by the numbers

Houston data science company expands pandemic-inspired research tool

Mercury Data Science has taken a tool it originally developed for COVID-19 research and applied it into new areas of research and innovation. Photo via Getty Images

Last fall, Houston-based Mercury Data Science released an AI-driven app designed to help researchers unlock COVID-19-related information tucked into biomedical literature. The app simplified access to data about subjects like genes, proteins, drugs, and diseases.

Now, a year into the coronavirus pandemic, Mercury Data Science is applying this technology to areas like agricultural biotech, cancer therapeutics, and neuroscience. It's an innovation that arose from the pandemic but that promises broader, long-lasting benefits.

Angela Holmes, chief operating officer of Mercury Data Science, says the platform relies on an AI concept known as natural language processing (NLP) to mine scientific literature and deliver real-time results to researchers.

"We developed this NLP platform as a publicly available app to enable scientists to efficiently discover biological relationships contained in COVID research publications," Holmes says.

The platform:

  • Contains dictionaries with synonyms to identify things like genes and proteins that may go by various names in scientific literature.
  • Produces data visualizations of relationships among various biological functions.
  • Summarizes the most important data points on a given topic from an array of publications.
  • Depends on data architecture to automate how data is retrieved and processed.

In agricultural biotech, the platform enables researchers to sift through literature to dig up data about plant genetics, Holmes says. The lack of gene-naming standards in the world of plants complicates efforts to search data about plant genetics, she says.


Angela Holmes is the COO of MDS. Photo via mercuryds.com


The platform's ability to easily ferret out information about plant genetics "allows companies seeking gene-editing targets to make crops more nutritious and more sustainable as the climate changes to have a rapid way to de-risk their genomic analyses by quickly assessing what is already known versus what is unknown," Holmes says.

The platform allowed one of Mercury Data Science's agricultural biotech customers to comb through scientific literature about plant genetics to support targeted gene editing in a bid to improve crop yields.

In the field of cancer therapeutics and other areas of pharmaceuticals, the platform helps prioritize drug candidates, Holmes says. One of Mercury Data Science's customers used the platform to extract data from about 2 terabytes (or 2 trillion bytes) of information to evaluate drug candidates. The information included drug studies, clinical trials, and patents. Armed with that data, Mercury Data Science's cancer therapy client signed agreements with new pharmaceutical partners.

The platform also applies to the hunt for biomarkers in neuroscience, including disorders such as depression, anxiety, autism and multiple sclerosis. Data delivered through the platform helps bring new neurobehavioral therapeutics to market, Holmes says.

"An NLP platform to automatically process newly published literature for more insight on the search for digital biomarkers represents a great opportunity to accelerate research in this area," she says.

Mercury Data Science has experience in the field of digital biomarkers, including work for one customer to develop a voice and video platform to improve insights into patients with depression and anxiety in order to improve treatment of those conditions.

The new platform — initially developed as a tool to combat COVID-19 — falls under the startup's vast umbrella of artificial intelligence and data science. Founded in 2017, Mercury Data Science emerged because portfolio companies of the Houston-based Mercury Fund were seeking to get a better handle on AI and data science.

Last April, Angela Wilkins, founder, co-CEO and chief technology officer of Mercury Data Science, left the company to lead Rice University's Ken Kennedy Institute. Dan Watkins, co-founder and managing director of the Mercury Fund, remains at Mercury Data Science as CEO.

The Ken Kennedy Institute fosters collaborations in computing and data. Wilkins replaced Jan Odegard as executive director of the institute. Odegard now is senior director of industry and academic partnerships at The Ion, the Rice-led innovation hub.

Wilkins "is an academic at heart with considerable experience working with faculty and students, and an entrepreneur who has helped build a successful technology company," Lydia Kavraki, director of the Ken Kennedy Institute, said in a news release announcing Wilkins' new role. "Over her career, Angela has worked on data and computing problems in a number of disciplines, including engineering, life sciences, health care, agriculture, policy, technology, and energy."

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Building Houston

 
 

For over a year now, scientists have been testing wastewater for COVID-19. Now, the public can access that information. Photo via Getty Images

In 2020, a group of researchers began testing Houston's wastewater to collect data to help identify trends at the community level. Now, the team's work has been rounded up to use as an online resource.

The Houston Health Department and Rice University launched the dashboard on September 22. The information comes from samples collected from the city's 39 wastewater treatment plants and many HISD schools.

"This new dashboard is another tool Houstonians can use to gauge the situation and make informed decisions to protect their families," says Dr. Loren Hopkins, chief environmental science officer for the health department and professor in the practice of statistics at Rice University, in a news release. "A high level of virus in your neighborhood's wastewater means virus is spreading locally and you should be even more stringent about masking up when visiting public places."

The health department, Houston Water, Rice University, and Baylor College of Medicine originally collaborated on the wastewater testing. Baylor microbiologist Dr. Anthony Maresso, director of BCM TAILOR Labs, led a part of the research.

"This is not Houston's first infectious disease crisis," Maresso says in an earlier news release. "Wastewater sampling was pioneered by Joseph Melnick, the first chair of Baylor's Department of Molecular Virology and Microbiology, to get ahead of polio outbreaks in Houston in the 1960s. This work essentially ushered in the field of environmental virology, and it began here at Baylor. TAILOR Labs is just continuing that tradition by providing advanced science measures to support local public health intervention."

It's an affordable way to track the virus, says experts. People with COVID-19 shed viral particles in their feces, according to the release, and by testing the wastewater, the health department can measure important infection rate changes.

The dashboard, which is accessible online now, is color-coded by the level of viral load in wastewater samples, as well as labeled with any recent trend changes. Houstonians can find the interactive COVID-19 wastewater monitoring dashboard, vaccination sites, testing sites, and more information at houstonemergency.org/covid19.

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