Centralized Model Organism Database (Biocuration 2014 poster)
Heart BD2K, Biocuration, and Citizen Science
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@andrewsu [email protected] http:// sulab.org The Heart BD2K Team Henning Hermjakob EMBL-EBI Andrew Su TSRI Karol Watson UCLA Merry Lindsey UMMC Peipei Ping UCLA
Transcript of Heart BD2K, Biocuration, and Citizen Science
@andrewsu
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
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Bainbridge et al., STM, 2011
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Photo: Retta Beery
Rare disease case study #26
7
… but no obvious treatments
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Bainbridge et al., STM, 2011
SPR
What differentiates SPR and NGLY1?9
SPR
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Sarah Olmsteadhttps://flic.kr/p/364dZW
NGLY1
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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
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0
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1,000,000
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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
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Goal: Assemble a network of biomedical knowledge that is comprehensive, current, computable and traceable.
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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?
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Experts versus crowd for concept identification
593 PubMed abstracts
6,900 mentions of “disease concepts”
F = 0.87F = 0.78
$$$
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Experts versus crowd for concept identification
593 PubMed abstracts
6,900 mentions of “disease concepts”
F = 0.87F = 0.87
$$$
• 9 days• 145 workers• Total: $630.96
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http://mark2cure.org
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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
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http://mark2cure.org
Went live today!
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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
[email protected]@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
