Heart BD2K, Biocuration, and Citizen Science
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This document provides information about the Heart BD2K Center and its efforts to map the biomedical network around the rare disease NGLY1. It discusses using crowdsourcing techniques like paid crowdsourcing platforms and citizen science to perform biomedical concept recognition and information extraction from literature. The document also introduces the Mark2Cure project, a new citizen science platform for mapping disease networks that went live on the day this presentation was given. Finally, it shares brief statements from some Mark2Cure volunteers on why they participate in citizen science initiatives.
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Heart BD2K, Biocuration, and Citizen Science
- 1. @andrewsu asu@scripps.edu http://sulab.org The Heart BD2K Team Henning Hermjakob EMBL-EBI Andrew Su TSRI Karol Watson UCLA Merry Lindsey UMMC Peipei Ping UCLA
- 2. Heart BD2K Center http://heartbd2k.org Cardiovascular biology (Prote)omics profiling Community science 2 Community infrastructure
- 3. Rare disease case study #1 3 Photo: Retta Beery
- 4. 4 Bainbridge et al., STM, 2011
- 6. Rare disease case study #2 6
- 7. 7 … but no obvious treatments
- 8. 8 Bainbridge et al., STM, 2011 SPR
- 9. What differentiates SPR and NGLY1? 9 SPR
- 11. 11 NGLY1 (11 PubMed articles) Congenital disorders of glycosylation (822) PNGase (686) ERAD (1330) glycosylation (48,862) alacrima (164) Genetic interactors (3016) symptoms (109,928) 24 million articles in PubMed
- 12. 12 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
- 13. 13 The biomedical literature is Pietro Bellini https://flic.kr/p/k5jmja BIG DATA
- 14. Information extraction from biomedical text 14 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
- 15. Information extraction from biomedical text 15 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
- 16. 16 Goal: Assemble a network of biomedical knowledge that is comprehensive, current, computable and traceable.
- 18. Question: Can a group of non-scientists collectively perform concept recognition in biomedical texts? 18
- 19. 19 Experts versus crowd for concept identification 593 PubMed abstracts 6,900 mentions of “disease concepts” F = 0.87F = 0.78 $$$
- 20. 20 Experts versus crowd for concept identification 593 PubMed abstracts 6,900 mentions of “disease concepts” F = 0.87F = 0.87 $$$ • 9 days • 145 workers • Total: $630.96
- 22. 22 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
- 23. Mapping the biomedical network around NGLY1 23 NGLY1
- 25. 25 Cyrus Afrasiabi Sebastian Burgstaller Ramya Gamini Louis Gioia Toby Li Salvatore Loguercio Adam Mark Erick Scott Greg Stupp Kevin Xin Other Group members Funding and Support BioGPS: GM83924 Gene Wiki: GM089820 BD2K COE: GM114833 Contact http://sulab.org asu@scripps.edu @andrewsu Mark2Cure Max Nanis Ginger Tsueng Ben Good Chunlei Wu All Mark2Curators! We are recruiting, join the team! http://bit.ly/JoinSuLab Slides: slideshare.net/andrewsu Icon credits (Noun Project, Wikimedia Commons): Zach VanDeHey, hunotika, Viktorvoigt, Alberto Rojas, Lloyd Humphreys Matt and Cristina Might NGLY1 community
- 26. Why do I Mark2Cure? 26 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