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This year marks the fifth anniversary of the ELIXIR Gateway on F1000Research. We have some big plans for the Gateway in 2021 with new advisors Xenia Perez Sitja, Erin Haskell and Corinne Martin (all from the ELIXIR Hub) on board. With that in mind, we have been looking at some of the best articles to come out of the Gateway, all of which exemplify the collaborative nature of ELIXIR and their commitment to best research practices and Open Science. The articles with the highest scientific impact greatly reflect ELIXIR’s mission to guide and coordinate amidst a complex and convoluted bioinformatics landscape.

Most views and downloads

Ten steps to get started in Genome Assembly and Annotation

“This paper does a good job of covering the big picture of what’s needed to assemble and annotate a genome.” – Dave Clements, John Hopkins University (MD, USA)

Published in 2018, this Opinion Article provides ten recommendations to help researchers get started with genome assembly and annotation. The authors highlight the importance of data management and offer advice on making data Findable, Accessible, Interoperable and Reproducible (the FAIR data principles). This advice is further emphasized in the follow-up blog by Henrik Lants (National Bioinformatics Infrastructure, Sweden).

As Bruno Contreras-Moreira (Fundación ARAID, Spain) explains in their reviewer report, the article is a “broad tutorial which will certainly be of help for anyone trying to sequence and assemble a genome sequence with little previous experience”. With over 55,000 views, 9,000 downloads and 50 citations on Dimensions, it is certainly well-read and well-used.

Identifying ELIXIR Core Data Resources

“This paper should be required reading for every panel and funding agency tasked with evaluating these resources.” – Helen Berman, The State University of New Jersey (NJ, USA).

This paper describes the process behind how ELIXIR’s Core Data Resources are identified and evaluated. These are important to the wider life science community and the long-term management of data. It has 23,000 views, 1,000 downloads and was recently cited by the Publications Office of the European Union in their recommendations on certifying services required to enable FAIR with EOSC. The Global Biodata Coalition of funders is currently considering this approach to identify Global Core Data Resources      

Top on Twitter

Four simple recommendations to encourage best practices in research software

Open Research practices, particularly around research software, are important topics for discussion that we have covered several times in our blog posts, from highlighting some of our best software tool articles to discussing the best ways to give credit for the software.

In this article, Rafael Jimenez formerly from the ELIXIR hub and his co-authors give recommendations to improve the quality and sustainability of research software. Their first recommendation is to make source code publicly accessible from the beginning of the project to encourage reuse and collaboration. These recommendations are not only for software developers, but also funders, journals, and policy makers. With over 170 tweets and 60 citations on Dimensions, it seems this opinion article has had its intended impact. In 2020, it was even used as one of the building blocks for the Research Data Alliance COVID-19 working group’s recommendations and guidelines on data sharing. 

Final Thoughts

The ELIXIR Gateway is a hub for outputs about ELIXIR and aspects of its work; full details on the Gateway’s scope can be found here. The Gateway also welcomes work that provides recommendations, criteria, and guidance (e.g. simple “rules” and “steps”) to the wider community, especially if these were developed collaboratively by ELIXIR partners. These works get much attention in the Gateway and illustrate the value of working together, which is what ELIXIR is all about!

You can submit to the Gateway through this link and you can contact the F1000Research team or the Gateway Advisors if you have questions.