Big Data for Oral Health Knowledge: Second Installment of Resources

Dr. Elsbeth Kalenderian, Associate Professor and Chair Oral Health Policy and Epidemiology Department and Chief of Quality at the Harvard Dental Center, presented “Standardized Diagnostic Terminology for Dental Research.”

Dr. Gil Alterovitz, Assistant Professor at Harvard Medical School in the Center for Biomedical Informatics, and Director of the Biomedical Cybernetics Laboratory presented about the “SMART Platform and API for Clinical Genomic Apps.” Remember, he also suggested this video that shows an external site (Vanderbilt) creating an app using the SMART on FHIR Genomics API that my team developed.

Dr. Helen Whelton who is Dean at the University of Leeds presented ADVOCATE, the Added Value Oral Care project for developing and comparing new models for safe and efficient, prevention-oriented and patient-centered health care systems.

Dr. Michael Sullivan, updated us on the “Global Collaboration in the Cloud,” reminding us to think globally in the cloud and to consider global collaborations.

IADR-I2 Workshop 3-14-2015
Figure 1: Participants interact during the Big Data for Oral Health Knowledge and get the work that lies ahead started.

Please stay tuned for more information from the Workshop and the next steps.

Chris, Khalil, Lynn and Heiko

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Big Data for Oral Health Knowledge; How to get the Big Answers–Successful Completion of the Workshop

After successful completion of the Workshop Big Data for Oral Health Knowledge; How to get the Big Answers that occurred in conjunction with 2015 IADR/AADR/CADR General Session & Exhibition in Boston on March 14, 2015, the participants sensed that there is still a lot of work ahead of the community.

This blog post will share a first batch of resources that were mentioned during the workshop by some of the presenters.

The organizers would also like to use the opportunity to thank all presenters as well as the participants for their time and efforts. Special thanks goes to IADR and Internet2, both have contributed substantial resources to make this event happen.

Dr. Charles Friedman’s Learning Health System (LHS): In addition to his presentation, he shared several resources that I list here: Brett James video “We Count Our Successes in Lives” for full version and here excerpts.

LHS case example Pancreatic Cancer
LHS case example Hypertension

Essential Standards to Enable Learning (ESTEL)

Department of Learning Health Sciences (DLHS)

Dr. Muhammad Walji’s presentation “Big Mouth Dental Data Repository”:

Big Mouth Data Repository:
A while ago, I interviewed Muhammad as part of our COHRI outreach efforts.

My presentation “Converting Data Cemeteries into Sources of Knowledge”:
The link that includes all the references is here.

Please stay tuned for more presentation slides and notes about the Workshop.

Chris, Khalil, Lynn and Heiko

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Big Data for Oral Health Knowledge: SMART Platform

Dr. Gil Alterovitz, Assistant Professor at Harvard Medical School in the Center for Biomedical Informatics, will speak about the “SMART Platform and API for Clinical Genomic Apps.”

Gil is Director of the Biomedical Cybernetics Laboratory and core faculty member of the Children’s Hospital Informatics Program. He is also affiliated with the Department of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology.

Gill will explain how a standard can spark innovation and expand Big Data usage. SMART accelerates medical application innovation and research removing roadblocks for developers. He suggested that we watch the video below that shows an external site (Vanderbilt) creating an app using the SMART on FHIR Genomics API that his team developed:

Please feel free to share your thoughts with us.

Chris, Khalil, Lynn and Heiko

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Big Data for Oral Health Knowledge: BigMouth for BigData?

Dr. Muhammad Walji, Associate Professor, Department of Diagnostic and Biomedical Sciences and Associate Dean for Technology Services & Informatics at the School of Dentistry, University of Texas Health Science Center at Houston, will present about BigMouth.

BigMouth is a unique dataset that has been developed by dental schools who are part of the Consortium for Oral Health Research and Informatics (COHRI). BigMouth currently contains data from over one million patients derived from electronic health records from five dental institutions. BigMouth contains demographics, diagnoses, procedures, periodontal measurements, odontogram/tooth measurements, medical and dental histories, medications, insurance and information about the provider type (hygienist, dentist, dental student, resident). In his presentation, Muhammad will review how these institutions came together, developed a data governance framework that promotes data sharing, and some of the benefits and challenges of using EHR data for secondary research.

A while ago, I interviewed him as part of our COHRI outreach efforts: http://vimeo.com/89624410

Please feel free to share your thoughts with us.

Chris, Khalil, Lynn and Heiko

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Big Data for Oral Health Knowledge: Preparing for the Workshop

Dr. Elsbeth Kalenderian, one of the presenters at the Workshop and Associate Professor and Chair Oral Health Policy and Epidemiology Department and Chief of Quality at the Harvard Dental Center, will talk about Standardized Terminology. She posted the following two questions to all the participants in order to trigger some discussions related to her presentation:

  1. What will make the average dental provider move to implement a diagnostic terminology, regardless if it is the DDS, ICD or a ref set?
  2. How can standardized terminologies be helpful in the integration of oral health into general health or more directly how can it facilitate inter-professional collaboration?

Please feel free to share your thoughts here with us.

Chris, Khalil, Lynn and Heiko

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Big Data for Oral Health Knowledge: Are we making a big mistake?

The preparations for the Big Data for Oral Health Knowledge; How to get the Big Answers workshop scheduled for March 14, 2015 are progressing nicely. The title for this blog post was paraphrased from Tim Hartford’s provocative article in The Financial Times:

Hartford summarizes in his article some of the inherent problems around Big Data. As always in technology, there is a lot of hype around a new concept and many snake oil sales people who attempt to promise easy solutions when in fact there are rarely easy ones available. It goes without saying that we need causation in medicine and dentistry and cannot rely on correlation alone. This is especially true as we need to remember that all our efforts in healthcare are ultimately geared towards the future—we are not (for the most part) historians. In other words, retrospective studies are only a means to figure out what can be done for future patients (dead people do not benefit from an autopsy). Or, to turn the argument around: We need prospective studies that allow the individual provider to determine what is the best therapy for the individual patient at hand—pure correlation without hypothesis and analysis of reasons will not get us there.

The other concerns associated with Big Data relate to the lack of randomization. Providers often wish that they could compare their patient at hand with all patients who had similar symptoms and conditions. Based on the aggregated outcomes for different therapy choices “for patients like mine” the provider could then determine which therapy is the best option for their individual patient. While this sounds like an intriguing concept, we should not forget that we cannot assume that the assignment of the treatment was randomly made like in a clinical trial—severe cases of a condition, for instance, might get preferably one of the available therapy options. Thus, results, even when using n=ALL, might not tell us which therapy is truly the best option, but only which one is most frequently applied.

How would we benefit if we had access to all patient data at all times from all places—I really mean ALL?

Lastly, we are excited that a few more invitees have accepted our invitation to the by-invitation-only workshop on March 14, 2015—again, just to drop a few names: Dr. Gregg Gilbert (PI of the National Dental PBRN), Dr. Chuck Friedman (Chair, Department of Learning Health Sciences, Medical School, Professor of Information and Public Health, University of Michigan), Dr. David Gesko (Dental Director and Senior Vice-President of HealthPartners Dental Group) and Dr. Elsbeth Kalenderian (Chair, Oral Health Policy and Epidemiology, Chief of Quality, Harvard Dental Center).

Please feel free to share your thoughts with us.

Chris, Khalil, Lynn and Heiko

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Data Management

The preparations for the Big Data for Oral Health Knowledge; How to get the Big Answers workshop scheduled for March 14, 2015 are well under way. The majority of the invitees have already accepted the invitation to the by-invitation-only workshop, such as Dr. Kathy Atchinson (UCLA, consulting for NIDCR), Dr. John Kusiak (Senior Advisory to the NIDCR Director and Acting Deputy, who will be playing an active role in the Big Data Research initiatives for NIDCR/NIH), Dr. Mary Marazita (one of the top-funded genetics researchers in dentistry), Dr. Patrick Ferrillo (Dean at the University of Pacific and representative of IFDEA), Hiroshi Ogawa (WHO Oral Health Program), Dr. Richard Valachovic (Executive Director, ADEA), Dr. Helen Whelton (Dean, University of Leeds), Dr. Peter Polverini (former Dean, University of Michigan), and Dr. Martha Somerman (Director, NIDCR).

During our preparatory meetings, Dr. Seth Weinberg, a faculty member at the University of Pittsburgh who is involved with several large research initiatives, recently conveyed to us that he believes data sharing – which is a key step in generating big data – should start with proper data management that makes research data available to the outside world in a way that can be used by others. He sees a lack of database management capacity as one of the biggest obstacles for Big Data.

We share his concerns and have found a related 4-minute video (that we wish we had produced, but it is from NYU):

This “data management horror story” might resemble some of the past experiences researchers have faced when it comes to storage, documentation and file formats.

Stay tuned to learn here at the DIOC blog more about the workshop.

Christopher Fox, Khalil Yazdi, Lynn Johnson, Heiko Spallek

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdhi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh

Big Data for Oral Health Knowledge; How to get the Big Answers

Researchers from the Universities of Michigan and Pittsburgh have been planning with IADR Global HQ staff and Internet2 a workshop about Big Data in conjunction with the 2015 IADR General Session in Boston. Many important stakeholders have been invited to this workshop that will explore new challenges now faced by dental researchers. Leading dental researchers from across the globe, such as Drs. Mary Marazita, Ira Lamster and Marjorie Jeffcoat; industry partners from organizations, such as Kaiser Permanente, ESPE, DentaQuest and Henry Schein; representatives from governmental organizations, such as NIH/NIDCR, WHO; representatives from organizations, such as ADEA, IFDEA and IADR; and technology leaders, such as Laura Patterson, the CIO of the University of Michigan and Michael Sullivan Associate Director at Internet2 have accepted the invitation.

Together, the participants want to explore some of the emerging challenges, such as development of standards for storage and retrieval of health data sets, dealing with larger and larger data sets; how to bring team science and collaborations, such as practice-based networks (PBRNs) to bear on big data research questions, how to transfer data quickly, and meet HIPAA security requirements; how to use sensors and mobile devices to gather health data continuously on numerous patients and how this data should be categorized and stored; and the need for computational needs for complex data sets. The goal is to connect dental researchers with Internet2 Big Data experts with the explicit goal of exploring solutions that will result in Big Answers.

Internet2 is helping researchers in healthcare and numerous other domains solve the challenges of data capture, curation, sharing, storage, visualization, securing and transfer. As those solutions are applied to dental research disease can be prevented and human health improved. It is these very issues that prompted the NIH to launch its Big Data to Knowledge (BD2K) program in 2012.

Internet2 is much more than a network. Internet2 is a community of U.S. and international leaders in research, academia, industry and government who create and collaborate via innovative technologies. The mission of Internet2 is to work with the research and education (R&E) community to accelerate research discovery, advance national and global education, and improve the delivery of public services. Internet2 is comprised of 252 universities, 82 leading corporations, 68 affiliate members (including CDC, NIH, NSF, HHS, among others), 41 state and regional networks, and more than 65 national R&E partners representing over 100 countries. The Internet2 community touches nearly every major innovation that defines our modern digital lives—and continues to define “what’s next.”

The Workshop will try to achieve the following goals:

  • Articulate the issues around big data that dental researchers are facing
  • Dental research community articulates what they need from vendors
  • Bring international stakeholders in dental research enterprise together
  • Educate about Internet2 NET+ program

Tentatively agenda:
Several presentations in the morning explaining concepts, such as the Learning Health System and data repositories’ role in facilitating dental research. Information about standardized terminologies will be presented and why they are important to convert our data cemeteries into sources of knowledge. In addition, participants will learn how Internet2 can support the dental research community and explore a case where this already happens.

During the interactive afternoon, the participants will try to accomplish the following goals:

  • Identify the research questions that Internet2 can help with
  • Identify how Internet2 can support the research of dental education
  • Identify how service providers (industry) can help

Stay tuned to learn here at the DIOC blog more about the workshop.

Christopher Fox, Khalil Yazdi, Lynn Johnson, Heiko Spallek

Christopher H. Fox, DMD, DMSc Executive Director International & American Associations for Dental Research

Khalil Yazdi, PhD CIO in Residence, Cloud Services Program Development at Internet2

Lynn Johnson, PhD Professor of Dentistry, School of Dentistry Associate Dean for Faculty Affairs and Institutional Effectiveness Clinical Professor, School of Information The University of Michigan

Heiko Spallek, DMD, PhD, MSBA Associate Professor, Dental Public Health Associate Dean for Faculty Affairs Executive Director, Center for Informatics in Oral Health Translational Research School of Dental Medicine, University of Pittsburgh