Metabiota's Collection of Open Data
•Download as PPTX, PDF•
1 like•453 views
Metabiota is an infectious disease research organization focused on the outbreak detection and tracking. As far as open data is concerned, Metabiota collects human and animal samples looking for evidence of disease emergence in field sites located in viral hot spots. They do so as part of formal and informal networks comprised of Ministries of Health, labs and universities, along with government partners in places like Cameroon, the Democratic Republic of Congo, Ukraine and China.
Recommended
Recommended
More Related Content
Recently uploaded
Recently uploaded (20)
Featured
Featured (20)
Metabiota's Collection of Open Data
Editor's Notes
- Thank you to the World Bank for inviting me here today. My name is Ash Casselman and I am a Product Manager at Metabiota, in San Francisco. Metabiota is an infectious disease research organization focused on the outbreak detection and tracking. As far as open data is concerned, Metabiota is on the other side of the fence from our friends at Climate Corp – we are the collectors. We collect human and animal samples looking for evidence of disease emergence in field sites located in viral hot spots. We do so as part of formal and informal networks comprised of Ministries of Health, labs and universities, along with government partners in places like Cameroon, the Democratic Republic of Congo, Ukraine and China.
- Following a decade of highly publicized outbreaks - SARS, H1N1, H5N1 – the developed world is aware of the risk of infectious diseases in a way it wasn’t before. For all their perceived randomness, pandemics are increasingly likely due to a confluence of environmental, cultural and economic factors.
- These include: the increased demand for animal protein and the farming processes used to satisfy this demand.
- To give you an idea, I’d like to show you this image from the Meat Atlas, a recent report on the state of meat production. I found this image particularly striking. That orange orb in the upper right hand corner of the frame is chicken. We slaughter 58 billion a year.
- The expansion of international travel which makes it possible for a virus to circumnavigate the globe in less than 36 hours.
- A good example of how climate change for instance might affect infectious diseases are the populations of malaria-carrying mosquitos that can now be found along the U.S.-Mexico border. As temperatures diverge from normal ranges, vectors sometimes relocate into previously uninhabited regions.
- It’s estimated that a severe flu pandemic could cost more than $3 trillion in GDP. The likelihood of a pandemic-level outbreak is no longer simply a troubling consideration for public health officials – but one which is also in the consciousness of the public itself. Your commute simply takes on a very different flavor once you become concerned about the person coughing next to you on the metro. In places where we work like Sierra Leone - where the risk of death from Malaria is the highest in the world – the people know intimately the reality of the effects on individuals and the greater community. But they also recognize that many infectious diseases, like Malaria, are highly preventable.
- The vast majority of human infectious diseases come from animals. HIV is a good example in that it originated in Chimpanzees and later became completely adapted to its human hosts. When most of us think about AIDS or HIV, we think of the early 80s, when observations of a rare form of pneumonia preceded the identification of the virus. Once it developed into one of the worst pandemics of our time, it was quickly imbued with deep social, cultural and political meaning. However, it is simply one of many viruses that has made such a jump. Identifying these outbreaks as the emerge from animals and into humans requires the cooperation of an international and interdisciplinary group looking both deeply and broadly at the interconnected state of health of people, animals and the environment. This concept, called One Health, recognizes the fluidity of life on our planet. This is a core tenet of our work at Metabiota.
- In a practical sense this effort necessitates the collection of vast quantities of health data. To capture this information we work within a substantial network comprised of Ministries of Health, labs, universities and NGOs. Our database currently houses over 200,000 specimens collected from over 20 countries. Our human sample collection focuses on individuals working at the human-animal interface, so for instance, hunters or people working in wet markets. Our animal sample collection includes known wildlife and domesticated vectors such as bats, rodents and poultry. The types of data range from the mundane such as the metadata on our samples to outcomes of diagnostic tests to terabytes of sequence data. We also prioritize the integration of digital epidemiology alongside field epi. For this we work with a group called Healthmap at Boston Children’s Hospital. Healthmap conducts hourly monitoring of over 50 thousand websites looking for indications of new outbreaks. The inputs range from the highly reputable official sources to eyewitness reports. We integrate this field reporting to gain a current picture of human and animal health as well as to determine a baseline for disease status in the hot spots where they occur most frequently. When we detect something new, we notify the appropriate local authorities and the information is subsequently released publically through the Healthmap website.
- For this we work with a group called Healthmap at Boston Children’s Hospital. Healthmap conducts hourly monitoring of over 50 thousand websites looking for indications of new outbreaks. The inputs range from the highly reputable official sources to eyewitness reports. We integrate this field reporting to gain a current picture of human and animal health as well as to determine a baseline for disease status in the hot spots where they occur most frequently. When we detect something new, we notify the appropriate local authorities and the information is subsequently released publically through the Healthmap website. You can see here a screenshot of the Healthmap site that I pulled up yesterday.To give an idea of what a tremendous cultural shift was required to entice and facilitate the kind of collaboration required for our data collection, let’s look back at SARS emergence.
- At the time, China was reluctant to report the outbreak to the WHO. Although there were indications of an issue as early as November of 2002, the first official report to the WHO came in February of 2003. SARS proceeded to infect more than 8,000 people in 29 countries across five continents, with 774 deaths. Estimates of the cost for the world economy range from $40-54 billion US.Last year, China was again faced with a challenging epidemic – one of many since SARS in 2002. This time, it is H7N9 avian influenza and this time, China has demonstrated its role as a leader in public health.
- Along with groups from around the world, our team was brought in to respond to H7N9. We worked with the Guangdong CDC to collect samples from sick individuals in sentinel hospitals. Additionally, environmental samples were collected from wet markets and poultry markets where live birds are sold, as well as swabs from wild birds in rural areas of the Guangdong Province. This is the embodiment of the One Health approach and when compared with the response to SARS, it is impressive progress by any measure. These efforts have made a tremendous impact on China’s ability to stem the spread of H7N9 within the country and within the region. So how can the World Bank contribute to and accelerate this kind progress?
- Invest in sustainable, consistent data collection systems.Current health surveillance systems do not facilitate ready comparison across human and animal populations. The WHO’s efforts to establish the International Health Regulations since 2005 have yielded tremendous progress but only with respect to capturing human data. FAO and OIE databases capture an incomplete picture of the state of animal health worldwide. Due to the latency of their reporting structures, our ability to act is greatly limited. Without a timely and complementary source of animal health surveillance, we lack a critical piece of information. It’s like crossing the road and deciding only to look left, because what’s on the right is unimportant. Given the risks of disease emergence from animal populations, we can no longer afford to silo human and animal health. I encourage the World Bank to promote the capture and dissemination of health data reflecting a unified One Health approach.
- The last 18 months have seen an uptick in support for open access research. In February of last year, the US government issued a memorandum requiring federally funded agencies to make research products, including data, available to the public within 12 months of publication. The World Bank has already taken tremendous steps to recognize the importance of open data. But in addition to playing a leadership role, the World Bank can and should continue to support open access through funding of open access publications and other mechanisms. I believe that open access journals are and will continue to be one of the cornerstones of scientific progress.
- In Silicon Valley, entrepreneurial failures are worn like badges of honor. Many investors seek founders who have previously pursued their ideas without commercial success. Strange as it might sound, it’s felt that by having been in the trenches, entrepreneurs develop the maturity and understanding necessary to succeed in their future pursuits. It’s even become popular to conduct a public post-mortem on a failed entrepreneurial endeavor. Sharing your story is cathartic but more importantly, it allows your peers to learn from your mistakes. In research, we often lack this kind transparency. The focus on publications as a measure of one’s contribution tells an incomplete story. If funders were to dictate that all outcomes – positive or negative - be captured and shared, it would more efficiently leverage the collective experience of the community.
- Obviously this kind of radical paradigm for transparency and collaboration invites questions about privacy as well as requiring a reformulation of the manner in which researchers seek prestige. But it undoubtedly furthers the cause of science not to shy away from the growing pains of approaching these issues. At Metabiota, we believe that detecting potential pandemics is an issue which is addressable within our lifetime. And once we recognize the implications of non-action, the need is self-evident. The primary obstacle to our success is our ability to convince the world of the shared value of collaboration in this effort. Thank you.