The case for an open biomedical knowledgebase

The case for an open biomedical knowledgebase

Andrew Su, Ph.D.@andrewsuasu@scripps.eduhttp://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