1. Federal Big Data Working Group Meetup: The Yosemite Project: A Roadmap for Healthcare Information Interoperability and The New Book: Building Ontologies with Basic Formal Ontology
Dr. Brand Niemann
Director and Senior Data Scientist/Data Journalist
Semantic Community
Federal Big Data Working Group Meetup
Data Science
August 31, 2015

2. Agenda
6:30 p.m. Welcome and Background (New Tutorial and Mentoring) Slides Data Science for EHRs
6:40 p.m. David Booth, PhD. HRG and Rancho BioSciences, Slides
7:30 pm. Brief Member Introductions
7:40 p.m. Professor Barry Smith, Department of Philosophy - University at Buffalo New Book: Building Ontologies with Basic Formal Ontology Slides
8:30 p.m. Open Discussion
8:45 p.m. Networking
9:00 p.m. Depart

3. Schedule
August 25th, Introduction to the American Community Survey Webinar (2-3 PM EST). (See October 5th Meetup Below)
September 1st, Data Science for EPA Hydraulic Fracturing Webinar.
September 14th, Big Data Science for Precision Farming Business Online Course.
September 16-17th, Building Ontologies with Basic Formal Ontology, Barry Smith
September 28th, Climate Change Data - Data Science Meetup of Meetups.
October 5th, Data Science for Census American Community Survey.
October 19th, Sensing Our Air: The Quest for Big Data About Our Air Quality.
November 2nd, Data Science for Random Forests
November 5-6th, OSTP/NSF Data Science Meetup of Meetups, Ballston, VA.
November 16th, Data Science for the DataAct Datathon
December 7th, TBA

4. Background
David Booth, PhD. HRG and Rancho BioSciences, The Yosemite Project. Slides 5-6.
Barry Smith, Professor of Philosophy and Co-Author of New Book on Ontology, Meeting with Intelligence Community. Slides 7-11.
Jonathan Hines, ORNL science writer, doing a story on Semantic Medline and the ORNL CADES – Compute and Data Environment for Science. Slides
Joan Aron and Brand Niemann, Data Mining - Science - Questions - Publication Process. Slides
Weifeng Li (Lexie) and Brand Niemann, FDA Precision Medicine, Slides
Chris Crawford and Jay Patkar, TIBCO Software Federal, Random Forests for Kaggle Competitions and Spotfire TERR. November 2nd.
Steve Hanmer, Mission Source, Allyson Ugarte, Treasury, co-planning Data Science for Data Act Datathon Meetup. He attended the Data Act Datathon and Forum this week and will report. November 16th.

6. About the Yosemite Project
The Yosemite Project is a collaborative effort to achieve semantic interoperability of all structured healthcare information, using RDF as a universal information representation.  It is a follow-up to the Yosemite Manifesto -- a position statement issued by participants of the 2013 workshop on RDF as a Universal Healthcare Exchange Language, held at the Semantic Technology and Business Conference, in response to the 2010 PCAST report's call for a universal exchange language for healthcare information.  The Yosemite Manifesto identifies RDF as the "best available candidate" to meet this need, and has been signed by over 100 healthcare and technology experts since it was issued.  Add your name!

7. https://mitpress. mit. edu/index. php

8. Building Ontologies with Basic Formal Ontology: Table of Contents
Introduction
1 What Is an Ontology?
2 Kinds of Ontologies and the Role of Taxonomies
3 Principles of Best Practice I: Domain Ontology Design
4 Principles of Best Practice II: Terms, Definitions, and Classification
5 Introduction to Basic Formal Ontology I: Continuants
6 Introduction to Basic Formal Ontology II: Occurrents
7 The Ontology of Relations
8 Basic Formal Ontology at Work
Appendix on Implementation: Languages, Editors, Reasoners, Browsers, Tools for Reuse
Glossary
Web Links Mentioned in the Text
Notes
Bibliography

9. Building Ontologies with Basic Formal Ontology By Robert Arp, Barry Smith and Andrew D. Spear
In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use.
After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies.

13. NIH Data Commons FAIR Principles: Cloud: Federal Science Policy:
Findable
Accessible
Interoperable
Reusable
Cloud:
Data
Software
Results
Federal Science Policy:
OSTP Public Access to Scientific Data Memo (February 2013)
New Program: Big-Data-to- Knowledge (2013)
New Position: Associate Director of Data Science (2014)
Digital Enterprise (2015): Data Commons
Metadata
Open APIs
Digital Objects
Containers
A NIH – Semantic Medline Data Science Data Publication Commons

14. OSTP/NSF Data Science Meetup of Meetups
Week of November 2nd:
NSF Data Science/Big Data Principal Investigators (About 300)
NSF Data Hubs (4)
Organizers of Largest Data Science/Big Data Meetups (About 65)
Pipeline for Return on Investment:
PIs put their data, tools and research results in the Data Hubs
Data Hubs provide those data, tools, and research results to the world, but especially to the Data Science/Big Data Meetups
Data Science/Big Data Meetups collaborate with PIs and Data Hubs to increase usage and feedback

15. We Already Do This!
Semantic Community:
Provides a Community Sandbox that is like a GitHub, Data Hub, Data Commons, etc.
Metadata (MindTouch)
Open APIs (MIndTouch)
Digital Objects (MindTouch)
Containers (Spotfire)
Organize the Federal Big Data Working Group Meetup
Support Agencies and Programs in Crowdsourcing Their Data Sets
Mentor Data Scientists (Tutorials and MOOCs) and Entrepreneurs (Eastern Foundry)
Federal Big Data Working Group Meetup:
Federal: Supports the Federal Big Data Initiative, but not endorsed by the Federal Government or its Agencies;
Big Data: Supports the Federal Digital Government Strategy which is "treating all content as data", so big data = all your content;
Working Group: Data Science Teams composed of Federal Government and Non- Federal Government experts producing big data products; and
Meetup: The world's largest network of local groups to revitalize local community and help people around the world self- organize like MOOCs (Massive Open On-line Classes) now embraced by the White House.

16. Data Mining - Science - Questions - Publication Process
Data Mining Process:
Business Understanding
Data Understanding
Data Preparation
Modeling
Evaluation
Deployment
Data Science Process:
Data Ecosystem
Data Story
Data Science Questions:
How was the data collected?
Where is the data stored?
What are the data results? and
Why should we believe the data results?
Data Science Data Publication:
Knowledge Base
Spreadsheet Index
Web & PDF Tables to Spreadsheet
Data Browser
Dynamically Linked Adjacent Visualizations

17. Data Science Data Curation for Sustainable Data Science Meetups of Meetups
I just finished four data science ecosystems:
RDA Climate Data Challenge (July 15):
ata_Challenge
RDA Information Week 2016 (Ebola Response and Nepal Earthquake) (July 17):
_Data
USDA Microsoft Innovation Challenge (July 27):
Business#Story
US Data Act (July 28):

18. Collaboration for Data Science Win-Wins
USDA Open Government Data Training, Innovation Competition, and Online Course in Data-Driven Farming:
_Farming_Business#Story
Many Curated Government Data Sets and Data Science Products:
Pick an Agency and/or a Data Set and Look for a Meetup on That:
Mentor Startups Partnership with Eastern Foundry:
Group/events/ /

19. USDA Collaboration Chronology
March 16th: USDA CIO and ACDO on Open Data Plan and Roundtable Meetup
March 25th: Government Technology & Innovation Incubator for Big Data Analytics II Meetup at Eastern Foundry
May 18th: USDA Data Science MOOC Meetup
May 21st, USDA Open Data Quarterly Submission to OMB on USDA Data Usage provided (USDA Data Science MOOC)
July 21st, Data-Driven Farming Online Course Announced by HeatSpring and Semantic Community
July 27th: USDA Microsoft Innovation Challenge Submission on Farm Data Dashboards
July 29th, Partnerships Sought for Data-Driven Farming Online Course
August 19, 2015, Data Science for USDA Big Data, Briefing and Demo
September 17th: Big Data Science for Precision Farming Business Online Course Meetup and Commercial Examples: Farmers Business Network, FarmLogs, etc.
October 26-December 18th, Data-Driven Farming Online Course with Partners

25.
Agriculture:
Data Type: 8 Pages
Industry Category: 3 Pages

26. CSV

27. Web Player

28. Web Player

29. FDA Mission
FDA plays an integral role in President Obama’s Precision Medicine Initiative, which foresees the day when an individual’s medical care will be tailored in part based on their unique characteristics and genetic make-up. Yet while more than 80 million genetic variants have been found in the human genome, we don’t understand the role that most of these variants play in health or disease.
The FDA, an agency within the U.S. Department of Health and Human Services, protects the public health by assuring the safety, effectiveness, and security of human and veterinary drugs, vaccines and other biological products for human use, and medical devices. The agency also is responsible for the safety and security of our nation’s food supply, cosmetics, dietary supplements, products that give off electronic radiation, and for regulating tobacco products.

31. precisionFDA
Planned for beta release (work in progress) in December 2015, precisionFDA will offer community members access to secure and independent work areas where, at their discretion, their software code or data can either be kept private, or shared with the owner’s choice of collaborators, FDA, or the public. Initially, precisionFDA’s public space will offer a wiki and a set of open source or open access reference genomic data models and analysis tools developed and vetted by standards bodies, such as the National Institute of Standards and Technology (e.g., Genome in a Bottle). We believe precisionFDA will help us advance the science around the accuracy and reproducibility of NGS-based tests, and in doing so, will advance consumer safety. We look forward to continuing to update the community on the development of these new tools.

32. Previous FDA-Related Meetups
July 7, 2014: Data Science of White House Big Data Review and Brooke Aker: Big Data Lens on OpenFDA
October 6, 2014: FDA Data Innovation Lab and Predictive Analytics
December 1, 2014: Data Science for NIH/FDA SEMOSS Data Federation and Analytics
April 6, 2015: Data Science for the FDA RFI