Project Tycho 2.0: a repository to improve the integration and reuse of data for global population health

Abstract

ObjectiveIn 2013, we released Project Tycho, an open-access database comprising 3.6 million counts of infectious disease cases and deaths reported for over a century by public health surveillance in the United States. Our objective is to describe how Project Tycho version 1 (v1) data has been used to create new knowledge and technology and to present improvements made in the newly released version 2.0 (v2).Materials and MethodsWe analyzed our user database and conducted online searches to analyze the use of Project Tycho v1 data. For v2, we added new US data and dengue data for other countries, and grouped data into 360 datasets, each with a digital object identifier and rich metadata. In addition, we used standard vocabularies to encode data where possible, improving compliance with FAIR (findable, accessible, interoperable, reusable) guiding principles for data management.ResultsSince release, 3174 people have registered to use Project Tycho data, leading to 18 new peer-reviewed papers and 27 other creative works, such as conference papers, student theses, and software applications. Project Tycho v2 comprises 5.7 million counts of infectious diseases in the United States and of dengue-related conditions in 98 additional countries.DiscussionProject Tycho v2 contributes to improving FAIR compliance of global health data, but more work is needed to develop community-accepted standard representations for global health data.ConclusionFAIR principles are a valuable guide for improving the integration and reuse of data in global health to improve disease control and save lives.

Predicting Dengue Outbreaks in Cambodia

“…Given the small number of such epidemics in our dataset, robustly demonstrating predictability from this dataset alone remains difficult. We therefore explored whether similar patterns could be observed in 4 other countries in South Asia: Thailand, Vietnam, Laos, and the Philippines ( 11 – 14 ). To be comparable with our analysis for Cambodia, we used the month at which >5% of cases have been observed on average (Appendix Tables 4, 5).…”

Transient indicators of tipping points in infectious diseases

“…As a specific example of infectious disease whose potential for elimination is of interest, we consider pertussis in the USA in the period of 1938–1956. The available data consist of weekly reports of the number of cases of pertussis in each US state, which have been provided in a digital format by Van Panhuis et al [63]. Pertussis may have moved closer to elimination in this period due to the rollout and increased coverage of whole-cell pertussis vaccines [64].…”

Nonparametric estimation of variable productivity Hawkes processes

“…The aim here is to see whether productivity appears to change significantly over time, by fitting a variable productivity Hawkes model. Cumulative Chlamydial infection counts during each year were obtained from Project Tycho (van Panhuis et al, 2018), https://www.tycho.pitt.edu, where the data were compiled from the United States Nationally Notifiable Disease Surveillance System. The records are purely temporal and consist of cumulative totals within various time periods; these cases were distributed uniformly during each temporal observation window as in for example, Meyer et al (2012), Althaus (2014), Chaffee (2017), Schoenberg et al (2018), Harrigan et al (2019), Schoenberg et al (2019), and Park et al (2020).…”