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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
Take-home #1
TOKeN is critical for biomedical research
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The biomedical literature is massive…3
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0200,000400,000600,000800,000
1,000,0001,200,0001,400,000
Number of new PubMed-indexed articles
… but it is very hard to query and compute4
… but it is very hard to query and compute5
ImatinibCrizotinibErlotinibGefitinibSorafenibLapatinibDasatinib
…
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!
Hyper-specialization…
… and decreased synergies at the interfaces
Take-home #2
Wikidata is an outstanding community platform
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#1: TOKeN is critical for biomedical research
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
“Show all tyrosine kinase inhibitors that are used to treat hematologic cancers.”
“Show all monoclonal antibodies used to treat melanoma.”
“Show all human membrane proteins associated with colorectal cancer.”
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”.
Raynaud disease and fish oil20
Raynaud disease
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
Raynaud disease and fish oil22
“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
B
B BB
BB
B
Take-home #4 (Bonus)
Data licensing is a massive obstacle
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Collaborate on the Knowledgebase
Compete on the Analyses
