ELIXIR UK: Our support in the fight against COVID-19
When the Covid-19 pandemic hit the UK in March 2020, many of our members, services and projects started to pivot their resources to help with research efforts to combat the virus. Below we detail how ELIXIR-UK has responded to the pandemic.
As it became clear that COVID-19 research was a race against time, several ELIXIR-UK services pivoted their work to produce useful resources. The group of researchers working at Rothamsted who developed our roadmapped service Knetminer responded to a call from the White House, Microsoft, Mark Zuckerberg and others to find a way to rapidly sift through the mountain of COVID-19 scientific data. Prior to the pandemic, Knetminer had been developed solely for plants (wheat, rice and Arabidopsis), but the team worked quickly to develop the same resources for Covid-19, providing a valuable resource for researchers working in this area during the pandemic.
Another ELIXIR-UK service which rapidly responded to the crisis was InterMine. InterMine integrates biological data sources, making it easy to query and analyse data, and you can install it on your own servers to make data available on the web. There were already many different InterMines worldwide, covering a broad range of model organisms and life science research areas, and with the fast work of the team CovidMine has now been added to this list.
The researchers behind the Guide to Pharmacology also worked quickly to curate a database of information on SARS-CoV-2 targets which captures some of the pharmacological strategies being investigated to mitigate against COVID-19. New ligands are being posted to a pre-release blog.
Even our services which were not directly linked to COVID-19 research saw a positive response during lockdown, with labs shut and researchers confined to desk work. Jalview has seen a trebling in interactions since the beginning of March 2020: in April 2019 there were around 30,000 interactions in April 2019, but in April 2020 this had increased to around 90,000.
Covid-19 and FAIR
There has been a fast expansion of FAIR resources around Covid-19. FAIRDOMHub now hosts the outputs of the Covid-19 Disease Map Consortium resource, which is a repository of known molecular host-pathogen interactions specific to SARS-CoV2. There is also a FAIRSharing covid-19 collection, which collates standards and databases relevant to covid-19 including clinical trials, virology studies, public health and patient registries.
Alongside this, a new initiative sees scholarly publishers working together to maximize the efficiency of peer review, ensuring that key work related to COVID-19 is reviewed and published as quickly and openly as possible. In January 2021 the initiative mandated that the journals involved in the initiative would require authors to deposit data in open data repositories rather than having data available on request. The ELIXIR-UK service FAIRsharing now hosts the data policies for these journals to increase transparency. This step is vital for facilitating the rapid work of COVID-19 researchers, and this work has shown how important FAIR data has been during the COVID-19 pandemic.
Other projects associated with ELIXIR-UK have also been adapting and rising to the challenge of fighting the pandemic.
Cyverse-UK, which is based at the Earlham Institute, has offered their cloud resource in the fight against COVID-19. This free resource allows users to store, annotate, and analyse their data, supporting a wide range of research projects and providing open source computational resources for those that need them.
EOSC-Life, a collaboration of 13 research infrastructures which aims to create an open digital space for life and medical sciences, has developed a COVID-19 specific instance for their WorkflowHub. This allows researchers working on COVID-19 to share their workflows for data analysis, increasing the knowledge and resources available to those working in this critical research area.
As illustrated by the hard work of our members outlined above, the response to the COVID-19 pandemic has been rapid and well coordinated, and has enabled a huge volume of work in this area to be carried out quickly by a large number of researchers in the UK and beyond. Without continued support and funding for e-infrastructure in the UK, this would not have been possible. This pandemic has demonstrated that if we are to be able to rise up to future emergencies such as this, we must continue to support the field of bioscience data, or those fundamental e-infrastructures will not be in place to respond to future crises.
Do you have COVID-19 related news that you would like featured here? Get in touch with us to contribute.
Articles for further reading:
- Read about how the researchers at Rothamsted Research responded to the call from the White House, Microsoft, Mark Zuckerberg and others to find a way to rapidly sift through the mountain of COVID-19 scientific data.
- The article about how the Earlham Institute has offered open access bioinformatics resources for COVID-19 research.
- The Global Research Data Alliance community response to the global COVID-19 pandemic
- OASPA announcement about the launch of a new initiative to see COVID-19 research published in a timely manner
- OASPA announcement on data deposition requirement for all C19 rapid review publishers