NCBI Celebrates International Love Data Week

Providing free and open access to scientific literature and data  Do you love biological data? Join NCBI in celebrating International Love Data Week, February 12-16, 2024! Love Data Week is an international celebration of data, which takes place every year during the week of Valentine’s Day. This year’s theme is “My Kind of Data,” focusing on … Continue reading NCBI Celebrates International Love Data Week

✚ The Process of Finding Data

Welcome to issue #211 of The Process, where we look closer at how the charts get made. I’m Nathan Yau, and this week I’m thinking about the process of finding data, because without data, there is no visualization.

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Moving data at the speed of a virus

Scientist reviews results from testing

by Rachel Shepherd, specialist, Informatics, APHL

The public health system serves as the backbone to our nation’s health and safety; there is nothing more collectively critical than making sure we are prepared to respond to threats. When a public health crisis like COVID-19 strikes, laboratories need to get mechanisms in place fast to test for a new pathogen. But there’s another, equally important side to that story. Without the technical infrastructure to send and receive data, and without agreed-upon language to communicate information, there could be no comprehensive response or strategy. In other words, you can build a car to get from Point A to Point B, but you won’t get very far if there are no roads. This is a story about roads.

In 2008, APHL built the APHL Informatics Messaging Services (AIMS) Platform, a messaging service for public health laboratories and agencies to transmit their influenza results to the US Centers for Disease Control and Prevention (CDC) for surveillance. Over time, AIMS went from having a handful of laboratories signed on to establishing connections with every state in the country, making, for the first time in history, near real-time national flu surveillance possible.

Today, most of the nation’s public health network—more than 200 public health laboratories and agencies, clinical and commercial labs, hospitals and medical providers, and federal agencies—uses AIMS to exchange critical health data, sending more than 25 million messages per month. AIMS now serves as a “super highway” on which testing data for several major public health initiatives flow, providing the means for national surveillance. While its functionality continues to expand, at its core AIMS ensures that important data travel fast into the right hands so that it can be actionable when it matters most.

When cases of COVID-19 began cropping up in the US, public health laboratories began getting testing up and running successfully. The public heard about assays not working, testing backlogs, overwhelmed staff, and reagent shortages. What the public didn’t hear about were the crises averted. Amidst all of the pandemic chaos, there has been at least one major positive: we already had a national data messaging platform that connects all of public health. No infrastructure had to be built; it’s been in place and growing since 2008.

When public health entities connect to AIMS, they enable faster transmission of a higher volume of data for surveillance or trend analysis. When information is exchanged through AIMS, what used to take days now takes minutes, and time saved—whether in a pandemic or in the routing and sharing of test orders and results—translates to lives saved. Doctors can make better informed decisions about patient-care when they have timely access to test results, and epidemiologists can analyze data to identify emergent threats before they become crises.

In addition to transporting data, AIMS also has portal services that automatically transform and translate data to different message formats and standards; in other words, users are able to communicate through AIMS, even if they are speaking different languages. AIMS converts messages and makes them readable to the receiver. Because of the sensitive nature of the data that flows through AIMS, AIMS takes security seriously and meets some of the most stringent security standards in the country.

AIMS also allows multiple users to take advantage of shared resources—for instance, laboratories can maintain one route on AIMS for all of their trading partners rather than having to establish and maintain an individual route with each. This is a major benefit to AIMS users. Typically, each laboratory would have to set up a connection with every entity with whom they exchange data—clinical laboratories, hospitals, public health agencies. When laboratories or agencies are on AIMS, they can condense all of their routes into a single connection and significantly reduce time and effort that would otherwise have to be dedicated to each.

In just over a month’s time, APHL worked with every single public health laboratory and agency to make sure they were able to electronically send their COVID-19 requests and results to CDC. They also worked on developing COVID-specific vocabulary and coding for testing so that when laboratories started conducting testing, they were all using the same terminology from the start. This means that all results sent to CDC were standardized—no effort or time had to be spent deciphering and comparing reports across laboratories to try and synthesize.

APHL’s job is to build and leverage technical solutions that will ease the burden on laboratories, not only for this response effort and a future of unknown threats, but to improve and simplify data exchange for public health at large on a day-to-day basis. When CDC launched its Data Modernization Initiative, it placed the urgent need for meaningful data to be sent and received faster; public health depends on information and results to be communicated quickly for surveillance, intervention and treatment. Time is critical. With the response to COVID-19, there is now a national recognition and comprehensive effort to modernize tools, technology, strategy and perceptions around data.

COVID-19 may very well prove to be a once-in-a-lifetime public health emergency. It may not. All we know is that we don’t know, and that our collective health and safety depends on having an efficient exchange mechanism in place to surveil, protect and be prepared.

The post Moving data at the speed of a virus appeared first on APHL Lab Blog.

APHL, partners garner $550M for data modernization initiative

Image depicting data transfer

Like many aspects of public health, the effective, efficient movement of public health data has been chronically underfunded. Faced with this perpetual issue—combined with a sharp increase in data production from new laboratory techniques that have added great volumes of data to an overburdened system—APHL joined with the Council of State and Territorial Epidemiologists, the National Association of Public Health Statistics and Information Services, and the Health Information and Management Systems Society in 2019 to engage in the first serious effort to secure federal funding for improved handling of public health data.

APHL contributed to the production of materials that quickly and easily explained the problem and urged Congress to provide $1 billion over the next ten years, at a rate of $100 million per year. With these materials in hand, APHL met with interested partners on Capitol Hill to press the case for funding. It also organized a Hill briefing for Congressional staff where subject matter experts, such as APHL member Dr. Joanne Bartkus, presented on the challenges with existing data handling processes. Dr. Anne Schuchat, Principal Deputy Director of the US Centers for Disease Control and Prevention (CDC), highlighted these same challenges in virtually every hearing where she testified on public health emergencies.

These educational activities culminated when Congresswoman Rosa DeLauro took up data modernization as one of her key initiatives in the Labor-HHS appropriations bill. Congresswoman DeLauro successfully included the first installment of $100 million for CDC to pursue the data modernization initiative in the Labor-HHS appropriations bill for fiscal year (FY) 2020. This is an unparalleled achievement in the first year of any significant effort, and one made even more remarkable considering that data management is not a particularly trendy or exciting topic.

Though the Senate never produced a Labor-HHS bill for FY 2020, but indicated that it would not accept the House amount of $100 million for data modernization, APHL persevered, continuing to work closely with Senate staff to advance the funding of the data modernization initiative. Ultimately, Congresswoman DeLauro was able to include $50 million in the final version of the bill. The COVID-19 response allowed for an additional $500 million to be directed to data modernization, and it appears that the balance of the $1 billion ($450 million) could be included in the next emergency supplemental funding bill.

APHL continues to pursue additional annual federal funding for the data management initiative, beginning with fiscal year 2021, and production of the required CDC report to Congress detailing how these federal funds will be expended in 2020 and the spend plan for the subsequent nine years.

While APHL looks forward to more nimble response to public health emergencies, such as COVID-19, due to improved public health data management, the association remains energized by the benefits to result from the $550 million already allocated to the data modernization initiative.

The post APHL, partners garner $550M for data modernization initiative appeared first on APHL Lab Blog.

APHL and partners: COVID aid package provides much needed funding for data modernization

Data illustration

FOR IMMEDIATE RELEASE
March 27, 2020

Washington, D.C. – Together, the Association of Public Health Laboratories (APHL), Association of State and Territorial Health Officials (ASTHO), Council of State and Territorial Epidemiologists (CSTE), Healthcare Information & Management Systems Society (HIMSS), National Association of County and City Health Officials (NACCHO), and National Association for Public Health Statistics and Information Systems (NAPHSIS) issued the following statement in response to the Coronavirus Aid, Relief, and Economic Security (CARES) Act:

We applaud members of Congress for providing $500 million for the Data Modernization Initiative at the Centers for Disease Control and Prevention (CDC) that will transform public health data systems and save lives.

The nation faces an unprecedented challenge to address the COVID-19 pandemic. Now, more than ever, it is critical to have a strong public health surveillance system that detects and facilitates immediate responses and containment of emerging health threats. The CDC—together with state, local, territorial, and tribal health departments—have taken important steps to improve the nation’s public health data infrastructure, but due to funding shortages, this has often been in a piecemeal approach.

The COVID-19 pandemic has exposed gaps in our nation’s outdated public health data systems and a workforce struggling to keep up. The United States currently relies on error-prone, sluggish and burdensome manual and paper-based data exchange methods such as faxing and phone calls to share critical public health data, especially with the health care sector. Simply put, the virus is moving faster than the data and when data move more slowly than diseases, the American people suffer. We are watching as our leaders struggle to make critical decisions without complete data.

An integrated, high-speed, networked health system—from laboratories to health care facilities to public health authorities—with fast and reliable data is necessary in order to protect Americans from COVID-19 and future health threats. Modernization is not just network upgrades; it is a commitment to building and sustaining a world-class data workforce and data systems that are ready for the next public health emergency. The funding provided in the CARES Act is an enterprise-level commitment to build a public health data superhighway of the 21st Century to speed the transmission of accurate, complete data.

We look forward to working with Congress to ensure sustained annual funding for CDC’s Data Modernization Initiative and with CDC in formulating its multi-year implementation plan.

Contact:  Erin Morton at 202.484.1100 or emorton@dc-crd.com

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New Lab Matters: Making data fly

Cover of Fall 2019 issue of Lab Matters magazine illustrating high volume of data

In today’s technology-connected world, information moves quickly. But in the world of public health, pathogens often travel faster than the data needed to diagnose, treat and prevent illness. Reporting delays and incomplete or incompatible data delay insights into pressing public health problems. The solution? Investing in public health infrastructure and resources to rapidly deliver data to public health and clinical decision makers.

Here are a few of this issue’s highlights:

Read the full issue.

Subscribe and get Lab Matters delivered to your inbox, or read Lab Matters on your mobile device.

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Supporting rapid exchange of public health data is urgent, crucial and laden with challenges

By Jody DeVoll, advisor, communications, APHL 

In an era when digital communications move at blazing speeds, public health laboratories still have to resort to fax, email or phone to exchange data with some partners. Yet, this is only one of the obstacles to rapid exchange of critical public health laboratory data needed for public health surveillance, emergency response and patient care.

The volume of public health laboratory data presents an obstacle in and of itself. Infectious diseases, environmental toxins, foodborne illnesses, radiological exposure, hazardous chemicals, high consequence pathogens, antibiotic resistance: public health laboratories test them all. Add to this exponential increases in volume from the expansion of advanced molecular technologies like next-generation and whole genome sequencing, and the result is terabytes of data that public health laboratories must manage, interpret, store and share.

In addition, dozens of different, stand-alone systems make programming and maintenance of laboratory reporting systems labor-intensive and costly. For example, the US Centers for Disease Control and Prevention (CDC) maintains over 100 surveillance programs, each with its own reporting system. Dari Shirazi, APHL’s health information technology manager, explains how these many systems affect public health laboratory operations: “It’s as though you have a houseful of furniture to arrange in dozens and dozens of different houses and, periodically, you receive shipments of additional furniture that also has to be arranged.”

Of course, CDC is not public health laboratories’ only data exchange partner. Other federal partners, state and local health agencies, hospitals and others also require laboratory data, and they too want it parsed and transmitted through their proprietary systems.

With all these demands, data scientists at public health laboratories face a mountain of work, yet their numbers are few. The number of graduates in public health informatics has not kept pace with demands for workers from public and private sector institutions. As a result, graduates can choose from an array of positions, and they often choose private sector jobs which tend to be higher paying and longer-term than lower-salaried, time-limited positions at a public health laboratory.

Huge data volumes, a multitude of reporting systems and a shortage of public health data scientists make data exchange a laborious, costly and frustrating enterprise for public health laboratories. However, the implications extend beyond laboratories to the populations the data is intended to protect, in other words, us. According to Peter Kyriacopoulos, APHL’s senior policy director, “We are fast approaching the confluence of events on the management of public health data that threatens the very relevance of governmental public health. The volume of data generated by new laboratory technologies adds to the burden of over 100 inefficient data reporting systems that each have been designed to move specific information to a point at CDC, which constrains the utility of that information.

Fortunately, there are signs of change. Four national health organizations — APHL, the Healthcare Information and Management Systems Society (HIMSS), the Council of State and Territorial Epidemiologists (CSTE) and the National Association for Public Health Statistics and Information Systems (NAPHSIS)  – launched the Data: Elemental to Health campaign calling for a $1 billion investment in congressional funding over the next decade to modernize public health data/IT systems and develop a skilled workforce of data/IT specialists. Under the plan, state, local, tribal and territorial health departments would receive direct funding for these purposes through the CDC.

Over the last six months, the campaign has convened stakeholders, made the case for improved data systems to congressional and administration staff, appeared before the House Appropriations Subcommittee, hosted Hill briefings and organized a Day of Digital Action. Already there are results:

  • The House appropriations bill includes $100 million in fiscal 2020 for public health data systems and workforce modernization
  • The House LIFT America Act authorizes $100 million per year for five years to develop public health data systems and train staff
  • The Senate Saving Lives Through Better Data Act authorizes $100 million per year for five years for systems and people
  • The Senate Lower Health Care Costs Act authorizes “such sums as may be necessary” over five years to modernize data systems.

How would legislation initiated through the campaign support public health laboratories? First and foremost, it would help them to strengthen their LIMS. Shirazi explains, “A LIMS is a living, breathing thing that has to grow with lab needs. These needs change every year as the lab takes on new and novel types of testing.” Building LIMS capacity would enable laboratories to expand capability for data capacity, exchange and analytics; eliminate manual entry of test results; and provide secure, instantaneous communication of results to health partners. In addition, legislation initiated through the campaign would underwrite laboratory systems for exchange of electronic health records, National Notifiable Disease Surveillance System data, vital health records (e.g., notices of births and deaths) and other public health surveillance data.

Looking forward, the US would do well to complement the advances initiated under the Data: Elemental to Health campaign with a data transfer solution that consolidates all public health data systems into one. Kyriacopoulos notes that: “the creation of a single reporting site, that multiple data providers and users can report to and receive information from, would be a significant improvement that would allow for the efficient and comprehensive use of this data throughout the federal/state/local public health system.”

 

Photo credit: James Marvin Phelps

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New Lab Matters: The ABCs of PFAS

New Lab Matters: The ABCs of PFAS | www.APHLblog.org

First discovered in the 1930s, per- and polyfluoroalkyl substances (PFAS) now pervade almost every aspect of modern life. In fact, PFAS compounds are found in everything from dental floss to cookware. But human exposure to PFAS comes at a cost, and as old compounds are removed from production, new compounds take their place. So how does a public health laboratory handle this challenge with limited resources? As our feature article shows, by establishing new public-private partnerships.

Here are just a few of this issue’s highlights:

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Gordon Research Conference on Craniofacial Morphogenesis and Tissue Regeneration (February 11 – 16, 2018): Licia Selleri & Ophir Klein

  Gordon Research Conference on Craniofacial Morphogenesis and Tissue Regeneration (February 11 – 16, 2018): Licia Selleri & Ophir Klein   Posted August 22, 2018 by post-info As part of its mission to encourage engagement

History of the word ‘data’

Sandra Rendgen describes the history of “data” the word and where it stands in present day.

All through the evolution of statistics through the 19th century, data was generated by humans, and the scientific methodology of measuring and recording data had been a constant topic of debate. This is not trivial, as the question of how data is generated also answers the question of whether and how it is capable of delivering a “true” (or at least “approximated”) representation of reality. The notion that data begins to exist when it is recorded by the machine completely obscures the role that human decisions play in its creation. Who decided which data to record, who programmed the cookie, who built the sensor? And more broadly – what is the specific relationship of any digital data set to reality?

Oh, so there’s more to it than just singular versus plural. Imagine that.

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