Welcome to Pathoplexus

What makes Pathoplexus different?

Pathoplexus offers flexible data-sharing: you can share openly, or with time-limited protections that help ensure proper attribution and credit. It integrates smoothly with the INSDC databases (NCBI, ENA, and DDBJ) — open data flows out to INSDC, and INSDC data can be browsed here too. It’s also built on modern tools for searching, filtering, and accessing data through both the website and API.

Can I use the data on Pathoplexus?

Yes! Pathoplexus is designed to be used by everyone, and so all data is accessible. Some data (“Restricted-Use Data”) does have restrictions on how it can be used — particularly in publications and preprints — and requirements on how it’s acknowledged. You can read the full details in our Data Use Terms, or our summaries for Open Data and Restricted-Use Data. Our stance on commercial use is described here.

How can I contribute data to Pathoplexus?

We’ve tried to make sharing your data as easy and flexible as possible! Just create an account and submit your sequences on the website or via the API (useful for computational pipelines). At submission you can choose to keep your data protected for up to one year or make it open immediately — and once it’s open, it also appears on INSDC-member databases.

How can I try Pathoplexus out?

You can always use our Demo Instance! It works just like the real Pathoplexus, but is wiped regularly and no data is sent onward to INSDC — perfect for trying it out or testing your API requests. You’ll just need to make a new account and group, and since the demo is public, don’t upload anything you can’t share. If you don’t have data to hand, try our example data. (See our Docs for more on creating an account, uploading sequences, and more.)

Who is behind Pathoplexus?

Pathoplexus is a transparent, non-profit association with members from 14 countries across 5 continents, and an Executive Board from around the globe — all committed to running it according to our Values. We work closely with PHA4GE, an international group setting better standards for public health and bioinformatics, which was also key in developing Pathoplexus. Pathoplexus was built out of a ground-roots effort by members of the microbial genomics research community, with many voluntary contributions.

Where can I read more?

• Our Pathoplexus Values and Statutes
• How data can be used and credited in our Data Use Terms
• Our Executive Board, Members, and Scientific Advisory Board
• Our list of Governance documents and ‘How-To’ documents
• Help drive Pathoplexus by joining PHA4GE’s Data Repositories Working Group