How bioinformatics is key to pandemic preparedness

22 Aug 2023

Colman O’Cathail. Image: Jeff Dowling/EMBL-EBI

Dr Colman O’Cathail discusses the new Pathogens portal and the value of bioinformatics for open, collaborative research.

Dr Colman O’Cathail is a bioinformatician who works at the European Bioinformatics Institute (EBI). The institute is part of the European Molecular Biology Laboratory (EMBL). Its tagline is “unleashing the potential of big data in biology”.

O’Cathail’s interest in microbiology grew during his undergraduate study and he decided to pursue a master’s degree with Prof Steve Diggle at the University of Nottingham, where he worked on ancient antibiotics. He stayed in Nottingham to pursue a PhD in microbial genomics, studying tuberculosis in cattle and badgers, among other topics.

O’Cathail’s current work focuses on creating open resources for collaborative biological research. Here, he explains his role and the value of bioinformatics to the wider scientific research community.

Tell us about your current research.

My current work is on the Pathogens Portal, which is a platform for pulling together open-access biological data resources for pathogens (disease-causing microbes), across the spectrum of life.

The Covid-19 pandemic brought into sharp focus the importance of open genomic data in battling pandemics, but even more importantly perhaps, connecting that genomic data with other biological data resources, such as literature, protein data and even clinical-epidemiological data.

I was a small part of an institute-wide response at EMBL-EBI to build the Covid-19 Data Portal, a platform which brought together all these types of open biodata for SARS-CoV-2 from the array of bioinformatics resources here at EMBL-EBI.

The Pathogens Portal is the ‘spiritual’ successor to the Covid-19 Data Portal, building on its success as a key resource during the pandemic.

The Pathogens Portal, mainly led by our team leader Dr Guy Cochrane at the European Nucleotide Archive, aims to do many of the same things the Covid-19 Data Portal did, but for many more pathogens – it already covers over 200,000 species and strains.

The core principle being that to be prepared for the next pandemic, we must enable open, connected access to as much biological data as possible, for researchers, clinicians and public health officials alike.

In your opinion, why is your research important?

Data has always been important in fighting disease and over the years, the data used to combat disease has come in many forms.

During the Covid-19 pandemic, genomic data was thrust into the limelight, being the primary data source used to battle SARS-CoV-2.

The global public health and research community showed it was possible to sequence a pathogen at scale and subsequently share that data rapidly in an open way.

To be ready for the next pandemic, we need to keep doing that. The Pathogens Portal is the cornerstone of that principle, putting pathogen biodata at the forefront and enabling people to share their data quickly and easily.

What inspired you to become a researcher?

Truthfully, for the longest time all I wanted was to be a medical doctor. Biology was the only subject that ever came to me naturally at school and I thought that medicine was the only career you could apply biology in. I didn’t get into medicine in Ireland, so I enrolled in the Biomedical, Health and Life Sciences degree at University College Dublin.

Within my first year, our course coordinator, Prof Bill Watson, had opened my eyes to research and to the application of life sciences in a spectrum of fields. I don’t think I ever reconsidered science as a career after that.

What are some of the biggest challenges or misconceptions you face as a researcher in your field?

I think bioinformatics has a reputation for being ‘push button’ science. You send your data to a bioinformatician, they push a button, you get some cool results. It’s much more complex than that and I think that perception is changing.

At a macro level, when running public data resources like the ones managed by the European Bioinformatics Institute, I think big tech companies have made it seem like producing high quality software is easy, but it really isn’t. Often some of the most critical bioinformatics services for life sciences are developed and maintained by small teams of people and require a lot of hard work.

Do you think public engagement with science has changed in recent years?

I think there’s much more interest in science, especially biology, since the Covid-19 pandemic. This is a great thing, but there’s a massive knowledge gap between the scientists working at the cutting edge and the public. That’s nobody’s fault, that’s just scientific advancement.

However, we need to give talented scientists and science communicators more funding and time to go out there and explain clearly what’s going on in the world, otherwise that knowledge gap will only widen and it becomes harder for the public to trust in the scientific process.

Personally, I like to shout about whatever we’re doing whenever I have a chance, be it on Twitter [now X] or interacting with the media. During my PhD, I loved organising outreach events and helped organise Pint of Science in Nottingham, which was a great informal outreach event for the public to engage with local academics.

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