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

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

5. 5
Photo: Retta Beery

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

10. 10
Sarah Olmstead
https://flic.kr/p/364dZW
NGLY1

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.

17. 17
http://www.navy.mil/management/photodb/photos/101104-N-6383T-508.jpg

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

21. 21
http://mark2cure.org

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

24. 24
http://mark2cure.org
Went live today!

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