Rapid and open sharing of data from research on pathogens is an essential part of preparedness. In addition to publishing scientific articles, access to the raw measurement data is important here, so that scientists worldwide can include the information in their analyses. With the launch of the Pathogens Portal Netherlands, the Pandemic Disaster & Preparedness Centre (PDPC) is participating in this movement.

The portal, sprung from an initiative by an international consortium led by Prof Marion Koopmans, provides convenient access to extensive datasets including genome sequences, measurement data from various laboratory studies, epidemiological information and clinical data. The result: a valuable counter to the global data infrastructure for biomedical research that enables researchers to offer their data to the world in an accessible way. ‘This is a first draft,’ stresses initiator Marion Koopmans, who set up the Dutch portal together with Ted Oliekan, Reina Sikkema and Clara Amid. ‘But with this, we have already taken a huge step.’

Preparedness

Data sharing is complicated because of the many types of data from different scientific disciplines. Moreover, each field tends to set up its own data infrastructure. Much valuable information is then restricted to its own circles. And then there are – often due to relative unfamiliarity – the restrictions around privacy. This also makes other, non-privacy-sensitive data in such a set, for instance on viruses or mosquitoes, inaccessible to other scientists. Much of the data from publicly funded research therefore remains inaccessible.

We need to do this in a different way, Koopmans believes, because: ‘It is important to share data as much and as quickly as possible – both nationally and internationally. During the Covid pandemic, the Covid19 Data Portal was developed, an assignment from the European commission to the research consortium VEO. We wanted to set up this concept for other pathogens – such as for Arboviruses – in a similar way.’

‘Marion was toying with the idea of such a portal well before Covid,’ Clara Amid adds. ‘The need was known even then, but the pandemic accelerated developments. Thanks to the Covid19 Data Portal, coronavirus research data were quickly shared worldwide, even before the research was published in scientific journals. Nothing like that had ever happened before. This allowed researchers worldwide to start developing vaccines and drugs.’

One-stop shop

With the further development of the pathogens portal came the request to set up these portals at the national level. The new Dutch Pathogens Portal aims to collect as much relevant data as possible and, where possible, make it publicly available. A one-stop shop for Dutch data and projects on pathogens, but in a structured way. ‘That makes life a lot easier for scientists,’ Koopmans said.

‘By sharing data quickly and openly, we increase our ability to intervene effectively in health problems, it promotes scientific progress and strengthens global health preparedness.

Data specialists Ted Oliekan and Clara Amid ensured that the data on the portal were standardised and linked. Sample data from patients, for example, are linked to virus sequences and t-cell/b-cell data. ‘This helps to make the complexity of the dataset more understandable,’ Amid explains. Furthermore, the data are provided with a download link and reference to the sources. Oliekan: ‘The portal even has experimental data that was never accessible before. People can decide for themselves whether and how they want to use the data for their own research.’

Reina Sikkema, researcher One Health PACT: “In the past few years, we collected many samples from mosquitoes, wild birds, and other animals. We used this for our research on how viruses spread through mosquitoes. By sharing our collection and the data, I hope other researchers can also use these samples again.

I had been looking for a way to share the data we collected from humans, animals and mosquitoes about these viruses. This new platform brings all the information together and lets us share the original data behind our future research papers.

European network

The Dutch Pathogens Portal is part of a network of national pathogens portals being set up to complement the European Pathogens Portal. The Netherlands is among the frontrunners; so far, only Sweden, Norway and Switzerland launched a similar project. The Dutch portal will initially offer comprehensive datasets on arboviruses – from the One Health PACT research consortium coordinated by Marion Koopmans to be completed this year. The intention is to expand this to other topics soon. The team therefore encourages Dutch researchers to share their data in line with the FAIR Data Principles. This also benefits the researchers themselves. Koopmans: ‘You can add an identifier to your research data and use it to keep track of how often your data is cited. You can then mention this on your CV. Moreover, funding bodies are increasingly asking how you plan to make your data available. This is a great way, and we hope many more people will start using it.’

Milestone

The development of the Dutch version of the Pathogens Portal involves a successful collaboration between various Dutch organisations and institutes such as the Pandemic Disaster and Preparedness Centre, NIOO, DWHC, Wageningen University, Erasmus MC, Leiden University, and various research projects such as Ecoalert (ZON MW), One Health PACT (NWO), ByCOVID (H2020), and VEO (H2020). Oliekan: ‘With this, we show that scientists from different institutes can jointly set up a data portal.’

‘We have been talking about the need for this way of working for years,’ adds Koopmans. ‘But there were always obstacles. We looked at what could be done, together with an enthusiastic club of supporters. For instance, we took the first step of turning a data-share problem into a data-share solution. That we can now share different types of data in a coherent form in the portal is really a milestone!’

Amid hopes that Dutch scientists will use the new portal intensively. ‘Who knows, nice new collaborations might emerge from it.’

Curious? Take a look at the new portal! Would you also like to contribute? Read more about sharing data.