About
This is a technical demonstrator built at FEMTO-ST, independent of the Institut Pasteur. It is not a reference database and does not replace Yersiniomics.
What this prototype shows
It demonstrates the layers a modernised Yersinia resource could carry, on real public data:
- A browsable taxonomy, from genus to species to Y. pestis SNP branches, with a bilingual fiche per taxon.
- Per-genome plasmid content (pCD1, pMT1, pPCP1) — the virulence determinants of Y. pestis, absent from existing browsers.
- Typing equivalences across rival systems, displayed side by side rather than arbitrated.
- The public sampling landscape by country and collection year, as an interactive map.
- Published ancient Y. pestis genomes with their historical period — a layer no other Yersinia resource exposes.
- A citable read-only REST API over every layer.
What it does not do yet
It carries no transcriptomic or proteomic data: those layers require the curated datasets of the existing resource, or a fresh ingestion from GEO and PRIDE. It carries no gene-level annotation and no genome browser. The phylogeny shown is a taxonomy, not an inferred tree.
Sources
- Yersiniomics — doi:10.1128/spectrum.03826-22
- BIGSdb-Pasteur Yersinia — doi:10.1128/spectrum.00504-24
- NCBI — assemblies, BioSample
- Cui et al. 2013, PNAS — Y. pestis SNP branch nomenclature (0.PE to 4.ANT)
20Taxa
41curated genomes
209ancient genomes
5606public BioSamples