Citizen Science and Rare Disease Research
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This document summarizes how citizen science and crowdsourcing can help advance rare disease research. It describes two case studies of rare diseases, SPR and NGLY1, that were advanced through citizen science efforts. The document discusses how the biomedical literature is massive but difficult to query, and how citizen science can help extract and organize knowledge from texts through crowdsourced concept identification and relationship annotation. It presents results showing non-experts can identify disease concepts in texts with similar accuracy to experts. The document concludes by describing the Mark2Cure project, which has mapped biological networks around NGLY1 through crowdsourced annotations by over 1,200 contributors.
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Citizen Science and Rare Disease Research
- 1. Citizen Science and Rare Disease Research Andrew Su, Ph.D. @andrewsu asu@scripps.edu http://sulab.org September 22, 2016 Personalized Health in the Digital Age Symposium Slides: slideshare.net/andrewsu
- 4. Rare disease case study #1 4 Photo: Retta Beery
- 5. 5 Bainbridge et al., STM, 2011
- 7. Rare disease case study #2 7
- 8. 8 … but no obvious treatments
- 9. 9 Bainbridge et al., STM, 2011 SPR
- 10. What differentiates SPR and NGLY1? 10 SPR
- 12. 12 NGLY1 (11 PubMed articles) Congenital disorders of glycosylation (822) PNGase (686) ERAD (1330) glycosylation (48,862) alacrima (164) Genetic interactors (3016) symptoms (109,928) 25 million articles in PubMed
- 13. The biomedical literature is massive… 13 0 200,000 400,000 600,000 800,000 1,000,000 1,200,000 1983 1988 1993 1998 2003 2008 2013 Number of new PubMed-indexed articles
- 14. … but it is very hard to query and compute 14
- 15. … but it is very hard to query and compute 15 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
- 16. 16 Personalized medicine relies on effective PietroBellini https://flic.kr/p/k5jmja KNOWELDGE MANAGEMENT
- 17. Information extraction from biomedical text 17 1. Identify biomedical concepts in text … We report a case of familial systemic mastocytosis with the rare KIT K509I germ line mutation. In vitro treatment with imatinib, dasatinib and PKC412 reduced cell viability of primary mast cells harboring KIT K509I mutation. Both patients with familial systemic mastocytosis had remarkable hematological and skin improvement after three months of imatinib treatment. Leuk Res. 2014 Oct;38(10):1245-51. doi: 10.1016/j.leukres. GENES DISEASES DRUGS VARIANTS
- 18. Information extraction from biomedical text 18 imatinib dasatinib PKC412 Familial systemic mastocytosis KIT K509I 1. Identify biomedical concepts in text 2. Identify relationships between concepts Mutation of Mutation causes causes treats inhibits
- 19. 19 Goal: Assemble a network of biomedical knowledge that is comprehensive, current, computable and traceable.
- 21. 21 Crowdsourcing
- 22. is to data is to text biomedical Provide a database of the world’s knowledge that anyone can edit - Denny Vrandečić
- 23. 23
- 24. Subclass of Regulates Physically interacts with Protein Neural development Property:P279 Property:P128 Property:P129 Q8054 Q1345738 VLDL receptor Q1979313 Amyloid beta A4 Q423510 Q13561329 http://www.wikidata.org/wiki/Q13561329 Decreased expression in Property:P1910 Schizophrenia Q41112 Bipolar disorder Q131755
- 26. We are seeding it with biomedical data • All human, mouse genes and proteins • All Gene Ontology terms • All FDA approved drugs • 9,000+ human diseases • 120 reference microbial genomes Burgstaller et al (2016) Database (preprint in BioRxiv) Mitraka et al (2015) Semantic Web Applications for the Life Sciences (best paper) (preprint in BioRxiv) Putman et al (2016) Database (preprint in BioRxiv)
- 27. Inter-item links form a giant knowledge graph Everything is connected Reelin, Heart disease, Barack Obama, everything.. https://query.wikidata.org SPARQL endpoint for Wikidata
- 28. 28 Crowdsourcing
- 29. Question: Can a group of non-scientists collectively perform concept recognition in biomedical texts? 29
- 30. 30 Experts versus crowd for concept identification 593 PubMed abstracts 6,900 mentions of “disease concepts” F = 0.87F = 0.78 $$$
- 31. 31 Experts versus crowd for concept identification 593 PubMed abstracts 6,900 mentions of “disease concepts” F = 0.87F = 0.87 $$$ • 9 days • 145 workers • Total: $630.96
- 33. 33 Paid crowdsourcing • F = 0.84 • 28 days • 212 workers • Total cost: $0 $$$ • F = 0.87 • 9 days • 145 workers • Total: $630.96 “Help science, please” Citizen Science
- 34. Mapping the biomedical network around NGLY1 34 NGLY1
- 36. 36 A preliminary view of the NGLY1- focused biological network 1,200 contributors 3,200 documents 787,400 annotations
- 37. 37 Personalized medicine relies on effective PietroBellini https://flic.kr/p/k5jmja KNOWELDGE MANAGEMENT
- 38. 38 If I have seen further than others, it is by standing on the shoulders of giants. - Sir Isaac Newton
- 39. 39 Jake Bruggeman Karthik G Ramya Gamini Louis Gioia Toby Li Greg Stupp Other group members Funding and Support BioGPS: GM83924 Gene Wiki: GM089820 BD2K COE: GM114833 Contact http://sulab.org asu@scripps.edu @andrewsu Mark2Cure Jennifer Fouquier Max Nanis Ginger Tsueng AMT volunteers and Mark2Curators! Slides: slideshare.net/andrewsu Icon credits (Noun Project, Wikimedia Commons): Zach VanDeHey, hunotika, Viktorvoigt, Alberto Rojas, Lloyd Humphreys Matt and Cristina Might NGLY1 community Gene Wiki Ben Good Sebastian Burgstaller Tim Putman Núria Queralt Rosinach Julia Turner Andra Waagmeester BioThings API Chunlei Wu Julee Adesara Cyrus Afrasiabi Sebastien Lelong Mike Mayers Kevin Xin
- 40. Why do I Mark2Cure? 40 I am retired, have a doctorate in medical humanities, and have two children with Gaucher disease. I am just looking for some way to put my education to use. My 4 year old daughter Phoebe is living with and battling rare disease. I have Ehlers Danlos Syndrome. I hope to help people learn about this painful and debilitating disorder, so that others like me can receive more effective medical care. Take part in something that helps humanity. I Mark2Cure in memory of my son Mike who had type 1 diabetes. Studied biology in college and I really miss it! In memory of my daughter who had Cystic Fibrosis Give back