Public dataset highlights: Antibiotic resistance

Friday, June 16, 2017

This is a big one and has been getting a lot more attention ever since the UN met last September to wring their hands over it. This week's Data is Plural features a publicly available dataset on antibiotic resistance genes:
Antibiotic resistance. ResistoMap is an interactive visualization of antibiotic drug resistance, based on more than 1,500 bacteria genome samples from people’s intestinal tracts. The data behind the visualization is available to download. It’s partly based on two prior datasets: McMaster University’s Comprehensive Antibiotic Resistance Database (“a bioinformatic database of resistance genes, their products and associated phenotypes”) and the University of Gothenburg’s BacMet (“an easy-to-use bioinformatics resource of antibacterial biocide- and metal-resistance genes”).

Public dataset highlights: Migrating scientists, workplace injuries, and beach bacteria

Wednesday, June 7, 2017

This week's Data is Plural features three datasets of public health and scientific interest - including one that includes yours truly! I have an ORCID, which means my research profile is included in the first dataset.
Millions of scientists, and their migrations. ORCID is a nonprofit organization that provides unique identifiers for researchers — mostly scientists so far — to make it easier to distinguish between them. It has issued more than 3 million IDs so far, and provides annual bulk downloads of all researchers’ public profiles . In many cases, the researchers have supplied their education and employment histories. That enabled Science magazine to analyze the migrations of more than 110,000 researchers who’ve listed multiple countries in these public CVs. (The data and code underlying the analysis are also available to download .)

Severe workplace injuries. Beginning in January 2015, the Occupational Safety and Health Administration began requiring U.S. employers to report “all severe work-related injuries, defined as an amputation, in-patient hospitalization, or loss of an eye.” You can download a spreadsheet of these injuries — some 20,000 in 2015 and 2016 combined. It contains the injury dates, descriptions, and outcomes, as well as the employers’ names and locations. Previously: OSHA’s more detailed (but slightly more cumbersome) inspection data and API (DIP 2016.07.13).

E. coli at Ocean Beach. The San Francisco Public Utilities Commission’s Beach Water Quality Monitoring Program measures bacteria levels at fifteen locations on the city’s shoreline. You can download the measurements by clicking the “raw data” link below this map . The data powers the (unsurprisingly) unofficial @BeachPooBot account on Twitter.