Department Blog

Health Sciences Libraries

Project Tycho: Data for health

December 5th, 2013 by Amy Studer

Announcing Project Tycho™, a web site which provides open access to newly digitized and integrated data from the entire 125 years history of United States weekly nationally notifiable disease surveillance data since 1888.  Read more about it:

The goal of Project Tycho™ is to aid scientists and public health officials in the eradication of deadly and devastating diseases. A recent NEJM article, documents how the Project Tycho team digitized and made public all weekly surveillance reports of nationally notifiable diseases for U.S. cities and states published between 1888 and 2011. The project derived a quantitative history of disease reduction in the United States over the past century, focusing particularly on the effect of vaccination programs.


van Panhuis WG, Grefenstette J, Jung SY, Chok NS, Cross A, Eng H, et al. Contagious diseases in the United States from 1888 to the present.N.Engl.J.Med. 2013 Nov 28;369(22):2152-2158.

Project Tycho Image

About Project Tycho

In the United States, cases of contagious diseases have been reported at weekly intervals to health authorities for more than a century, but these data have not been publicly available in a computable format, so their use and value have been limited. The University of Pittsburgh has released a collection of surveillance reports about diseases in the United States going back 125 years. “The researchers obtained all weekly notifiable disease surveillance tables published between 1888 and 2013 – approximately 6,500 tables – in various historical reports, including the U.S. Centers for Disease Control and Prevention’s Morbidity and Mortality Weekly Report. These tables were available only in paper format or as PDF scans in online repositories that could not be read by computers and had to be hand-entered. With an estimated 200 million keystrokes, the data – including death counts, reporting locations, time periods and diseases – were digitized. A total of 56 diseases were reported for at least some period of time during the 125-year time span, with no single disease reported continuously.”

Blog entry re-posted from Rudolph Mata Library Blog by, with permission.

Predicting Emerging Diseases

April 23rd, 2013 by Mary Wood

Which Primate is the Most Likely Source of the Next Pandemic?
Smithsonian Surprising Science Blog April 22, 2013

photo by AfrikaForce

photo by AfrikaForce

“…Most emerging infectious diseases in humans have indeed arisen from animals… Therefore, experts prioritize the task of figuring out which animals in which regions of the world are most prone to delivering the latest novel pathogen to hapless humanity.

With this in mind, researchers at Harvard University, the University of Granada and the University of Valencia set out to develop a new strategy for predicting the risk and rise of new diseases transmitted from animals before they happen, describing their efforts in the journal Proceedings of the National Academy of Sciences, Centrality in primate–parasite networks reveals the potential for the transmission of emerging infectious diseases to humans
doi: 10.1073/pnas.1220716110 PNAS April 22, 2013


School of Veterinary Medicine | One Health Institute |
:  Building global surveillance to detect and prevent spillover of pathogens of pandemic potential


.Morse SS, Mazet JA, Woolhouse M, Parrish CR, Carroll D, Karesh WB, Zambrana-Torrelio C, Lipkin WI, Daszak P.
Prediction and prevention of the next pandemic zoonosis
Lancet 2012 Dec 1;380(9857):1956-65 PMID: 23200504

“…In order to predict, respond to, and prevent the emergence of novel infectious diseases in humans, pathogens must be identified at their source. The PREDICT project, led by Principal Investigator and Co-Director Dr. Jonna A.K. Mazet, DVM, MVPM, PhD of the UC Davis School of Veterinary Medicine and Co-Director Stephen S. Morse, PhD of the Columbia University Mailman School of Public Health, recognizes that explosive human population growth and environmental changes have resulted in increased numbers of people living in close contact with animals.

PREDICT, a project of USAID’s Emerging Pandemic Threats Program, is building a global early warning system to detect and reduce the impacts of emerging diseases that move between wildlife and people (zoonotic diseases)…”

Epidemiology and gun violence

January 17th, 2013 by Mary Wood

UC Davis Violence Prevention Research Program
Garen Wintemute, Director, MD MPH
Professor Emergency Medicine
Inaugural Susan P. Baker-Stephen P. Teret Chair in Violence Prevention, UC Davis

Dr. Wintemute researches and publishes in the field of injury epidemiology and the prevention of firearm violence; he studies the problem of guns and violence as a public-health issue and emphasizes the importance of prevention.

NEJM December 2012
Tragedy’s legacy

JAMA December 2012
Silencing the science on gun research

Journal of Urban Health August 2012
Characteristics of federally licensed firearms retailers and retail establishments in the US: Initial findings from the firearms licensee survey

Journal of trauma and acute care surgery July 2012
Epidemiology and clinical aspects of stray bullet shootings in the US

American journal of public health September 2011
Opportunities for state-level action to reduce firearm violence: proceedings from the evidence

Injury prevention December 2011
Association between firearm ownership, firearm-related risk and risk reduction behaviours and alcohol-related risk behaviours

additional articles:
PubMed author search Wintemute GJ

American Medical Association
American Medical News 2001
Target Prevention

New Resource: Social Explorer

December 9th, 2011 by Bruce Abbott

The library has licensed a new resource which provides provides quick and easy access to current and historical census data and demographic information.

Link to Social Explorer :

From the description:

The easy-to-use web interface lets users create maps and reports to better illustrate, analyze and understand demography and social change. In addition to being a comprehensive data resource, Social Explorer also offers features and tools to meet the needs of both demography experts and novices. From research libraries to classrooms to the front page of the New York Times, Social Explorer is helping people engage with society and science.

Key content
  • Provides easy access to current and historical demographic data:
    • Including over 40 billion data elements, 200,000 variables and more than 18,000 interactive maps from 1790 to 2010.
    • The entire US Census from 1790 to 2000, plus the first 2010 census data release.
    • All annual updates from the American Community Survey.
    • InfoGroup data on religious congregations for the United States for 2009, including maps for counties, and special census areas, as well as point maps of the actual congregation locations (to be updated yearly).
    • The Religious Congregations and Membership Study (RCMS) from 1980 to 2000. (To be updated in 2012.)
    • Carbon Emissions Data for 2002 from the Vulcan Project.
  • Creates thematic and interactive maps that make it easy to visually explore all historical and modern US census data across the centuries and even down to street level detail where available.
  • Creates reports at all geographic levels including the state, county, census tract, block group, zip code and census place (where the data exist).

Large Dataset Inventory

November 23rd, 2011 by Bruce Abbott

UCSF, specifically CTSI’s CELDAC initiative, has created an inventory, or catalog, of publicly available datasets.
The link to the search form is:

Among the criteria which can be searched:

By Domain:

Health Care (including utilization, costs, and quality) 
Health Status
Health Risk Behaviors
Children’s Health
Population Characteristics
Infectious Disease
Global Health
Cardiovascular Health

By Population:

Health Data Tools and Statistics

November 17th, 2011 by Bruce Abbott

The Partners in Information Access for the Public Health Workforce (or “PHPartners”) alliance has recreated its webpage and pulled together a comprehensive collection of resources.

From the announcement:

The Health Data Tools and Statistics page on the website,, has been recently reorganized to make public health data and statistics easier to find and use.

New Public Health Data Tools and Statistics Categories:

* County and Local Health Data
* State Health Data
* Individual State Data
* National Health Data
* Global Health Data
* Statistical Reports
* Demographic Data
* Geographic Information Systems (GIS)
* Training and Education
* Health Information Technology and Standards
* Tools for Data Collection and Planning

Census Bureau Publishes Health Insurance Coverage Estimates for All Counties

October 15th, 2011 by Bruce Abbott

from the announcement:

The U.S. Census Bureau today (Oct. 13, 2011) released 2008 and 2009 estimates of health insurance coverage for each of the nation’s roughly 3,140 counties. Small Area Health Insurance Estimates (SAHIE) are currently the only source for estimates of health insurance coverage status for every county in the nation.

These estimates are available by sex, age groups, race and Hispanic origin (for states only), and income-to-poverty ratios relevant to the new health care reform legislation and other health programs. They enable local planners to determine, for instance, the counties in which low-income children are most likely to lack health insurance coverage. The data pertain to those under age 65.


link to Small Area Health Insurance Estimates: