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1st Network-of-BioThings Hackathon

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Despite the massive amount of biomedical literature, only a small amount is available in a form that is readily computable. The National Center for Biomedical Ontology (NCBO) is hosting the first hackathon to develop a comprehensive Network of BioThings (proteins, genes, pathways, mutations, drugs, diseases) extracted from scientific research articles and integrated with public biomedical data (see blog post http://goo.gl/i91ngK). During this hackathon, we will (1) identify motivating use cases, (2) define a shared, sustainable, multi-component infrastructure to build the NoB, and (3) implement common data representations, ontology-based programmatic interfaces, and develop cool applications. We will do this in an open, scalable, responsive manner so that it becomes a major asset for hackers and biomedical researchers worldwide.

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1st Network-of-BioThings Hackathon

  1. 1. 1st NoB Hackathon April 26-27 @Stanford University @Maastrict University
  2. 2. • Michel Dumontier • Natasha Haulman (superadmin) • Mark Musen • Andrew Su • Ben Good • Chris EveloData FAIRport • Mark Wilkinson
  3. 3. European site @ Maastricht University • Chris Evelo (NoB) • Mark Wilkinson (FAIRport)
  4. 4. What is it?
  5. 5. 5 Pathways Diseases Proteins Variants Genes Drugs Goal: Assemble a network of biomedical entities that is comprehensive, current, and computable.
  6. 6. The biomedical literature is growing fast 6 In 2013, there were 1,108,920 new articles indexed in PubMed, bringing the current total to over 23 million. 0 200,000 400,000 600,000 800,000 1,000,000 1,200,000 1983 1988 1993 1998 2003 2008 2013 Number of new PubMed-indexed articles
  7. 7. The biomedical literature is growing fast 7 In 2013, there were 1,108,920 new articles indexed in PubMed, bringing the current total to over 23 million. 0 200,000 400,000 600,000 800,000 1,000,000 1,200,000 1983 1988 1993 1998 2003 2008 2013 Number of new PubMed-indexed articles k n o w l e d g e
  8. 8. The Kitchen Sink approach • Biocuration • Text-mining • Crowdsourcing • Citizen science • Semantic web • Bio-ontologies • Network biology • Biomedical domain experts • Scientific publishers • Bio-IT • … 8
  9. 9. 1. Knowledgebase infrastructure • Scaling to billions or trillions of relationships • Efficient query and access • Generic and extensible data model • Interoperability with other resources 9
  10. 10. 2. Populating the knowledgebase • Scalability with biomedical research • Synergies between methods • Assessing confidence • Preserving provenance 10
  11. 11. 3. Driving Biological Projects • Defining the domain area • N-of-1 cancer • Drug repurposing • Neuroscience • Defining the specific data needed • Defining the mining/analysis strategy • Defining the testable hypotheses 11
  12. 12. Overarching goals • Demonstrate feasibility • Demonstrate collaboration • Demonstrate synergy • Secure funding for multi-center multi-PI consortium 12
  13. 13. Schedule Saturday April 26 8:30AM: Registration and Breakfast 9:00AM: Introductions, Problem Statement, Ideas session 10:15AM: Project Pitches and Team Formation 11:00AM: Tutorials 12:15PM: Lunch is served 6:00PM: Progress Reports 7:00PM: Transportation leaves for restaurant 7:15-8:00PM: Cocktails @ Left Bank 8:00PM: Dinner @ Left bank Sunday April 27 8:00AM : Breakfast is served 12:15PM: Lunch is served 4:30PM : Pitches and Demos 6:00PM : Winners announced, prizes awarded, final remarks.
  14. 14. Prizes • $500 for best motivating use case • $500 for most sustainable infrastructure design • 2x$500 for best applications
  15. 15. Format • Form groups of at most 5 • Must contain at least 2 local participants • Up to 3 additional remote participants (total of 8) • All code must be open and available • GitHub repo https://github.com/Network-of-BioThings/
  16. 16. Judges • Mark Musen (NCBO) • Bob Stanley (IO Informatics) • Paul Alexander (NCBO) • Manuel Salvadores (NCBO) • Michel Dumontier (NCBO) • Andrew Su (Scripps – Use Cases) • Criteria • Innovation • Integration • Sustainability / Scalability • Impact Potential
  17. 17. Other Stuff • Wifi • Bathrooms • Room configuration • projectors
  18. 18. Let’s Get Started! • GitHub • https://github.com/Network-of-BioThings/ • Hackathon repo • Use Cases • Resources • Participant Profiles

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