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June 24 2011

Big data and open source unlock genetic secrets

Replicating Nanomachines by jurvetson, on FlickrThe world is experiencing an unprecedented data deluge, a reality that my colleague Edd Dumbill described as another "industrial revolution" at February's Strata Conference. Many sectors of the global economy are waking up to the need to use data as a strategic resource, whether in media, medicine, or moving trucks. Open data has been a major focus of Gov 2.0, as federal and state governments move forward with creating new online platforms for open government data.

The explosion of data requires new tools and management strategies. These new approaches include more than technical evolution, as a recent conversation with Charlie Quinn, director of data integration technologies at the Benaroya Research Institute, revealed: they involve cultural changes that create greater value by sharing data between institutions. In Quinn's field, genomics, big data is far from a buzzword, with scanned sequences now rating on the terabyte scale.

In the interview below, Quinn shares insights about applying open source to data management and combining public data with experimental data. You can hear more about open data and open source in advancing personalized medicine from Quinn at the upcoming OSCON Conference.

How did you become involved in data science?

Charlie QuinnCharlie Quinn: I got into the field through a friend of mine. I had been doing data mining for fraud on credit cards and the principal investigator, who I work with now, was going to work in Texas. We had a novel idea that to build the tools for researchers, we should hire software people. What had happened in the past was you had bioinformaticians writing scripts. They found the programs that they needed did about 80% of what they wanted, and they had a hard time gaining the last 20%. So we had had a talk way back when saying, "if you really want proper software tools, you ought to hire software people to build them for you." He called my boss to come on down and take a look. I did, and the rest is history.

You've said that there's a "data explosion" in genomics research. What do you mean? What does this mean for your field?

Charlie Quinn: It's like the difference between analog and digital technology. The amount of data you'd have with analog is still substantial, but as we move toward digital, it grows exponentially. If we're looking at technology in gene expression values, which is what we've been focusing on in genomics, it's about a gigabyte per scan. As we move into doing targeted RNA sequencing, or even high frequency sequencing, if you take the raw output from the sequence, you're looking at terabytes per scan. It's orders of magnitude more data.

What that means from a practical perspective is there's more data being generated than just for your request. There's more data being generated than a single researcher could possibly ever hope to get their head wrapped around. Where the data explosion becomes interesting is how we engage researchers to take data they're generating and share it with others, so that we can reuse data, and other people might be able to find something interesting in it.

Health IT at OSCON 2011 — The conjunction of open source and open data with health technology promises to improve creaking infrastructure and give greater control and engagement for patients. These topics will be explored in the healthcare track at OSCON (July 25-29 in Portland, Ore.)

Save 20% on registration with the code OS11RAD

What are the tools you're using to organize and make sense of all that data?

Charlie Quinn: A lot of it's been homegrown so far, which is a bit of an issue as you start to integrate with other organizations because everybody seems to have their own homegrown system. There's an open source group in Seattle called Lab Key, which a lot of people have started to use. We're taking another look at them to see if we might be able to use some of their technology to help us move forward in organizing the backend. A lot of this is so new. It's hard to keep up with where we're at and quite often, we're outpacing it. It's a question of homegrown and integrating with other applications as we can.

How does open source relate to that work?

Charlie Quinn: We try and use open source as much as we can. We try and contribute back where we can. We haven't been contributing back anywhere near as much as we'd like to, but we're going to try and get into that more.

We're huge proponents not only of open source, but of open data. What we've been doing is going around and trying to convince people that we understand they have to keep data private up to a certain point, but let's try and release as much data as we can as early as we can.

When we go back to talking about the explosion of data, if we're looking at Gene X and we happen to see something that might be interesting on Y or Z, we can post a quick discovery note or a short blurb. In that way, you're trying to push ideas out and take the data behind those ideas and make it public. That's where I think we're going to get traction: trying to share data earlier rather than later.

At OSCON, you'll talk about how experimental data combines with public data. When did you start folding the two together?

Charlie Quinn: We've been playing with it for a while. What we're hoping to do is make more of it public, now that we're getting the institutional support for it. Years ago, we went and indexed all of the abstracts at Pubnet by gene so that when people went to a text engine, you could type in your query and you would get a list of genes, as opposed to a list of articles. That helped researchers find what they were looking for — and that's just leveraging openly available data. Now, with NIH's mandate for more people to publish their results back into repositories, we're downloading that data and combining it with the data we have internally. Now, as we go across a project or across a disease trying to find how a gene is acting or how a protein is acting, it's just giving us a bigger dataset to work with.

What are some of the challenges you've encountered in your work?

Charlie Quinn: The issues we've had are with the quality of the datasets in the public repositories. You need to hire a curator to validate if the data is going to be usable or not, to make sure it's comparable to the data that we want to use it with.

What's the future of open data in research and personalized medicine?

Charlie Quinn: We're going to be seeing multiple tiers of data sharing. In the long run, you've going to have very well curated public repositories of data. We're a fair ways away from there in reality because there's still a lot of inertia against doing that within the research community. The half-step to get there will be large project consortiums where we start sharing data inter-institutionally. As people get more comfortable with that, we'll be able to open it up to a wider audience.

This interview was edited and condensed.

Photo: Replicating Nanomachines by jurvetson, on Flickr


February 23 2011

Health care projects could yield templates for tackling big problems

I will be attending the HIMSS conference again this year and look forward to a great week exploring new opportunities in health information technology.

There was an excellent panel discussion Sunday at HIMSS that looked at innovation in health care with Aneesh Chopra, CTO of the United States, Peter Levin, CTO at the Department of Veterans Affairs, and Farzad Mostashari, Deputy National Coordinator at the ONC. They discussed a three-pronged approach to health care innovation:

  1. Invest in the building blocks of innovation, such as R&D and human capital
  2. Set the right policy conditions to foster market-based innovations
  3. Foster an all-hands-on-deck approach to R&D and standards

There was a great deal of focus on the government in its role as a convener and collaborator and using government as a platform for innovation. Using the examples of the Direct Project and the Blue Button initiative as templates for how government can solve not only problems we face in health care in this country, but other sectors such as energy and education as well.

I spoke with Chopra after the panel. He touched on general topics ranging from the Direct Project, to open government, to ways government can act as a platform for innovation. He also discussed:

  • The work of the the Smart Grid Interoperability Standards Project at the National Institute of Standards and Technology (NIST).
  • How we can use the open and transparent process that led to the Direct Project as a template for other efforts to solve our country's problems.

The full interview is available in the following video:

Thanks to Open Affairs Television for providing the video for this conversation. They will also be posting video from the entire panel discussion on their site.


July 15 2010

Health Care Challenge combines patient empowerment and data crunching

I looked over the five applications requested by the Health Care Challenge launched last week. This challenge was set up by the organizers of the Health 2.0 Conference along with the Department of Health and Human Services and other partners (including O'Reilly Media). Two unifying threads tie together all the challenges, indirectly showing the way the health care field is heading.

The first thread is involving the patients in their own
-- sometimes collaboratively. The health care field has come
to realize that as we pick off and solve the obvious problems that
surgery or drugs can take care of, and as the population's general health
and hygeine increase, diseases are getting harder to deal with. The
patient has to be responsible for his or her own well-being.

This is fairly clear in problems such as high blood pressure and
obesity, but applies even to conditions that are immediately treatable
by health care professionals. Take surgery, for instance. It would
seem the ultimate occasion for passivity on the part of the patient,
but every surgery requires a lengthy recovery. If the patient fails to
follow orders or doesn't understand the need to report a complication,
she could end up worse than she started.

The second thread is collecting and sharing data. Sometimes
this involves existing standards for electronic storage, but many
vendors are creating their own APIs and data structures to fill the
gap left by these standards -- especially to record patient activity, as
part the previous thread involving the patients.

Together, these threads take health out of specialized, clinical
settings and integrate it into everyday routines -- the way true health
has always been attained.

Take a look at the five challenges and see whether you'd like to try
your hand at them. More challenges will hopefully be added.

Real-Time Patient-Driven Data Challenge
, by Practice Fusion

There has been a lot of talk about health care providers giving patients access to patient data in the hands of the provider--most recently in the final meaningful use rules, covered in recent blogs on the Radar site by me and by Brian Ahier. But what about using electronic systems to let patients report data to their doctors?

That's the goal of this challenge. Practice Fusion here is showcasing an API that allows data to be set in and retrieved from their web service for physicians. They are challenging programmers to develop apps that make it easy for patients to input real-time data about exercise, heart rate, etc.--perhaps collecting that data directly from devices, including GPS systems, instead of requiring the patient to type it in. Programmers have to provide their own authentication system for patients.

Improving Health Together
, by Keas

The challenge is to produce a text messaging application, using the Keas RESTful API, that pushes reminders to participants. The app can remind them to take medication, give feedback on their exercise, etc. Somewhat in the mode of PatientsLikeMe, an app might allow users to post their data and compare it to others.

The Keas API is quite rich--providing control flow, for instance--and includes calls and data tables manipulating common information of medical interest. You can report height, weight, cholesterol level, medications taken, etc., create a care plan to deal with such issues as weight and exercise, and create your own categories of information.

Move Your App! Developer Challenge
, by href=">">Snaptic and href="">Hope Lab

The challenge is a mobile app, based on Snaptics's RESTful API, that
encourages people to pick up their pace--something that makes them
want to dance or run or do some other form of movement for fun--and
then record data about that movement for medical use. Snaptic provides
APIs for several languages--including the iPhone's Objective-C and
Android's Java--but seems to offer a much less detailed, more high-level set
of calls than Keas.

Why-Health ?!?!
, by Whyville

The challenge is a game or graphical display of health data for Whyville's audience of children aged 9 to 15.

The Living Record: Rethinking Medical Record Documentation, by the
Szollosi Healthcare Innovation Program

The challenge is an application than can document the course of a patient's condition or treatement: a hospital stay, for instance, or a series of visits to different health care providers. Most data about patients, currently, is broken up into the reports of individual visits by a doctor or nurse. A fundamental requirement for the app is to accept data from multiple sources and combine it all accurately.


Analysis: A defining moment for "meaningful use"

We have reached a fulcrum point in the history of health care in our country. The announcement on Tuesday of the final rule establishing Medicare and Medicaid incentive programs for the meaningful use of electronic health records (EHR) creates a framework for change that will have reverberations throughout the health care industry. An important companion rule (pdf) was also released that establishes standards, specifications and certification criteria for EHRs.

Health IT at OSCON 2010David Blumenthal, the national coordinator for health information technology at Health and Human Services (HHS), and Marilyn Tavenner, principal deputy administrator of the Centers for Medicare and Medicaid Services (CMS), published an overview of the meaningful use rule in the the New England Journal of Medicine. John D. Halamka, of both Harvard Medical School and Beth Israel Deaconess Medical Center, wrote an excellent analysis of the final standards rule on his blog. I expect in the coming months there will be a great deal of parsing of the language of these two rules, which total 1,092 pages.

The rule defining meaningful use will now allow health care providers to adopt health information technology that aligns with the goals of the incentive program included in the American Recovery and Reinvestment Act. The criteria for achieving meaningful use has been substantially scaled back from the proposed rule, which came out at the beginning of the year. After receiving more than 2,000 comments, the rule has some significant changes that could make reaching stage one of meaningful use easier.

A major shift is the move away from an all-or-nothing approach, where providers had to meet every single measure to be eligible for payments. Instead, there's now a set of must-have core requirements and an a la carte menu of discretionary options. There are 15 core requirements for physicians and 14 for hospitals. Health care providers can then choose five of 10 menu options to meet phase one of meaningful use. This strategy will enable a great many hospitals and small practices in rural and underserved areas to have a shot at cashing in on incentive payments.

Meaningful use in action

It's important to note there will still be second and third phases of meaningful use. Ultimately, the final stage must be met. After 2015, when the incentive payments end, penalties will kick in. By lowering expectations for the first phase the slope to reach succeeding phases only gets steeper.

Let's take Computerized Physician Order Entry (CPOE): more than 30 percent of unique patients being seen by an eligible provider or admitted to a hospital, must have at least one medication order entered using CPOE. But the final rule actually states that phase two will require a 60 percent threshold:

For stage 1, we are finalizing a threshold for CPOE of 30 percent for EPs, eligible hospitals, and CAHS. We believe this relatively low threshold, in combination with the limitation to only medication orders, will allow hospitals and EPs to gain experience with CPOE. However, as providers gain greater experience with CPOE, we believe it is reasonable to expect greater use of the function."

As difficult as small physician practices and critical access hospitals might find initial adoption and implementation, it will take a sustained effort to attain the results we need to see so that costs can actually be lowered and the quality of care will improve.

The Emergency Department (ED) is now included in the mix for hospital CPOE. "Nearly every commenter who commented on CPOE objected to our proposal to limit this measure to the inpatient department," the rule says. "Commenters stated that this limitation was inappropriate given the manner in which hospitals use EHR technology. To account for current practice, the commenters recommended the measures be expanded to include the emergency department." The rule then goes on to say: "We agree with the commenters, and therefore are expanding this objective and its associated measure to the emergency room."

This is significant because many hospitals are depending on CPOE orders coming from the ED to meet their 30 percent adoption requirement for meaningful use. Since orders coming from the ED, which is actually an outpatient department, are not included in ambulatory care, it wouldn't make sense to exclude them from hospital orders.

Another important relaxation is in the area of e-prescribing. This is the ability to electronically send an accurate and understandable prescription directly to a pharmacy. The e-prescribing requirement was lowered from the 75 percent under the proposed rule, to only 40 percent in the final rule for phase one. The requirements for phases two and three are not yet spelled out clearly. Eventually we need to reach 100 percent, and a lower initial bar only makes it a steeper climb to get to the goal line in the succeeding stages.

One huge barrier to physician adoption of e-prescribing has been the restriction on electronically sending prescriptions for narcotics. The Drug Enforcement Agency proposed a rule on June 27, 2010 that will allow e-prescribing controlled substances. This move has been cheered by providers and pharmacies alike. However, the rule will require two-factor authentication, which is going to require vendors to set up systems to enable this technology. So the final rule on meaningful use for phase one is not going to include requiring e-prescribing for the newly allowed controlled substances prescriptions.

The final rule also decreased the number of clinical quality measures that must be met to demonstrate meaningful use. The proposed rule listed 90 measures, of which eligible providers had to select and comply with three general measures and three specialty-specific measures. The final rule lists 44 measures for physicians with a requirement to comply with six, with no requirement to meet specialty-specific measures. Hospital clinical quality measures have been reduced from 35 to 15. For 2011, reporting will be through attestation; for 2012, electronic submissions will be required. HHS stated that they cut the clinical quality measures to reduce the burden on EHR vendors to meet the criteria. But since quality is such an important aspect of the overall goals of the program, these measures will certainly need to be ramped up in succeeding phases.

The final rule on meaningful use defers until phase two the requirement to submit claims and eligibility transactions electronically. With the forthcoming HIPAA 5010 and ICD-10 adoption, and creation of operating rules to make HIPAA standards more uniform, additional transaction processing criteria will be coming in 2013. The rule states, "In order to meet these and other administrative simplification provisions, most providers will have to upgrade their practice management systems or implement new ones."

Electronic copy of medical records required

The rule has added the recording of advanced directives and a provision for providing patients with educational materials, which were not included in the proposed rule. However, the proposed rule's requirement to provide an electronic copy of a patient's medical record is maintained in the final rule. This record must contain diagnostic test results, problem list, medication list, medication allergies, and for hospitals, discharge summary and procedures for at least 50 percent of patients within three business days. This requirement may prove to be one of the most difficult to achieve, but as Regina Holliday's poignant testimony during the press conference proves (video below), it is vital to include consumers in the process.

Regina Holliday is a 37-year old mother of two and an art teacher. Last summer, her husband, Fred, died from kidney cancer at the age of 39. She writes at the Medical Advocacy Blog and tweets at @ReginaHolliday.


June 29 2010

Open source and the VA's health transformation

Joseph Dal Molin, one of founders of the WorldVistA project and a speaker in the health care track at the upcoming OSCON convention, recently spoke with me about the Department of Veterans Affairs' historic VistA system and its expansion as an open source effort.

OSCON Health IT - Save 20%Specific topics covered in the 31-minute audio interview include:

  • How VistA evolved within a feedback loop.
  • How organizations outside the Department of Veterans Affairs use VistA.
  • How WorldVistA and other groups in the VistA community adapt the system to civilian needs and health care requirements.
  • A look at some of the tools for developing with VistA.

Dal Molin also provided links to projects and resources touched upon in the interview:

Joseph Dal Molin will be part of two health-related sessions at next month's OSCON convention (running July 19-23 in Portland, Ore.). Learn more about OSCON's new health track.

June 24 2010

Open source and health care already have a history

Fred Trotter, organizer of the annual OSHealthCon summit, has developed open source software for the health care field for many years. Most recently, he released a new national provider identifier search tool based on publicly available data.

Trotter will provide an overview of the open source health care IT space at next month's OSCON convention.

Health IT at OSCON 2010He previews his OSCON session and discusses the following in the associated podcast:

  • How mashing up data about doctors and treatment quality reveals trends and helps health care professionals make assessments.
  • How he curated and organized information on 3 million health care providers to create the NPIdentify project.
  • How open source data applies to the health care space, and where the real costs of software lie.

Fred Trotter will examine the history of the open source health care movement and its near-term future at the OSCON convention (running July 19-23 in Portland, Ore.). Learn more about OSCON's new health track.

June 21 2010

Giving patient data meaningful use

Arien Malec is coordinator of NHIN Direct, a new open-source effort sponsored by the Department of Health and Human Services (HHS) to improve health care through the secure exchange of patient data. Malec, a speaker in the health track at next month's OSCON conference, has led a uniquely open, community-based project to define standards for NHIN Direct.

Health IT at OSCON 2010In this 27-minute audio interview, Malec talks about:

  • Why privacy concerns make communication standards in health care more difficult than e-commerce.
  • The difficulties doctors face when trying to send data needed to treat patients.
  • The learning process HHS went through in deciding NHIN Direct was needed, as well as the steps it took to develop standards in the Internet's "rough consensus and running code" fashion.
  • The kinds of applications and services that should be facilitated by NHIN Direct.

Arien Malec will discuss the collaboration and framework that made NHIH Direct possible at the OSCON convention (running July 19-23 in Portland, Ore.). Learn more about OSCON's new health track.

June 17 2010

From Apache to Health and Human Services

Brian Behlendorf, one of the founders of the Apache web server project and the CollabNet cooperative software development company, is contracting now with the Department of Health and Human Services (HHS) on the CONNECT software project. CONNECT helps hospitals and agencies exchange medical data, which gives doctors critical information to improve patient care.

Behlendorf, along with project leader David Riley, will speak at OSCON about the importance of CONNECT and the way they and their colleagues built a robust community of government staff, volunteers, and healthcare IT vendors around it.

Health IT at OSCON 2010Behlendorf discusses the following in this 18-minute podcast:

  • The role of health data in promoting quality care, in improving our knowledge of what works, and in reducing healthcare costs.
  • How HHS is trying to improve the exchange of patient data for hospitals and doctors, agencies monitoring quality of care, and eventually patients themselves.
  • How, with Behlendorf's help, HHS opened up the CONNECT project, attracted both volunteers and vendors to improve it, and created a community with a sense of ownership.

June 16 2010

NASA technology leads to better medical decisions

Can a data-sharing technology developed at NASA'S Jet Propulsion Laboratory create better outcomes for medicine?

In fact, it already is.

In this podcast, Chris Mattmann, a senior computer scientist at the NASA Jet Propulsion Laboratory, talks with me about objected-oriented data technology (OODT) and health IT.

Mattman dives in to the following questions:

  • What is object-oriented data technology (OODT) and how does it relate to health IT?
  • How did NASA's Jet Propulsion Laboratory get involved with applying OODT to health IT?
  • What's it been like for a NASA project to work within the Apache Incubator and the open source community?
  • What is the Virtual Pediatric Intensive Care Unit?
  • How will data-driven tools help doctors, researchers and patients make better medical decisions?

Health IT at OSCON 2010Chris Mattmann will speak about grid software and healthcare IT in the health track at next month's OSCON conference.

June 11 2010

Here come the healthcare apps

"People in communities can improve their healthcare if they just have the information to do it," said Kathleen Sebelius, Secretary of Health and Human Services (HHS), at the Community Health Data Forum in D.C. last week.

The forum took place almost exactly a decade after President Clinton announced he would unscramble global positioning system data (GPS) for civilian use. Now, the potential for private enterprise to provision services using open data from the Community Health Data Initiative could match the billions of dollars made when the government unlocked GPS and NOAA weather data. Last week, in fact, I wrote about how HHS is making community health information as useful as weather data.

Sebelius delivered her remarks to both an online audience at and the collection of government officials, technologists and researchers gathered at the Institute of Medicine at the National Academy of Science. Her speech is embedded below.

After the jump, learn more about the healthcare apps that were featured at the forum's showcase.

Apps that use open health data

Health IT at OSCON 2010I covered the healthcare apps developed by National Association of Counties (NACO), GE, Bing, Healthways and Google last week.

Glimpses of a nascent ecosystem of innovation around community health data were on further display in the apps at the Community Health Data Forum. The selections included games, visualizations, web services, crowdsourcing platforms, and smartphone software.

Walking around the expo, I learned about the following apps:

  •, an interactive database that provides state- and country-level health data.
  •, an in-development iPhone app that engages healthcare practitioners about drug safety alerts
  •, an interactive website for describing the overall health of a community
  •, a web-based mapping platform that mashes up community and health resource data. It includes a HIPAA-compliant means for uploading patient information.

The following are six different apps / web services that also caught my eye at the forum.

Finding connections with Palantir

analyzetheus.jpgPalantir wowed the crowd in the main hall with its tech demonstration, which can be viewed in the video embedded above. Alex Fishman, an engineer, also announced at the forum that Palantir had integrated community health data into Analyze The US, a web application that allows citizens, researchers and government officials to explore community health data. A video comparing Medicare quality to Medicare spending -- an example of this tool in use -- is available at Palantir's Government data analysis blog.

Game mechanics and health data

scvngr.jpgCommunity Clash isn't the only game that's using community health data: SCVNGR combines the location-based technology that has become familiar to many through Foursquare and Gowalla with specific challenges to earn points. SCVNGR provides a platform for organizations to build games upon. To date, more than 550 institutions in 44 states and 20 countries have taken them up on the opportunity as clients, including museums, conferences, universities and cities.

John Valentine, SCVNGR's conference and events manager, says that SCVNGR now has more than 20 million locations in its system and is being downloaded thousands of times daily from the iTunes and Android app stores. In D.C., SCVNGR will be a part of the upcoming Digital Capital Week.

Medicare data gets mapped

The Community Health Map is being used by HHS internally to visualize and organize data, says Sohit Karol, a PhD student in the kinesthesiology department of the University of Maryland. The video below provides an overview of the core features of Community Health Map, a web application for visualizing Medicare datasets.

The tool was developed as a part of a course on Information Visualization at the University of Maryland. More information on the project is available through the class wiki.

iTriage puts hospitals in patients' hands

itriage.jpgThe iTriage app combines open health data with a large database of symptoms and a directory of healthcare service providers. A pair of emergency physicians, Peter Hudson and Wayne Guerra, developed iTriage to empower consumers to make better decisions.

"People are making bad decisions with third-party information," said Hudson at the expo. "The people making those decisions are costing the system money, mostly because they don't have the tools they need to understand."

Now, users can get quality reports on doctors, research symptoms, click to see nearby healthcare facilities and, where available, view emergency room wait times. "We're seeing a high level of engagement," said Hudson. "With people using it to find doctors, hospitals and pharmacists. We've seen 2 million page views on mobile already." Hudson said an iTriage API is in development.

Pillbox turns FDA drug label data into a platform

pillbox-screenshot.jpgPillbox, an open data initiative developed within the National Library of Medicine and the Food and Drug Administration (FDA), makes pill identification easier. Pillbox lets developers build applications for the web and smartphones through an open API.

David Hale, Pillbox's project manager, says a call to a poison control center for a pharmaceutical identification costs $45. With Pillbox and a web browser, that cost can be substantially reduced.

Hale explains more in this video from the USP Annual Scientific Meeting in September 2009:

Asthmapolis crowdsources better health for asthma patients

asthmapolis-screenshot.jpgAsthmapolis has developed a specialized device called a "Spiroscout" that, when attached to an asthma inhaler, uses GPS to track use, and share the time and location of symptoms.

Asthmapolis aggregates the data voluntarily provided by users and gives it to physicians, scientists and health agencies. The goal is to identify environmental exposures that trigger attacks. Asthmapolis has released a web app and its building a mobile phone diary and website for later release to the public.


The opportunities in healthcare IT will be explored at the upcoming OSCON conference. Learn more about OSCON's health track here.

June 02 2010

Making community health information as useful as weather data

hhsframeworks.jpgThe chief technology office of Health and Human Services, Todd Park, is fond of using the National Ocean and Oceanographic Association (NOAA) as a metaphor for the innovation that may be unlocked through releasing public data. NOAA data underpins and nearly every commercial meteorological service in the United States. Park has been working closely with other government officials and the technology community to put community healthcare data into a parallel role as a catalyst for innovation. In other words, HHS is creating a framework for government to act as a platform through the Community Health Data Initiative.

"The idea to make our community data as useful to the world as weather data or other types of data is to other parts of American life," said Park yesterday at a media briefing. "The real magic is that HHS put data out there on March 11 and the world responded. Innovators responded -- from Google to Microsoft to startups -- and have built amazing apps that HHS could never have built itself. That's built amazing value for citizens."

It's clear that at HHS, as Tim O'Reilly observed in his post on NHIN Connect and open healthcare records, "there's some fresh thinking going on here, influenced by the best practices of open standards and rapid Internet development."

This morning, Park will join HHS Secretary Kathleen Sebelius and White House CTO Aneesh Chopra at the Institute of Medicine at the National Academy of Science, where they will host the Community Health Data Forum.

For those unable to attend the event in person, the CHDI event will be streamed at and through this livestream. The agenda is available online. After the jump, you can get a sneak preview of some of the applications that will be going live today.

Apps, games and platforms for open health data

Yesterday's preview featured fascinating creations from the National Association of Counties (NACO), GE, Bing, Healthways and Google. Collectively, they hold promise for enabling citizens to make better health decisions and providers to make data-driven policy.

Google Fusion Tables and health data

hospital finder.jpgGoogle's Fusion Tables are essentially a lightweight online database powered by Google's cloud that allow users to examine data, combine it and share. Instead of the "best place to live," users can search through community health data, mash it up with maps and see which regions are, for instance, the "best places to have chest pain."

Using Fusion Tables and CHDI data, Dr. Ronnie Zieger, Google's chief health strategist (and a practicing doctor) showed at the media briefing how to filter for region and a certain value, like heart attack mortality. He called his particular mashup Hospital Finder, though the datasets could be adapted for may other users. Users can restrict a search to just hospitals with a "lower than" value, zoom in to maps or customize search results with metrics aggregated under "Heart friendly" or "People friendly" labels.

Bing visualizes health data

bing-search.jpgEarlier this year, Bing quietly began adding public health data provided by patient ratings immediately below search results for hospitals. The box also includes nearby facilities, ranked by distance, and the ability for searchers to share with their social networks.

Bing's product managers say they'll be introducing a “virtual supermarket” program that lets policy makers identify "food deserts." A new app called Bing HealthMaps -- live today -- allows users to search using geolocated data and add overlays for the incidence of health conditions, like Diabetes or obesity. Bing will also integrate Oodle classifieds with health data, enabling searches to load rentals, school ratings and layer on different conditions.

Network of Care for Healthy Communities

network-care.jpgNetwork of Care for Healthy Communities is a web-based portal that targets individuals and policy makers. The portal includes multiple components, including:

  • A service directory of every service that deals with health for a region, with more than 2,000 entries.
  • A library with more than 50,000 volumes. Both the directory or library can be dropped with a click into a personal health record.
  • A selection of links, including nearly 20,000 health-related links from around the country.
  • A legislative section that includes every bill dealing with health in state legislature and in Congress

The web portal could be adopted by other counties. For example, the template that's applied to Sonoma County can be replicated fairly easily. The portal is built upon a number of open source and proprietary applications. As it's also a service, there would be a cost associated with customization.

General Electric commits to health apps


GE launched in May of 2009, focusing on showing data to drive change. Infographics and visualizations, like those that show the cost of getting sick, have received hundreds of thousands of views with no promotion. An interactive health visualizer has been particularly popular. GE will be adding new apps that present more health data in aggregate, including community health rankings. An interactive map, for instance, provides visualization for regional public health data all across the United States.

Social gaming for better health?

community-clash.jpgA health game called Community Clash will marry public health data to game mechanics. Users can get their own "well-being score" and then share their results with friends.

The game mashes up four data sources: CHDI, Twitter, Gallup polls and well-being assessments. In the future, the game's creators hope to build leader boards, encourage social comparison, and add geo-location and sentiment analysis.

Open data as a means to healthier communities

By releasing data and empowering the technology to build applications, HHS CTO Todd Park hopes to catalyze healthcare policy, delivery and services. The same evidence-based medicine that bids to make healthcare better could be applied on an even grander scale, and yet only for the cost of releasing good data. That's a bargain Park seems willing to make. "In less than 90 days, we've had a growing number of innovators team up to take ideas that originated on March 11 and then expand upon them to turn into beta applications," he said.

Park formally announced the launch of an interim CHDI website, which is already accessible through under the "Connect with data" button. He also said that there will be a new HHS Health Indicators Warehouse, launching in December 2010, that will have Medicare community-level indicators.

The Community Health Data Forum will kick off the Health 2.0 Developer Challenge (, which will extend through this fall. Over the next four months, the Challenge will host a series of code-a-thons and team competitions to build apps based upon CHDI data.

"We're going to ask developers to submit the coolest apps they could use to improve the mission," said Park. Regional events will culminate in a final challenge during the fourth annual Health 2.0 Conference in San Francisco.

Todd Park on open health data and innovation

At the recent Gov 2.0 Expo in Washington, I spoke with Park about the Community Health Data Forum, NHIN Direct, innovation and much more.

May 01 2010

Report from Health Information Technology in Massachusetts

When politicians organize a conference, there's obviously an agenda--beyond the published program--but I suspect that it differed from the impressions left by speakers and break-out session attendees at Health Information Technology: Creating Jobs, Reducing Costs, & Improving Quality.

A quick overview of what I took away from the conference is sobering.
Health care costs will remain high for many years while
institutionalize measures intended to reduce them. Patients will still
have trouble getting their records in electronic form to a different
doctor (much less access it themselves). And quality control will make
slow headway against the reluctance of doctors to share data on
treatment outcomes.

Still, I have to give the optimists their due, and chief among the
optimists is Richard Shoup, director of the href="">Massachusetts eHealth Institute and one
of the conference's key organizers. He points out that the quality
control measures emerging at the federal level (the "meaningful use"
criteria for electronic health records) meshes excellently with both
the principles and the timing legislated in href="">Section
305 in the Massachusetts health care bill. Massachusetts has a
long history of health care IT deployment and of collaboration to
improve quality. "All stakeholders are at the table," he says, and the
Massachusetts eHealth Institute recently floated a href="">statewide plan for
implementing health care IT.

A conference fraught with political meaning

Gov 2.0 Expo 2010There was no doubt that politicians high up in the federal and Massachusetts governments respected the significance of this conference, which was also called the Governors National Conference (no missing apostrophe here; the conference really did draw representatives from many governors). Attendees included Massachusetts governor Deval Patrick (who came straight from the airport to speak), Senate president Therese Murray, US Surgeon General Regina Benjamin, and health care national coordinator David Blumenthal. I haven't even mentioned the many other scheduled speakers who could not attend for one reason or another.

As Governor Patrick indicated, Massachusetts is an excellent locale
for this conference. Besides the high concentration of medical
institutions that attract patients from around the world, and a decent
number of innovative research facilities, we are leaders in electronic
physician order entry and other aspects of health care IT.

I wondered, though, why no venue for this conference could be found in
the Longwood medical area. It would require handling the crowds
differently, but perhaps the main drawback is that Longwood would
swamp the out-of-towners in attendees from local institutions. But
instead, we were located in the new conference center area of Boston,
a place devoid of signs of life even though it's only a fifteen-minute
walk from the bustling financial district.

The conference met the needs of both the state and federal
administrations. Patrick hit on three major topics on many people's
minds: adding jobs, lowering health care premiums for small
businesses, and reducing the burden of health care in local

The pressures at the state level are out in full view. A recent flap
frightened the health care industry when insurers proposed annual
insurance policy increases of up to 22% and the administration slapped
them down. Although an annual 22% raise is clearly unsustainable,
imposing arbitrary limits (known as capitation) usually leads to
equally arbitrary denials of care instead of the creative fine-tuning
required to intelligently eliminate waste. I noted today that Paul
Tang, who is responsible for defining meaningful use for the federal
stimulus bill, says that to improve quality, the health care system
has to move from fee-for-service to paying for outcomes, but that we
don't yet know how to do make such a major change.

As mentioned earlier, the Massachusetts health care bill as well as
the federal recovery and health care bills include ways to collect
data, analyze it, and disseminate results meant to raise quality while
lowering costs. I have to say that I'll believe it when I see it,
because "doing the right thing" (as David Blumenthal called the
implementation of electronic health records) has to fight barriers put
up consciously or unconsciously by medical institutions, individual
doctors, and electronic health record vendors.

Nationally, both the stimulus package and the health care bill
stipulate very ambitious goals and extremely accelerated
schedules--and still, many people worry that the incentives aren't
strong enough to make them come to pass.

David Blumenthal lays out the stimulus package

The Department of Health and Human Services, to administer the
billions of dollars provided in the stimulus package and the demands
on health care providers that may dwarf that appropriation, set up the
Office of the National Coordinator with the task of making and
administering regulations. David Blumenthal came from Boston back to
Washington to take on the job of National Coordinator, and
practitioners in health care now hang on his every word.

Under such circumstances, one has to look beyond the official aspects
of Blumenthal's keynote and look at particular inflections or
emphases. Most telling to me was his metaphor of putting heath care
providers on an escalator. The point was that no matter what problems
they encounter, they should keep moving. It's OK to start slow (he
spoke of making the first step low enough) as long as the institution
keeps adding functions along the sequence specified in the ONC

Given the extensive goals in using electronic records, sharing data
with relevant agencies, and improving clinical care, Blumenthal made
some statements one could see as defending the initiatives. He pointed
out that when the goals were circulated for public comment, many
people questioned the ambitiousness or timing, but hardly anybody
challenged the direction they were taking or the value of the goals.

He did admit some of the barriers we are collectively facing:

  • The unmatched diversity this country presents in geography,
    demographics, income and educational levels, political philosophies,

  • The risk of holding back innovation. As standards are specified in
    more detail, they increase the chance that conforming implementations
    will interoperate, but also the chance that future advances in a field
    will be hard to reflect in product improvements. (John Halamka, CIO of
    Harvard Medical School and an advisor to the federal government on
    implementing health care policy, issued a similar warning on his panel
    the next day.)

  • Resilient problems with privacy. It's worth mentioning, in this
    regard, a study cited by a lawyer on a a later panel, David Szabo.
    Fears of privacy hold back many people from using personal health
    records, and are cited even by a large percentage of people who use
    them. Only 4% of respondents trusted HIPAA to protect them. But many
    say they would start using personal health records if privacy laws
    were improved.

The high-level priorities cited by Blumenthal were to help small and
rural providers who have few resources (the task of Regional Extension
Centers, a new institution in health care created by the stimulus
bill) to get data in the hands of patients, and to "make electronic
systems so easy to use that doctors can't wait to turn them on in the
morning." I'll return to this sunny notion later.

Patient-centered care

As I claimed in an href="">
earlier blog, the revolution that will really crack open the
electronic health record field is the need to share data with and
among patients. The same point was raised today by Paul Tang.

One of the barriers to giving data to patients is that, frankly, it's
not in a form they can use. Current records are fashioned more toward
insurance claims than clinical needs. They can be confusing and
positively frightening to someone who doesn't understand the peculiar
circumstances that drive the entries. Doctors are consequently
reluctant to open current records to patients. Barbra Rabson also said
that this dominance of billing data makes it hard to collect useful
data for quality control, but that it will be several years before
doctors provide the clinical data that will provide a better basis for

Themes that came up throughout the conference suggested that
improvements in health require patient education. Some speakers
objected to using the term "patient" because that already implies
ill-health and sets up a situation where the professional health
provider is in control.

John Halamka said that the recently passed federal health care bill
requires health care systems to make it possible for all patients to
get electronic access to their data.

How can we get patients to use this power? They need to understand,
first of all, the benefits of having access to their data. John Moore,
who promotes patient-centered care at href="">Chilmark Research, said that
for many people this will begin at the office, because some companies
require employees to take some responsibility for managing their own
insurance. Patient records may become more widely used as patients
find value in them far beyond tracking their treatment: to order
refills of medicine, make follow-up appointments, and so on.

Next, patients have to learn the value of adding to that data, and how
to do so. (Another problem with patient-centered care is that some
patients deliberately or mistakenly enter incorrect information or
fail to record important events.) As US Surgeon General Regina
Benjamin pointed out in a teleconferenced talk, we have to design a
patient-centered system that can be used even by illiterate patients,
who are quite common in our country and who need perhaps even more
assistance than the people who can read this blog.

With all these practices in place, patients can turn to comprehending
the information they get back and using it to improve the quality of
their lives. One doctor even pushed to pay patients for complying with
treatment plans, to put some responsibility for outcomes on the

Girish Kumar Navani, CEO of the eClinicalWorks health record vendor,
mentioned that involving patients in their care provides a powerful
motivation to expand access to high-bandwidth Internet.

Privacy came up in this talk, as it did in nearly every one. David
Szabo reassured us that there are more legal protections in place than
we tend to admit. Many patient record sites post privacy policies. The
FTC, and many state attorneys general, vigorously these policies. What
Szabo did not address--because, I suppose, it fell outside legal
considerations--was the risk of data breaches, which should concern us
because attacks on health care repositories are on the rise.

Data exchange

One pediatrician recounted a teeth-clenching story of a doctor who
moved his practice to another hospital and instantly lost electronic
access to all his records. Any patient who wants to stay with him will
have to obtain records in printed form and have them re-entered at the
new hospital. This frustrating scenario gets repeated at every level
of the national health system as systems trap data in proprietary

Several members of the ONC have boasted how their specifications for
electronic records and health information exchanges say nothing about
architecture, being "technology neutral." One can interpret this as
modest caution, but could we also see in it a veiled plea for help, an
acknowledgment that current standards and protocols aren't up to the

While many people criticize the vendors of electronic health systems
for incompatibility, Micky Tripathi, president of the Massachusetts
eHealth Collaborative, said that doctors are more to blame. The
doctors have assigned no importance to sharing data with other doctors
or with responsible agencies, and just demand electronic systems that
allow them to continue with their old workflows and require the least
possible change in behavior. One doctor in a break-out session
reported that doctors use the systems inconsistently or enter data in
unstructured comments instead of fields designated for that data, so
that automatic searching and aggregation of data becomes impossible.

Tripathi pointed out that standards in themselves don't get people to
communicate. The history in every field is that people start to feel a
burning need to communicate; systems and standards then emerge from
that. The very early days of telephony resembled today's health
information exchanges: you needed a separate phone and a
point-to-point line for each person you wanted to talk to. Even in
1901, the United States had 2,811 independent phone networks.
(Tripathi didn't point out that it took heavy-handed government
mandates to bring that number down to one, and that this AT&T
network eventually became a bottleneck--if not a chokepoint--for
innovation.) His main point remains valid: most systems start out
cumbersome and expensive before best practices and standards help them
converge on elegant solutions.

Along those lines, a commenter in one forum praised the New England
hospital network, NEHEN, and claimed that it started before
applications were available, but generated innovative applications.
J. Marc Overhage, a leader in the use of electronic records for
clinical decision support, added a cute reference to McDonald's, which
waits for a highway to be built before putting a restaurant at the

Daniel Nigrin, CIO of Children's Hospital, also praised NEHEN but
reminded us it was designed only for doctors, not patients.

I talked to managers at Coping
, a firm that helps hospitals assess their quality of care
by analyzing statistics and presenting them in visual displays. The
biggest barrier Coping Systems face is the willingness of hospitals to
share data. Patient data must be anonymized, of course, but sometimes
hospitals won't share data about quality of care unless the name of
the institution is removed. Even by looking at their own data in
isolation, though, a hospital or an individual doctor can discover
insights that change treatment. They can check the expected versus
actual outcomes for individual doctors, for a doctor working with a
particular nurse, for a particular time of the day, etc.

Tang mentioned a simple example of how public health could be improved
by data collection. During last year's rush to provide H1N1 flu
vaccines to the most critical people, the government divided the
limited supplies up geographically. Some areas with high
concentrations of vulnerable people were severely constrained, and if
we had data about the locations of people who needed the vaccine, we
could have distributed it on a much fairer basis.

John Halamka, while acknowledging that many current standards for
electronic records are adequate for the task, called for better
standards to classify patients and treatments. Right now, for
instance, it's hard to define who is diabetic, which makes it hard to
compare statistics about the treatment of diabetics by different
doctors. A recent ONC meeting, covered in href="">another
Radar post, discussed standards for health IT.

Halamka said that electronic records, for which he is a strong
advocate, will catch on when doctors realize they facilitate new
activities that the doctors could never do before. In this way Halamka
fleshed out and energized Blumenthal's dream of "electronic systems so
easy to use that doctors can't wait to turn them on in the morning."
Whether this involves improvements to public health or something more
closely aligned to doctors' day-to-day practices, good planning will
help doctors, patients, and researchers all move toward a brighter
health care future.


March 24 2010

First impression: Health reform and Health IT

President Obama has signed the health reform package (PDF). Love it or hate it, the health reform passed by the Senate and the House has now become law. The Senate will grapple with the fixes proposed by the House and we may end up with some changes, but the existing law will have a wide-ranging impact on the health IT industry. I am slogging my way through reading the bill and thought I would point out highlights I've found so far.

There are sections on Quality Reporting, Administrative Simplification, creation of a National Medical Device Registry, a new Center for Comparative Effectiveness Research, and the creation of the Assistant Secretary for Health Information. I'm sure there is still a great deal more that I will uncover over the coming weeks, but some of the pertinent sections of the bill are:

Under the section, Part D - Implementation of best practices in the delivery of healthcare, the health reform package establishes within HHS an Assistant Secretary for Health Information. This will certainly raise the level of the conversation surrounding health IT. The Assistant Secretary will work “in consultation with the Director of the Office of Minority Health, and the Director of the Office of Civil Rights, of the Department, develop standards for the collection of data on health and health care with respect to primary language.” The Assistant Secretary will also coordinate with the head of the Office of the National Coordinator for Health Information Technology to ensure optimal use of health information technology. So this position will certainly augment the work of the ONC.

I think the creation of a National Medical Device Registry will have a profound impact on health IT. The registry would list devices by type, model and serial number or other unique identifier. It is intended to help HHS assess the post-market safety and effectiveness of all class III devices, and all class II devices that are implantable, life-supporting or life-sustaining, according to the bill. The registry, to be established by HHS, would link data provided by manufacturers to the FDA, with outcomes data from multiple sources. The bill also authorizes HHS to require device makers to submit "such other information as is necessary to facilitate post-market assessments of device safety and effectiveness and notification of device risks."

The section under subtitle A - Comparative Effectiveness Research, states that “the Secretary shall establish within the Agency for Healthcare Research and Quality a Center for Comparative Effectiveness Research” and that “the Center may secure directly from any department or agency of the United States information necessary.” This new Center for CER will be encouraging “the development and use of clinical registries and the development of clinical effectiveness research data networks from electronic health records, post marketing drug and medical device surveillance efforts, and other forms of electronic health data.”

There is significant language dealing with administrative simplification as Health Data Management reports:

The bill requires HHS to seek public input and consider whether to standardize the application form for insurance enrollment, as well as worker's compensation transactions, and automobile insurance-related health care transactions ... Further, HHS is mandated to consider "whether there could be greater transparency and consistency of methodologies and processes used to establish claim edits used by health plans," and whether plans should be required to publish their timeliness of payment rules.

There is also a section referring to health IT regarding enrollment standards and protocols: "Not later than 180 days after the date of enactment of this title, the Secretary, in consultation with the HIT Policy Committee and the HIT Standards Committee, shall develop interoperable and secure standards and protocols that facilitate enrollment of individuals in Federal and State health and human services programs."

The section under subtitle E - Public Reporting on Health Care-Associated Infections, is also very interesting. Aside from the technology involved in collecting data, the requirement that "information shall be set forth in a manner that allows for the comparison of information on health care-associated infections" provides some interesting possibilities for mashups with existing data sources.

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