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@andrewsu
asu@scripps.edu
http://sulab.org
The Heart BD2K Team
Henning
Hermjakob
EMBL-EBI
Andrew Su
TSRI
Karol Watson
UCLA...
Heart BD2K Center
http://heartbd2k.org
Cardiovascular
biology
(Prote)omics
profiling
Community
science
2
Community infrast...
Rare disease case study #1
3
Photo: Retta Beery
4
Bainbridge et al., STM, 2011
5
Photo: Retta Beery
Rare disease case study #2
6
7
… but no obvious treatments
8
Bainbridge et al., STM, 2011
SPR
What differentiates SPR and NGLY1?
9
SPR
10
Sarah Olmstead
https://flic.kr/p/364dZW
NGLY1
11
NGLY1
(11 PubMed articles)
Congenital disorders of
glycosylation
(822)
PNGase
(686)
ERAD
(1330)
glycosylation
(48,862)
...
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 a...
13
The biomedical literature is
Pietro Bellini
https://flic.kr/p/k5jmja
BIG DATA
Information extraction from biomedical text
14
1. Identify biomedical concepts in text
… We report a case of familial syst...
Information extraction from biomedical text
15
imatinib
dasatinib
PKC412
Familial systemic
mastocytosis
KIT
K509I
1. Ident...
16
Goal: Assemble a network of biomedical
knowledge that is comprehensive,
current, computable and traceable.
17
http://www.navy.mil/management/photodb/photos/101104-N-6383T-508.jpg
Question: Can a group of non-scientists
collectively perform concept recognition in
biomedical texts?
18
19
Experts versus crowd for concept identification
593 PubMed abstracts
6,900 mentions of
“disease concepts”
F = 0.87F = 0...
20
Experts versus crowd for concept identification
593 PubMed abstracts
6,900 mentions of
“disease concepts”
F = 0.87F = 0...
21
http://mark2cure.org
22
Paid crowdsourcing
• F = 0.84
• 28 days
• 212 workers
• Total cost: $0
$$$
• F = 0.87
• 9 days
• 145 workers
• Total: $...
Mapping the biomedical network around NGLY1
23
NGLY1
24
http://mark2cure.org
Went live today!
25
Cyrus Afrasiabi
Sebastian Burgstaller
Ramya Gamini
Louis Gioia
Toby Li
Salvatore Loguercio
Adam Mark
Erick Scott
Greg S...
Why do I Mark2Cure?
26
I am retired, have a doctorate in
medical humanities, and have two
children with Gaucher disease. I...
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Heart BD2K, Biocuration, and Citizen Science

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Talk given at Big Data in Biomedicine Conference May 21, 2015.

Published in: Science
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Heart BD2K, Biocuration, and Citizen Science

  1. 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. 2. Heart BD2K Center http://heartbd2k.org Cardiovascular biology (Prote)omics profiling Community science 2 Community infrastructure
  3. 3. Rare disease case study #1 3 Photo: Retta Beery
  4. 4. 4 Bainbridge et al., STM, 2011
  5. 5. 5 Photo: Retta Beery
  6. 6. Rare disease case study #2 6
  7. 7. 7 … but no obvious treatments
  8. 8. 8 Bainbridge et al., STM, 2011 SPR
  9. 9. What differentiates SPR and NGLY1? 9 SPR
  10. 10. 10 Sarah Olmstead https://flic.kr/p/364dZW NGLY1
  11. 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. 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. 13 The biomedical literature is Pietro Bellini https://flic.kr/p/k5jmja BIG DATA
  14. 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. 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. 16 Goal: Assemble a network of biomedical knowledge that is comprehensive, current, computable and traceable.
  17. 17. 17 http://www.navy.mil/management/photodb/photos/101104-N-6383T-508.jpg
  18. 18. Question: Can a group of non-scientists collectively perform concept recognition in biomedical texts? 18
  19. 19. 19 Experts versus crowd for concept identification 593 PubMed abstracts 6,900 mentions of “disease concepts” F = 0.87F = 0.78 $$$
  20. 20. 20 Experts versus crowd for concept identification 593 PubMed abstracts 6,900 mentions of “disease concepts” F = 0.87F = 0.87 $$$ • 9 days • 145 workers • Total: $630.96
  21. 21. 21 http://mark2cure.org
  22. 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. 23. Mapping the biomedical network around NGLY1 23 NGLY1
  24. 24. 24 http://mark2cure.org Went live today!
  25. 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. 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

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