Citizen Science: Empowering the Public to Help Solve Biomedical - - PowerPoint PPT Presentation

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Citizen Science: Empowering the Public to Help Solve Biomedical - - PowerPoint PPT Presentation

Dec 20, 2022 140 likes •673 views

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

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Citizen Science: Empowering the Public to Help Solve Biomedical Challenges

September 10, 2020 Andrew Su, Ph.D. @andrewsu http://sulab.org

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Acknowledgements

Ginger Tsueng Benjamin Good Max Nanis Jennifer Fouquier Ricardo Avila Marco Cano Karthik Gangavarapu Paul Gaudin Andrea Hom Eric Hu Laura Hughes Janet Joy Mike Mayers Julia Mullen Zhongchao Qian Roger Tu Sabah Ul-Hasan Kevin Xin Colleen Xu Jerry Zhou Chunlei Wu

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A quick poll

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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.”

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Credit: The Eterna Project

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Phylo

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Credit: Alex Norton, Seung Lab, MIT

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What is Citizen Science?

CITIZEN SCIENCE

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Source: http://www.flickr.com/photos/bcmphoto/110887045/

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Source: http://www.flickr.com/photos/tsoumplekas/7248449256/

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Source: http://www.flickr.com/photos/inesnjers/9348711741/

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The biomedical literature is massive

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200,000 400,000 600,000 800,000 1,000,000 1,200,000 1,400,000 1,600,000 1985 1990 1995 2000 2005 2010 2015

Number of new PubMed-indexed articles

Over 30 million articles total in PubMed 1,392,836 new articles published in 2019

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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

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… 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.

Demo #1: Identifying the entities

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… 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. familial systemic mastocytosis

Demo #1: Identifying the entities

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… 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. familial systemic mastocytosis KIT

Demo #1: Identifying the entities

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… 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. familial systemic mastocytosis KIT Imatinib

Demo #1: Identifying the entities

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Demo #1: Instructions

For each of these entities …

familial systemic mastocytosis KIT Imatinib

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Demo #1: Instructions

For each of these entities … … select the entity type … GENE / PROTEIN DRUG / CHEMICAL DISEASE OTHER

familial systemic mastocytosis KIT Imatinib

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Demo #1: Instructions

For each of these entities … … select the entity type … … using this poll GENE / PROTEIN DRUG / CHEMICAL DISEASE OTHER

familial systemic mastocytosis KIT Imatinib

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GENE / PROTEIN DRUG / CHEMICAL DISEASE OTHER

Demo #1: Identifying the entities

familial systemic mastocytosis KIT Imatinib … 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.

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GENE / PROTEIN DRUG / CHEMICAL DISEASE OTHER

Demo #1: --- 30 seconds, GO! ---

familial systemic mastocytosis KIT Imatinib … 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.

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Demo #1: Results

familial systemic mastocytosis

DISEASE

is a KIT

GENE / PROTEIN

is a Imatinib

DRUG / CHEMICAL

is a

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Demo #2: Defining the relationships

… 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. KIT

GENE / PROTEIN How are these related?

  • Altered gene

expression causes

  • Mutation causes
  • Biomarker of
  • No relation

familial systemic mastocytosis

DISEASE

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Demo #2: Defining the relationships

How are these related?

  • Treats
  • Causes / exacerbates
  • Increases risk for
  • Prevents
  • No relation

Imatinib

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 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. KIT

GENE / PROTEIN How are these related?

  • Altered gene

expression causes

  • Mutation causes
  • Biomarker of
  • No relation

familial systemic mastocytosis

DISEASE

familial systemic mastocytosis

DISEASE

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familial systemic mastocytosis

DISEASE

Demo #2: Defining the relationships – 30 s --- GO! ---

How are these related?

  • Treats
  • Causes / exacerbates
  • Increases risk for
  • Prevents
  • No relation

Imatinib

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 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. KIT

GENE / PROTEIN How are these related?

  • Altered gene

expression causes

  • Mutation causes
  • Biomarker of
  • No relation

familial systemic mastocytosis

DISEASE

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imatinib KIT Familial systemic mastocytosis

Demo #2: Results

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Mutation causes treats

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PKC412 dasatinib K509I KIT Familial systemic mastocytosis

Demo #2: Results

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Mutation

  • f

Mutation causes causes treats inhibits

imatinib

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http://mark2cure.org

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A preliminary view of the NGLY1- focused co-occurrence network 3,200 documents 1,300 contributors 787,400 annotations

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“Why do you Mark2Cure?”

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

  • thers like me can receive more effective medical care.

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

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Mark2Cure community of Citizen Scientists

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

  • thers like me can receive more effective medical care.

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

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A preliminary view of the NGLY1- focused co-occurrence network 3,200 documents 1,300 contributors 787,400 annotations

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Goal: Assemble a network of biomedical knowledge that is comprehensive, current, and computable.

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Drug repurposing

… identifying and developing new uses for existing drugs

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Drug repurposing using knowledge graphs

DRUGS

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Drug repurposing using knowledge graphs

DRUGS DISEASES

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Drug repurposing using knowledge graphs

DRUGS

Genes, proteins, pathways, genetic variants, metabolites, …

DISEASES

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Drug repurposing using knowledge graphs

DRUGS

Genes, proteins, pathways, genetic variants, metabolites, …

DISEASES

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Drug repurposing using knowledge graphs

DRUGS

Genes, proteins, pathways, genetic variants, metabolites, …

DISEASES

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Drug repurposing using knowledge graphs

DRUGS

Genes, proteins, pathways, genetic variants, metabolites, …

DISEASES PREDICTIONS

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Drug repurposing using knowledge graphs

DRUGS

Genes, proteins, pathways, genetic variants, metabolites, …

DISEASES PREDICTIONS

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Drug repurposing using knowledge graphs

DRUGS

Genes, proteins, pathways, genetic variants, metabolites, …

DISEASES PREDICTIONS PEOPLE

Friends, Coworkers, Websites, Tweets/Updates, Apps, Movies, Music, Schools, Places, Car, …

PRODUCTS

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Knowledge graphs in high tech

https://www.microsoft.com/en-us/research/publication/model-ensemble-click-prediction-bing-search-ads/

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https://www.flickr.com/photos/castellersdevilafranca/39681358724

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How you can engage in research

Citizen Science Portals

  • www.citizenscience.gov
  • scistarter.org
  • zooniverse.org

Biomedical Citizen Science

  • crowd.cochrane.org – organize healthcare evidence
  • curate.outbreak.info – COVID-19 resources
  • eternagame.org – RNA folding
  • eyewire.org – 3D neuronal structure
  • foldit.it – protein folding
  • phylogame.org – sequence alignment
  • stallcatchers.com – Alzheimer’s disease
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