What makes Pathoplexus different?

Pathoplexus offers flexible data-sharing options: users can choose to share their data openly, or with time-limited protections to help ensure proper attribution and credit. Pathoplexus integrates smoothly with existing INSDC-member databases (NCBI, ENA, and DDBJ), enabling data that’s ‘open’ on Pathoplexus to also appear on INSDC, and INSDC data to be accessed through Pathoplexus. Pathoplexus is built on the latest tools for filtering, searching, and accessing data, making data sharing and analysis more accessible (through both the website and API) and fostering a connected, collaborative global research community.

Can I use the data on Pathoplexus?

Yes! Pathoplexus is designed to be used by everyone, and so all data is accessible. However, Pathoplexus does have restrictions on how some data (“Restricted-Use Data”) can be used, particularly in publications and preprints, and has requirements on how all Restricted-Use Data is acknowledged. You can find out more about these protections and how you can use data by reading our Data Use Terms. We also have summaries on you can use Open Data and Restricted-Use Data.

How can I contribute data to Pathoplexus?

We’ve tried to make sharing your data as easy and flexible as possible!

You can upload data to any of our supported pathogens by first creating an account and then submitting your sequences on the website or via the API (useful for computational pipelines). At submission, you can choose whether you’d like your data to be protected for up to one year, or open immediately. Once the data is open, it also appears on INSDC-member databases.

How can I try Pathoplexus out?

If you don’t have sequences to upload for the pathogens we currently support - or just want to try out Pathoplexus before deciding if you want to use it - you can always use our Demo Instance! Our Demo Instance works just like the ‘real’ Pathoplexus, but is wiped regularly and no data is sent onward to INSDC.

It’s perfect for trying out Pathoplexus or testing your API requests. Do note that since it is wiped regularly, you will have to make a new account and group - but it’s ok if these aren’t as detailed as your ‘real’ accounts. Remember that the Demo Instance is public, so don’t upload data that you can’t or don’t want to share. If you’d like to try out Pathoplexus but don’t have any data to hand, you can use our example data for the pathogens we support!

(See our Docs for more information on how to do things like create an account, upload sequences, and more in Pathoplexus!)

Who is behind Pathoplexus?

Pathoplexus is a transparent, non-profit association with members from 10 countries in 5 continents, and an Executive Board from around the globe. Pathoplexus’ members and Executive Board are committed to running Pathoplexus according to our Values. Pathoplexus is proud to work closely with PHA4GE, an international group working to establish better standards for public health and bioinformatics. PHA4GE was also key in helping to develop Pathoplexus from the ground up.

At the moment, Pathoplexus is run completely on donations and volunteer efforts, thus is independent of influence by larger players, and is truly a community-driven project. See our About page for more information about Pathoplexus, and our Executive Board, Scientific Advisory Board, Members page and Development Team pages for more information about some of the people involved.

Where can I read more?

See more of our Frequently Asked Questions here!