1st Network-of-BioThings Hackathon

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    23-Aug-2014
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    Science

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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.

Transcript of 1st Network-of-BioThings Hackathon

  • 1st NoB Hackathon April 26-27 @Stanford University @Maastrict University
  • Michel Dumontier Natasha Haulman (superadmin) Mark Musen Andrew Su Ben Good Chris EveloData FAIRport Mark Wilkinson
  • European site @ Maastricht University Chris Evelo (NoB) Mark Wilkinson (FAIRport)
  • What is it?
  • 5 Pathways Diseases Proteins Variants Genes Drugs Goal: Assemble a network of biomedical entities that is comprehensive, current, and computable.
  • 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
  • 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
  • The Kitchen Sink approach Biocuration Text-mining Crowdsourcing Citizen science Semantic web Bio-ontologies Network biology Biomedical domain experts Scientific publishers Bio-IT 8
  • 1. Knowledgebase infrastructure Scaling to billions or trillions of relationships Efficient query and access Generic and extensible data model Interoperability with other resources 9
  • 2. Populating the knowledgebase Scalability with biomedical research Synergies between methods Assessing confidence Preserving provenance 10
  • 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
  • Overarching goals Demonstrate feasibility Demonstrate collaboration Demonstrate synergy Secure funding for multi-center multi-PI consortium 12
  • 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.
  • Prizes $500 for best motivating use case $500 for most sustainable infrastructure design 2x$500 for best applications
  • 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/
  • 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
  • Other Stuff Wifi Bathrooms Room configuration projectors
  • Lets Get Started! GitHub https://github.com/Network-of-BioThings/ Hackathon repo Use Cases Resources Participant Profiles