Citizen Science: Empowering the Public to Help Solve Biomedical Challenges Andrew Su, Ph.D. @andrewsu http://sulab.org September 10, 2020 1
Acknowledgements Ricardo Avila Marco Cano Max Nanis Karthik Gangavarapu Paul Gaudin Andrea Hom Chunlei Wu Eric Hu Laura Hughes Janet Joy Jennifer Mike Mayers Fouquier Ginger Tsueng Benjamin Good Julia Mullen Zhongchao Qian Roger Tu Sabah Ul-Hasan Kevin Xin Colleen Xu Jerry Zhou 2
A quick poll 3
4 https://www.sdss.org/science/m51/
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https://www.zooniverse.org/projects/zookeeper/galaxy-zoo/about/results “…within 24 hours of launch we were stunned to be receiving almost 70,000 classifications an hour . In the end, more than 50 million classifications were received by the project during its first year, contributed by more than 150,000 people .” 6
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8 Credit: The Eterna Project
Phylo 9
10 Credit: Alex Norton, Seung Lab, MIT
What is Citizen Science? CITIZEN SCIENCE 11
Source: http://www.flickr.com/photos/bcmphoto/110887045/ 12
Source: http://www.flickr.com/photos/tsoumplekas/7248449256/ 13
14 Source: http://www.flickr.com/photos/inesnjers/9348711741/
15 The biomedical literature is massive Number of new PubMed-indexed articles 1,600,000 1,400,000 1,200,000 1,392,836 new articles 1,000,000 published in 2019 800,000 600,000 400,000 200,000 0 1985 1990 1995 2000 2005 2010 2015 Over 30 million articles total in PubMed 15
Citizen Science Demo • Participate only if your day job does NOT include biomedical research • We will read a bit of text together, and a zoom poll will ask you a series of questions • Answer based only on what the text says, not what is “true” • Don’t worry too much about being sure – make your best guess within the allotted time 16
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Demo #1: Identifying the entities … 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. 19
Demo #1: Identifying the entities … We report a case of familial systemic mastocytosis with the rare KIT K509I familial systemic germ line mutation. In vitro treatment mastocytosis 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. 20
Demo #1: Identifying the entities … We report a case of familial systemic mastocytosis with the rare KIT K509I familial systemic germ line mutation. In vitro treatment mastocytosis with imatinib, dasatinib and PKC412 reduced cell viability of primary mast cells harboring KIT K509I mutation. Both patients with familial systemic KIT mastocytosis had remarkable hematological and skin improvement after three months of imatinib treatment. 21
Demo #1: Identifying the entities … We report a case of familial systemic mastocytosis with the rare KIT K509I familial systemic germ line mutation. In vitro treatment mastocytosis with imatinib, dasatinib and PKC412 reduced cell viability of primary mast cells harboring KIT K509I mutation. Both patients with familial systemic KIT mastocytosis had remarkable hematological and skin improvement after three months of imatinib Imatinib treatment. 22
Demo #1: Instructions For each of these entities … familial systemic mastocytosis KIT Imatinib 23
Demo #1: Instructions For each of these … select the entities … entity type … GENE / PROTEIN familial systemic mastocytosis DRUG / CHEMICAL KIT DISEASE Imatinib OTHER 24
Demo #1: Instructions For each of these … select the … using this poll entities … entity type … GENE / PROTEIN familial systemic mastocytosis DRUG / CHEMICAL KIT DISEASE Imatinib OTHER 25
Demo #1: Identifying the entities … We report a case of familial systemic mastocytosis with the rare KIT K509I GENE / PROTEIN familial systemic germ line mutation. In vitro treatment mastocytosis with imatinib, dasatinib and PKC412 reduced cell viability of primary mast DRUG / CHEMICAL cells harboring KIT K509I mutation. Both patients with familial systemic KIT mastocytosis had remarkable DISEASE hematological and skin improvement after three months of imatinib Imatinib treatment. OTHER 26
Demo #1: --- 30 seconds, GO! --- … We report a case of familial systemic mastocytosis with the rare KIT K509I GENE / PROTEIN familial systemic germ line mutation. In vitro treatment mastocytosis with imatinib, dasatinib and PKC412 reduced cell viability of primary mast DRUG / CHEMICAL cells harboring KIT K509I mutation. Both patients with familial systemic KIT mastocytosis had remarkable DISEASE hematological and skin improvement after three months of imatinib Imatinib treatment. OTHER 27
Demo #1: Results familial systemic is a DISEASE mastocytosis KIT is a GENE / PROTEIN Imatinib is a DRUG / CHEMICAL 28
Demo #2: Defining the relationships KIT GENE / PROTEIN … We report a case of familial systemic mastocytosis with the rare KIT K509I germ line mutation. In vitro treatment with imatinib, dasatinib and PKC412 How are these related? reduced cell viability of primary mast Altered gene • cells harboring KIT K509I mutation. expression causes Mutation causes Both patients with familial systemic • Biomarker of • mastocytosis had remarkable No relation • hematological and skin improvement after three months of imatinib treatment. familial systemic mastocytosis DISEASE 29
Demo #2: Defining the relationships KIT Imatinib GENE / PROTEIN DRUG / CHEMICAL … We report a case of familial systemic mastocytosis with the rare KIT K509I germ line mutation. In vitro treatment with imatinib, dasatinib and PKC412 How are these related? How are these related? reduced cell viability of primary mast Altered gene • Treats • cells harboring KIT K509I mutation. expression causes Causes / exacerbates • Mutation causes Both patients with familial systemic • Increases risk for • Biomarker of • mastocytosis had remarkable Prevents • No relation • No relation hematological and skin improvement • after three months of imatinib treatment. familial systemic familial systemic mastocytosis mastocytosis DISEASE DISEASE 30
Demo #2: Defining the relationships – 30 s --- GO! --- KIT Imatinib GENE / PROTEIN DRUG / CHEMICAL … We report a case of familial systemic mastocytosis with the rare KIT K509I germ line mutation. In vitro treatment with imatinib, dasatinib and PKC412 How are these related? How are these related? reduced cell viability of primary mast Altered gene • Treats • cells harboring KIT K509I mutation. expression causes Causes / exacerbates • Mutation causes Both patients with familial systemic • Increases risk for • Biomarker of • mastocytosis had remarkable Prevents • No relation • No relation hematological and skin improvement • after three months of imatinib treatment. familial systemic familial systemic mastocytosis mastocytosis DISEASE DISEASE 31
32 Demo #2: Results KIT imatinib Mutation treats causes Familial systemic mastocytosis 32
33 Demo #2: Results inhibits KIT imatinib Mutation treats causes Mutation Familial systemic of dasatinib mastocytosis PKC412 causes K509I 33
http://mark2cure.org 34
A preliminary view of the NGLY1- focused co-occurrence network 3,200 documents 1,300 contributors 787,400 annotations 35
“Why do you Mark2Cure?” I am retired, have a doctorate in In memory of my daughter who medical humanities, and have two had Cystic Fibrosis children with Gaucher disease. I am just looking for some way to put my Studied biology in college education to use. and I really miss it! Give back My 4 year old daughter Phoebe is living with and I Mark2Cure in memory of my son Mike who had type 1 diabetes. 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. 36
Mark2Cure community of Citizen Scientists I am retired, have a doctorate in In memory of my daughter who medical humanities, and have two had Cystic Fibrosis children with Gaucher disease. I am just looking for some way to put my Studied biology in college education to use. and I really miss it! Give back My 4 year old daughter Phoebe is living with and I Mark2Cure in memory of my son Mike who had type 1 diabetes. 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. 37
A preliminary view of the NGLY1- focused co-occurrence network 3,200 documents 1,300 contributors 787,400 annotations 38
Goal : Assemble a network of biomedical knowledge that is comprehensive, current, and computable. 39
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