Pathoplexus

An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.

[Pathoplexus @pathoplexus]

3/ 📤 Ready to try it? Upload raw reads files alongside your next submission (individual or bulk), add them to your existing consensus sequences, and check out our docs for the details on required metadata.

🔗 https://t.co/cN7WXUI5Fp

#OpenData #OpenScience #PathogenGenomics

[Pathoplexus @pathoplexus]

1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences!

Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.

📰 Read more: https://t.co/cN7WXUI5Fp

[Pathoplexus @pathoplexus]

2/ ⚙️ How it works: raw reads follow all the same policies as consensus sequences - your chosen Data Use Terms apply to both, and raw reads are openly downloadable as soon as processing completes.

Pathoplexus handles INSDC submission for you, just like today.

[Pathoplexus @pathoplexus]

9/ ❤️ To everyone who's submitted a sequence, flagged a curation issue, joined our Scientific Advisory Board, presented a poster, funded our work, or told a colleague about us - thank you.

2️⃣ Here's to year two, and many more to come! 🎊

🔗 Full post: https://t.co/PdxcUJ2Vfi

[Pathoplexus @pathoplexus]

1/ 🎂 Pathoplexus turns TWO! 🎉

Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:

📰 Read the full update: https://t.co/PdxcUJ2Vfi

[Pathoplexus @pathoplexus]

8/ 🙏 None of this happens on its own. Thank you to our Executive Board, our members who guide and hold us accountable, our developer team, and every researcher, lab, and institute who has chosen to share data through Pathoplexus.

[Pathoplexus @pathoplexus]

2/ 🧬 ZIKV often causes mild or no symptoms - but can rarely lead to Guillain-Barré syndrome or birth defects, making surveillance important.

🙏 Thanks to @ArthurShem for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!

[Pathoplexus @pathoplexus]

1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens.

Read more: https://t.co/EEcIr1G6BG 📰

[Pathoplexus @pathoplexus]

4/ That's it! 🎉

Now, as soon as CrossRef indexes your manuscript, your SeqSet, and all sequences within that SeqSet, will show that paper/preprint!

See examples - A preprint citation in a SeqSet: https://t.co/e60iVA5pbK

A preprint on a sequence page: https://t.co/gvOzSoZ7Vf

[Pathoplexus @pathoplexus]

1/ Using @pathoplexus sequences in a preprint or publication? Remember to cite them correctly!
It's easy - here how!

1. 🧺Create a SeqSet containing all the sequences used. You can divide them into Focal & Background

https://t.co/hGGeLkwaaB

[Pathoplexus @pathoplexus]

3/

3. ✒️Cite the DOI *in the references*, like a paper!
(This is how CrossRef 'sees' it & how we track it)

Getting a citation is easy - click the 'Export/Cite' button & pick your style

Copy this *into the references* just like you'd cite a paper!

[Pathoplexus @pathoplexus]

10/ As always - share sequences, cite your SeqSets & DOIs, and let us know what you'd like to see next 💬

🔗 Full July update: https://t.co/FWPsskJ2SJ

#OpenData #OpenScience #PathogenGenomics #PublicHealth

[Pathoplexus @pathoplexus]

1/ 🛠️ Our July update is here - and it's a technical one! New features for citations, search, submission, and more. Here's what's new in #Pathoplexus 👇

🔗 Full post: https://t.co/FWPsskJ2SJ

[Pathoplexus @pathoplexus]

9/ 🏛️ Governance update: Pathoplexus held its General Assembly on 10 June, approving the annual report & planning next year. Minutes & report here 👉 https://t.co/sIxmI9q1vE

We're also delighted to welcome Prof. Placide Mbala @PlacideMbala to our Scientific Advisory Board! 🎉