We are announcing Pathoplexus, a specialised genomic database for viruses of public health importance. By combining modern open-source software with transparent governance structures, Pathoplexus fills a niche within the existing genomic sequencing database landscape, aiming to meet requests from both data submitters and users and striving to improve equity. Today we launch with four virus species, Ebolavirus sudan, Ebolavirus zaire, West Nile virus and Crimean-Congo haemorrhagic fever virus.
Pathoplexus aims to offer the best features of existing platforms, and to supplement these with new approaches that optimise data utility and preserve data autonomy. In particular, data submitters can easily share their data via Pathoplexus and receive credit through citable Pathoplexus datasets. Submitters can choose to have their data immediately deposited in the International Nucleotide Sequence Database Collaboration (INSDC) databases, without additional effort. Alternatively, submitters can choose to submit data with a time-limited restriction, during which use in publications is not permitted without involvement of the submitters. Only after this restriction ends is the data released to the INSDC. However, all users can freely access, explore, and download all data hosted in Pathoplexus. Data querying can be done both in an interactive and programmable fashion, the latter enabling the embedding of Pathoplexus into other tools.
Pathoplexus is powered by a new open-source software package, Loculus. Loculus is a general purpose tool for running virus sequence databases: anyone can use it to launch their own database for their pathogens of interest. These might include internal laboratory databases, or databases for collaborations or consortia.
Pathoplexus is a transparent, non-profit association with members from 10 countries in 5 continents. The Executive Board of Pathoplexus consists of five members from North and South America, Africa, Asia, and Europe. We are really excited to engage with the community - please check out our website, connect with us on Mastodon, Bluesky, or Twitter or join our open-source community on GitHub.
To read more please check out our announcement at: