Open biomedical knowledge using crowdsourcing and citizen science
The case for an open biomedical knowledgebase
Transcript of The case for an open biomedical knowledgebase
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The case for an open biomedical knowledgebase
Andrew Su, Ph.D.@[email protected]://sulab.org
February 27, 2017
Slides: slideshare.net/andrewsu
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Take-home #1
TOKeN is critical for biomedical research
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The biomedical literature is massive…3
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1,000,0001,200,0001,400,000
Number of new PubMed-indexed articles
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… but it is very hard to query and compute4
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… but it is very hard to query and compute5
ImatinibCrizotinibErlotinibGefitinibSorafenibLapatinibDasatinib
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Acute myeloid leukemiaAcute lymphoblastic leukemia
Chronic myelogenous leukemiaChronic lymphocytic leukemia
Hodgkin lymphomaNon-Hodgkin lymphoma
Myeloma…
AND
GleevecGlivecSTI-571STI 571STI571ST1571ST 1571CGP-57148CGP 57148CGP57148CGP57148B…
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Identified 517 operons and 103 small regulatory RNAs...
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A 35 page PDF!
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Hyper-specialization…
… and decreased synergies at the interfaces
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Take-home #2
Wikidata is an outstanding community platform
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#1: TOKeN is critical for biomedical research
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Seeding Wikidata with biomedical data
• All human, mouse genes and proteins (~175k items)
• All FDA approved drugs (~2k items)• All human diseases from Disease
Ontology (~7k items)• 120 reference microbial genomes
Mitraka et al (2015) Semantic Web Applications for the Life SciencesBurgstaller-Muelbacher et al (2016) DatabasePutman et al (2016) Database
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“Show all operons present in Listeria monocytogenes.”
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The Stone Soup of Knowledge…
HT: Jamie Taylor, The Stone Soup of Data, WWW2007
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“Show all tyrosine kinase inhibitors that are used to treat hematologic cancers.”
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“Show all monoclonal antibodies used to treat melanoma.”
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“Show all human membrane proteins associated with colorectal cancer.”
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Appealing to domain experts’ selfish motives16
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Take-home #3
Drug repurposing is a promising application
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#2: Wikidata is an outstanding community platform
#1: TOKeN is critical for biomedical research
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“Repurposing generally refers to studying drugs that are already approved to treat one disease or condition to see if they are safe and effective for treating other diseases”.
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Raynaud disease and fish oil20
Raynaud disease
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Raynaud disease and fish oil21
Raynaud disease
Fish oil / EPA
Abnormal platelet activity
Abnormal blood
viscosity
High blood viscosity
Elevated RBC rigidity
Vasodilation
Low blood triglycerides
Increased prostacyclins
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Raynaud disease and fish oil22
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“Undiscovered public knowledge”23
Raynaud disease
Fish oil / EPA
Abnormal platelet activity
Abnormal blood
viscosity
High blood viscosity
Elevated RBC rigidity
Vasodilation
Low blood triglycerides
Increased prostacyclins
A
C
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B BB
BB
B
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Take-home #4 (Bonus)
Data licensing is a massive obstacle
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Collaborate on the Knowledgebase
Compete on the Analyses