About・Abstract・Questions・See also
1854: Cholera・2005: H5N1・2005: Hurricane Katrina・2009: H1N1・2010: Haiti earthquake・2011: Tōhoku earthquake・2011: E. coli O104:H4・2013: Typhoon Hiyan・2015: Ebola・2016: Zika・Future?
John Snow's original map of the 1854 Broad Street cholera outbreak in London. Cholera cases are highlighted in black, as are water pumps (data available here). The pump on Broad Street was identified as the one through which the contaiminated water was distributed. Removing its handle then essentially stopped the outbreak, and when the next Cholera outbreak hit London in 1866, sanitary measures had been improved.
- PLOS Currents: Influenza was started: "The key goal of PLoS: Currents is to accelerate scientific discovery by allowing researchers to share their latest findings and ideas immediately with the world's scientific and medical communities."
- OpenStreetMap
- coordination page
- sinsai.info
- run by OpenStreetMap Japan using Ushahidi
- saveMLAK
- Geigermap
- Japan’s Nuclear Woes Give Rise to Crowd-Sourced Radiation Maps In Asia and US
- Japan’s Radiation Levels: Real-Time Crowd Sourcing
- Crowdsourcing Japan’s Nuclear Crisis
- How Citizen Science Changed the Way Fukushima Radiation is Reported
- Open StreetMap coordination page
- A set of three poster maps printed in response to the 2013 Typhoon Haiyan based on data from OpenStreetMap
- Ebola teaches tough lessons about rapid research
- Data sharing: Make outbreak research open access
- Special issue of Journal of Empirical Research on Human Research Ethics: Ethics and sharing individual-level health research data from low and middle income settings (13 papers, 2015)
- Ebola outbeak data scraped from government PDF
- WHO Report of the Ebola Interim Assessment Panel - July 2015
- Open Data's Impact: Battling Ebola in Sierra Leone — Data Sharing to Improve Crisis Response
- Wikipedia became the most used internet site in Liberia, Sierra Leone and Guinea for Ebola during 2014 outbreak (greater than CNN, CDC and WHO)
- WHO: Developing Global Norms for Sharing Data and Results during Public Health Emergencies
- Ebola tracking
- Well covered in IMED session "Data Sharing and Ethics of Big Data" (yesterday)
- Statement on data sharing in public health emergencies
- Policy Statement on Data Sharing by the World Health Organization in the Context of Public Health Emergencies
- Public Health Surveillance: A Call to Share Data
- Science, get over yourself: Zika data-sharing should be the norm, not the exception
- "Several participants noted that it is critical to study ZIKV in humans in the countries most affected and highlighted the importance of establishing a coordinated and well-resourced research approach to ZIKV, which would include the efficient sharing of biospecimens across international borders, availability of rapid funding announcements, better communication among scientists about the types of research being conducted, and the availability of datasets."
- Partnerships, Not Parachutists, for Zika Research:
- "But we believe the experience with recent outbreaks makes clear that if open sharing of data and specimens becomes the norm among scientists and epidemiologists around the world, we will be far more likely to succeed in improving international public health capacity and strengthening our collective health — and human — security.
- To avoid having to make this argument again every time we face an outbreak with the potential for becoming a global crisis, we believe the global health community should develop and agree on a framework of principles for sharing data and biologic samples during any such public health emergency. It would be best if the researchers themselves developed such a framework, as the genomics community did in the Human Genome Project."
- Zika Open research Portal
- other open datasets
- Open Zika
- Zika tracking
- ContentMine: mining PubMed Central for data
- preprints
- from the Zibra blog (comparing Ebola versus Zika project): "there we were limited by upload speed and here throughput"
- Final Rule for FDAAA 801 and NIH Policy on Clinical Trial Reporting
- PCORI consultation on their data sharing policy
- An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
- Jupyter notebook
- Docker image
- could in principle be run on a mobile phone
- Data-driven identification of potential Zika virus vectors
- Visualization of selected information mined from the Zika literature
- Do vacant properties explain Miami's Zika outbreak? (follow-up post)
- How mobile data visualization helped reduce malaria cases by 93% — Zika could be next
- Mapping the global geographic potential of Zika virus spread
- Dynamic forecasting of Zika epidemics using Google Trends
- many Zika-themed hackathons
- Make Data Sharing Routine to Prepare for Public Health Emergencies
- Quantifying the global attention to public health threats through Wikipedia pageview data
- Feel free to post them on GitHub or via Twitter.
This file hosts my "slide" for a talk for the International Meeting on Emerging Diseases and Surveillance (IMED 2016), which took place on 4-7 November, 2016, in Vienna, Austria. It was submitted as an abstract to the "Public communication of outbreaks and emerging diseases" track on July 10 and received the abstract number 1124 in their system. On August 17, the abstract was accepted for the poster session. Upon confirming my attendance on September 16, I requested whether this contribution could be turned into a talk, and this was granted on September 18.
The talk then became part of the session "Innovative Approaches to Emerging Disease Surveillance" at 8.30-10.30am on Monday, November 7, in Room Klimt 2&3.
Data sharing in public health emergencies
Public health emergencies caused by emerging diseases pose special challenges in terms of gathering relevant information and making it available to the research and public health communities as well as the public more broadly. In response, a growing number of initiatives are focusing on the role of data sharing under these circumstances.
In this contribution, I am reviewing existing efforts around data sharing in recent public health emergencies from around the globe, focusing on cases where emerging diseases played a major role, as in the ongoing Zika virus outbreak.
The underlying project is conducted by way of open notebook science that can be followed and contributed to via https://github.com/Daniel-Mietchen/datascience/blob/master/emergency-response.md .
Data sharing can increase the speed of responses to emerging diseases. It may also affect the quality, the nature or the range of the responses and other variables. Conversely, a lack of adequate data sharing may pose a considerable barrier to effective responses.
Data sharing is becoming an important aspect of responses to public health emergencies, and strategies for communicating outbreaks and emerging diseases are evolving around this notion, complementing traditional means of research and public health communication with faster, more transparent, more collaborative and more responsive channels.
- Zika virus outbreak
- Ebola virus outbreak
- E. coli O104:H4 outbreak
The submission process had two mandatory affirmations:
Copyright (mandatory) By submission of this abstract I hereby confer the copyright for conference publication of all text and tables in this abstract to the organizers of the IMED 2016
Authors confirmation (mandatory) I hereby confirm, that all authors mentioned in the author block of this abstract have been informed about, and agreed to this submission.
I actually object to the transfer of copyright to the IMED organizers (and will try to submit without that statement clicked), but since my copy here is available earlier and under CC0, there should in practice be no hurdle in terms of reuse of this text by others. In any case, this is work for the US government and as such not copyrightable in the US.
Update: they would indeed not let me submit the abstract without that confirmation. So I opted for submitting, took some screenshots in the process and sent them an email expressing my dissent with that point.
- Data sharing in public health emergencies — a presentation given at SciDataCon 2016 in Denver on September 12, 2016
- SciDataCon session Disasters and Disasters Risk Data
- World Health Organization Member States and Open Health Data: An Observational Study
- More details on sharing in response to public health emergencies
- "Due to an effective quarantine policy, most Danish cities experienced only a single [Cholera] epidemic in 1853 and detailed data are available."