Global participation in biodata: Building equitable partnerships

A new report, entitled Towards global biodata partnerships, explores the adoption practices, drivers and barriers for scientists in low resource settings who use open biodata resources. The report, commissioned by EMBL-EBI and funded by Wellcome, was produced by Research Consulting.

“This report explores a number of challenges and opportunities that must be addressed if we are to improve the global biodata ecosystem,” said Chiann-Mun Chen, Senior Research Manager for Discovery Research at Wellcome. “It includes valuable recommendations, drawing attention to the importance of engaging with researchers in low-resource settings to build towards truly global, equitable and inclusive biodata resources for the future.”

Below, ThankGod Ebenezer, who is the Global Engagement Manager for EMBL-EBI Data Services, shares report findings and how to build sustainable global partnerships to help improve biodata access and usage. 

What does the global biodata ecosystem look like? 

In a word: fragmented, but not necessarily in a bad way. There are many databases managed by different people and organisations worldwide. Biology is vast and databases often grow organically from community efforts. There are also ‘biodata hubs’, such as EMBL-EBI, which manages a suite of open data resources used by millions of scientists worldwide. But no single organisation can manage the world’s data, so partnerships, collaboration and trust are essential. 

What are the findings of the report?

The report is based on an analysis of EMBL-EBI data resource usage patterns and interviews with researchers in low resource settings. 

Research Consulting found that EMBL-EBI data resource users are spread out globally. The usage patterns reflect population sizes, economic parameters, and the level of investment in research and innovation. We’re also seeing a direct correlation between data contribution and usage: the more a region contributes data, the more it uses the data resources.

In summary, results show that high income countries are heavy users, upper middle income and lower middle income countries are medium users, while low income countries have the lowest usage levels. We used the OECD’s list of recipients of development assistance for country classification.

Looking at 2024, EMBL-EBI data resources saw 18 million unique IP addresses from low and middle income countries (LMICs), from a total of 41 million. But although one in every two IPs visiting our databases are from LMICs, they are not using data resources as intensively as scientists in higher resource environments.

What are the benefits of participating in open data resources like the ones managed by EMBL-EBI?

The benefits of an open data ecosystem go right down to the individual level because public data resources enable scientists to ask new research questions, gain new insights and skills, and to share their own research data with the community.

At a regional level, access to open data resources can help scientists prioritise and find solutions for local problems. For instance, African researchers working on cassava mosaic disease – which leads to massive crop losses – can compare viral genomes of infected cassava leaves, to sequences available in EMBL-EBI’s European Nucleotide Archive. This tells them whether they’ve found new or emerging variants. They can use the Ensembl genome browser to study genetic variation, and build phylogenetic trees to see how local strains relate to those in other countries. By linking cassava genome data from Ensembl with viral interaction studies, they can identify candidate resistance genes in cassava. This could help local plant breeding programmes to develop cassava varieties that are resistant to viral strains found in their region.

These kinds of initiatives have to be built from the ground up. Local scientists need to point their national institutions and ministries in the right direction, but to do so, they also need the foundations: funding, skills and infrastructure, including data. 

On a national level, existing open data resources provide examples of how countries can set up their own data infrastructures and potential partnerships. Many of EMBL-EBI’s data resources are built on international collaborations, while others operate using a federated model where sensitive data doesn’t leave national jurisdictions (for example the Federated EGA). National infrastructural resources strengthen the global scientific ecosystem through interoperability, while also providing resources tailored to local needs. 

Each region has its own challenges and priorities, but producing data in isolation duplicates efforts and limits insights. By working together, the breadth and usage of biodata increases, enabling the scientific community to work on global and local challenges alike.

What are some of the barriers for scientists in low resource settings to leveraging open data resources?

Our interviews revealed three types of challenges: technical infrastructure, norms and customs, and policies and funding. 

Technical infrastructure challenges included connectivity issues, limited data storage and high-performance computing. The report also highlighted projects that are managing to overcome some of these challenges, for example the Indian Biological Data Centre – which is democratising access to essential infrastructure for local scientists – or the Brazilian Biosciences National Laboratory, which houses a cutting-edge computational biology facility.

The invisible architecture of local norms and practices also shapes how researchers engage with biodata resources. Our interviewees expressed that there is apprehension about data sharing, some of which can be traced back to historical and structural factors. Scientists are wary of potential issues with data ownership, attribution and misuse.

Other challenges include integrating local research workflows into global data standards, and reduced workforce capacity in bioinformatics. Resolving this requires capacity building and shifts in ways of working. 

Finally, our report showed funding barriers, including comparatively limited short-term funding, which undermines sustainability. This is sometimes linked to changing national priorities. Resource disparities can sometimes push scientists into inequitable collaborations, limiting capacity building or leaving critical regional research needs unmet. 

What are some of the key ways in which public data resources can support scientists in low resource settings?

The report proposes a suite of recommendations, many of which go beyond the scope of EMBL-EBI. The fundamental point is to work with scientists in low resource settings to build sustainable partnerships based on trust. By working together, we can explore options for technical solutions, for example whether it’s possible to develop lightweight versions of data resources and tools. This could improve usage where internet connectivity is a challenge. Another possible option for sensitive data sharing would be to participate in federated data solutions that mean the data remain within national boundaries. 

Other recommendations include the development of new recognition mechanisms for data producers. There has been encouraging progress already but more work is needed. Researchers can now ‘link’ datasets to their ORCID record, using systems such as EBI Search or DataCite Commons. This is a move towards acknowledging that data generation and sharing are valuable outputs of research activities, similarly to scientific publications. 

Finally, capacity building is important so initiatives that support train-the-trainer type activities, knowledge exchanges and skills cascading can upskill more scientists and reduce dependencies on international training.

What next for EMBL-EBI’s Global Engagement Programme?

This report is a first step in EMBL-EBI’s Global Engagement Programme, funded by Wellcome. We’re still in the listening and awareness phase, and the next steps are to identify partners in low resource settings that can work with us to explore ways of making our data resources and training more accessible. We aim for this to be an interactive and mutually beneficial process. Interested parties can reach out to us on globalengagementds@ebi.ac.uk.