heart bd2k, biocuration, and citizen science

@andrewsu

asu@scripps.edu

http://sulab.org

The Heart BD2K Team

Henning Hermjakob

EMBL-EBI

Andrew Su

TSRIKarol Watson

UCLAMerry Lindsey

UMMCPeipei Ping

UCLA

Heart BD2K Centerhttp://heartbd2k.org

Cardiovascular biology

(Prote)omics profiling

Community science

2

Community infrastructure

Rare disease case study #13

Photo: Retta Beery

4

Bainbridge et al., STM, 2011

5

Photo: Retta Beery

Rare disease case study #26

7

… but no obvious treatments

8

Bainbridge et al., STM, 2011

SPR

What differentiates SPR and NGLY1?9

SPR

10

Sarah Olmsteadhttps://flic.kr/p/364dZW

NGLY1

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

1983

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0

200,000

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1,000,000

1,200,000

Number of new PubMed-indexed articles

13

The biomedical literature is

Pietro Bellinihttps://flic.kr/p/k5jmja

BIG DATA

Information extraction from biomedical text14

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

Information extraction from biomedical text15

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

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

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Experts versus crowd for concept identification

593 PubMed abstracts

6,900 mentions of “disease concepts”

F = 0.87F = 0.78

$$$

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

http://mark2cure.org

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

Mapping the biomedical network around NGLY1 23

NGLY1

24

http://mark2cure.org

Went live today!

25

Cyrus AfrasiabiSebastian BurgstallerRamya GaminiLouis GioiaToby Li

Salvatore LoguercioAdam MarkErick ScottGreg StuppKevin Xin

Other Group members

Funding and Support

BioGPS: GM83924Gene Wiki: GM089820BD2K COE: GM114833

Contacthttp://sulab.org

asu@scripps.edu@andrewsu

Mark2Cure

Max NanisGinger Tsueng

Ben GoodChunlei Wu

All Mark2Curators!

We are recruiting, join the team!

http://bit.ly/JoinSuLab

Slides: slideshare.net/andrewsuIcon credits (Noun Project, Wikimedia Commons): Zach VanDeHey, hunotika, Viktorvoigt, Alberto Rojas, Lloyd Humphreys

Matt and Cristina MightNGLY1 community

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