Harvest: Data Discovery for Humans


I'm Speaking at OSCON 2013 (size 125 X 125)

Biomedical data can be a pain to work with. Data lives in multiple places: electronic health records, proprietary vendor databases,  MS Access databases, and even flat files. Furthermore, healthcare data models are often incredibly complex, with multiple temporal attributes and a dizzying array of tables.

This kind of environment puts a damper on biomedical research, making it hard for analysts and clinicians to explore and and test hypotheses about their patient populations. We believe that as medicine and biomedical research becomes increasingly data-driven we need to democratize access to data across a wide number of people with varying skill sets to maximize its utility. For this reason, we created the Harvest framework: a toolkit for building highly interactive data-intensive biomedical applications. Harvest was built using several guiding principles:

  1. Promote data discovery
  2. Enable real time query and reporting
  3. Render data in a way that makes sense to the clinician/researcher
  4. Give easy routes to customizing data sets for export to popular analysis software

We think Harvest is going to be very popular inside the biomedical research community, but we are also excited to see who else might want to use it too. So where do you go if you want to reach the biggest audience of open source developers, users, and fans? You go the O’Reilly Open Source Convention in Portland, Oregon. OSCON is the sort of place where never know who you’re going to meet sitting at breakfast or lunch, and that’s part of the magic of it all. If you’re at OSCON Thursday, come check out our talk Harvest: Data Discovery for Humans and let us know what you think!

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Insightful Metrics in Translational Health Care Informatics

CBMi’s Translational Informatics Unit (TiU) uses various software technologies to “get the job done.”  This approach leaves us at liberty to find the right tool for a research project and not be limited by the weaknesses of any one technology.  Many tools and frameworks are developed in house and we also make wide use of open source programs.

Use of the Electronic Medical Record (EMR)

The EMR (Electronic Medical  Record ) used in the clinical services of the hospital however, is not thought of as an “open” piece of software.  It instead is highly proprietary.  Its code base is locked down and its new versions are installed less than annually.  It is the protector and keeper of patient health records.  Tools developed in the TiU to work with it must “play nice”, with nice meaning, “don’t mess anything up.”  So in a sense, in a quarrel between TiU software and the EMR, which is Epic in our case, Epic must win.

20130124_response_time_xyscatter_v0.5

Figure 1. shows a scatter plot of response times recorded on January 11, 2013.  The response time is the time it took for one of our patient portals to receive a response from Epic/Interconnect.  The tests were triggered every five minutes but only response times greater than 1000 milliseconds were captured.  The average response time was 2328 milliseconds, the standard deviation was 834 milliseconds, and the maximum response time was 5310 milliseconds.  The Interconnect is a network bound service of Epic and thus our waiting could be a factor Epic itself or the network traffic during the time of the request.  In either case we must “wait” to receive a response from Epic.

 2013-01-23_11-52-23

Prior to January 17, 2013, there were clusters of response times above 1000 milliseconds as show in Figure 1.  Figure 2. shows how the number of response times greater than 1000 milliseconds drops off dramatically after January 17th.  Average response times are dramatically lower for that week and the clusters would be less dense.   CHOP is a major hospital and research institute.

Dealing with the variations in load and processing time.

Variations in network load and processing times by our EMR must be expected.  We at the TiU have at least two choices; (1)  We can design our software such that its usefulness will be minimally affected by these variations or (2) we can design our software such that it is not at all dependent on processes will make us “wait.”  In reality, a useful and impactful translational software tool will be a blending of the two options.

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Genome Wowser Listed in Best Science Apps in Genetic Engineering & Biotechnology News

Genetic Engineering and Biotechnology News lists Genome Wowser as one of the Best Science Apps in the February, 2013 issue of the journal. Check it out here.

About Genome Wowser

Genome WowserGenome Wowser provides a functional presentation of the popular UCSC Genome Browser that is intuitive, highly portable, and allows a “Google Maps”-like navigation experience. Users can view genomic annotation tracks, zoom in, out, and across a chromosome, search for genomic elements, and download displayed data of interest.Developed by the Center for Biomedical Informatics (CBMi) at The Children’s Hospital of Philadelphia, the application is a customized mobile interface of the Genome Browser compiled by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz (UCSC).

Features include:

  • Standard whole genome assembly as provided by the Genome Reference Consortium.
  • Comprehensive standard annotations as compiled by the UCSC Genome Bioinformatics Group via their numerous collaborations with annotators worldwide.
  • Multiple annotation tracks: select the tracks you want to see and view them concurrently in an intuitive stacked configuration for any chromosome section.
  • Pinch-and-spread zoom capability.
  • Drag-and-swipe navigation.

To download the Genome Wowser free of charge, visit the app’s iTunes page at http://itunes.apple.com/us/app/genome-wowser/id437044318?mt=8 or search for “Genome Wowser” in the iTunes store.
This application is one example of the many ways in which CBMi helps to transform clinical care and research at our institution and across the industry.

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CBMi Coordinates Data Analysis for ePROS Project

EHRs Centerpiece of Studies on Hypertension, Medication Use in Children.

Pediatric Research in Office Settings (PROS), the Academy’s practice-based research network, has received federal funding for a five-year $5million project to do pharmacoepidemiological studies using electronic health records (EHRs) from approximately 800,000 children across the country. The project builds on the PROS ePROS subnetwork, but also extends to noted EHR research collaborators at the Children’s Hospital of Philadelphia (CHOP), Boston University, MetroHealth/Case Western Reserve University, and the American Academy of Family Physicians. PROS is the largest and most well established pediatric primary care network and now by adding the EHR information, the most innovative. CBMi serves as the data coordination and analysis center for this project drawing on the expertise of the Center for Biomedical Informatics (CBMi)’s data reporting and management group and the healthcare analytics experience of PolicyLab and the Center for Pediatric Clinical Effectiveness (CPCE) Healthcare Analytics Unit. CHOP’s Pediatric Research Consortium (PERC) will be providing the data for the studies.

The study has been funded by the Health Resources and Services Administration Maternal and Child Health Bureau in collaboration with the Eunice Kennedy Shriver National Institute of Child Health & Human Development. The new über-network of EHR networks has been dubbed by one of the collaborators as “CER2,” which stands for “Comparative Effectiveness Research through Collaborative Electronic Reporting.” Working together, the CER2 collaborators will use EHR-based practice systems and other electronic data to conduct observational comparative effectiveness research on the long-term side effects of pharmaceutical treatments in children, including atypical antipsychotic medications, psychotropic medication polypharmacy, and the off-label asthma medications. In addition, the CER2 collaborators will also conduct investigations on the prevalence and management of pediatric hypertension, and will launch a trial of EHR-based clinical decision support in the management of elevated blood pressure.

Principal investigators of CER2 are PROS Director Richard C. “Mort” Wasserman, M.D., FAAP and Alexander G. Fiks, MD, MSCE of CHOP. Key collaborating investigators include Robert Grundmeier, M.D., FAAP (CHOP), William Adams, M.D. FAAP (Boston University), David Kaelber, M.D., FAAP (MetroHealth/Case Western Reserve), and Wilson Pace, M.D., FAAFP.

Read the full article from the November 2012 issue of AAP News here.

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Keynotes Announced for 6th Annual CHOP Healthcare Informatics Symposium

Keynote speakers were announced for the 6th Annual CHOP Healthcare Informatics Symposium presented by The Children’s Hospital of Philadelphia’s Center for Biomedical Informatics on April 26, 2013 at the Sheraton Philadelphia Downtown Hotel.  This year’s conference will focus on  patient centered medicine.

Keynotes

Murphy

Judy Murphy, RN, FACMI, FHIMSS, FAAN
Deputy National Coordinator for Programs & Policy
Office of the National Coordinator for Health IT
Department of Health & Human Services, Washington, DC

Judy Murphy is Deputy National Coordinator for Programs & Policy at the Office of the National Coordinator for Health IT, Department of Health and Human Services in Washington D.C.  She is a nurse, who came to the ONC in December of 2011 with more than 25 years of health informatics experience at Aurora Health Care in Wisconsin.   Most recently she was Vice President-EHR Applications, and managed the organization’s successful achievement of Stage 1 EHR Meaningful, with incentive payments beginning in September 2011.

Dan Masys

Daniel R. Masys, MD
ACMI Fellow
Affiliate Professor of Biomedical and Health Informatics
University of Washington School of Medicine

Dr. Daniel R. Masys is an Affiliate Professor of Biomedical and Health Informatics, joining the Department of Biomedical Informatics and Medical Education in 2011.  Previously he served as Professor and Chair of the Department of Biomedical Informatics and Professor of Medicine at the Vanderbilt University School of Medicine .

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See the Latest CBMi YouTube Videos

See the latest videos from our 2012 CBMi Fall Speaker Series.

Dr. Nancy Hanrahan’s October 2012 presentation “Technology and Game Solutions in Health Care” was highly attended and wer had many requests to post the video.

You can find it at http://bit.ly/RzoYRR.

In addition, AMIA President Dr. Kevin Fickenscher’s “Healthcare 2020: From Gutenberg to Zuckerberg – Informatics and Technology for the New Care Delivery Models” is also available on CBMi’s YouTube channel.

The CBMi YouTube channel also has archived videos from past symposiums and speaker sessions that you may find interesting as well.  Check out the selection at http://cbmi.chop.edu.

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CBMi Featured in 2012 CHOP Research Institute Annual Report

The Center for Biomedical Informatics is featured in the 2012 Children’s Hospital of Philadelphia Research Institute Annual Report,

The Cornerstone of Personalized Medicine.”

Led by Peter White, PhD, CBMi develops innovative solutions that address the informatics needs of the Research Institute — and beyond. It provides the aptitude and infrastructure critical to maximizing the value of the data and other information relevant to research and clinical activities at Children’s Hospital.

CBMi’s expertise in medicine, biology, statistics, mathematics, linguistics, and computer science empowers it to help investigators, clinicians, and families alike best use the ever-evolving and expanding pediatric health information.

Read about CBMi’s efforts in

SDM Asthma Portal

CBMi’s Dr. Robert Grundmeier and lead Human Computer Interaction Specialist Dean Karavite collaborated with Dr. Alexander Fiks on the creation of the Shared Decision Making Portal for Pediatric Chronic Illness. Drs. Fiks and Grundmeier’s portal is a modification of MyChart that greatly expands MyChart’s capabilities. While the pilot version of the portal is focused solely on asthma, Dr. Fiks and his team hope to eventually introduce versions geared toward other diseases, such as ADHD. Read more about Making Families Active Partners in Care.

Genome Wowser

With the iPad® application Genome Wowser, investigators can quickly and efficiently navigate the vast information on the human genome. Developed by the Center for Biomedical Informatics (CBMi) at Children’s Hospital, Genome Wowser provides for the convenient, intuitive, and highly mobile exploration of genomic information.

Since its launch, Genome Wowser has been consistently ranked as a top 10 “What’s Hot” medical app on iTunes, downloaded more than 7,000 times and updated more than 25,000 times from researchers in 79 countries. A second version of the app, released in August 2012, includes access to the genome sequences of more than three dozen non-human species, including dogs, cats, mice, chimpanzees, elephants, and 11 species of fruit fly, plus further improvements in the touch interface.

Read more about Genome Wowser

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