a massive obstacle 24
- 25. 25
- 26. 26 Collaborate on the Knowledgebase Compete on the Analyses