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pr2database

INFRA · APIS
Velocity0.0

PR2 database with shiny web interface

github.com/pr2database/pr2database ↗

The protist reference database keeps widening past the rRNA gene it was built on.

reference-databaseprotiststaxonomymetabarcodingcuration
◆Current state
PR2 curates ribosomal reference sequences for eukaryotes, distributed as flat files and through a web interface, with each release crediting the specialists who curated individual clades. Since 2022 the structural changes have outweighed the curation: one combined SSU database replaced the separate ones, the taxonomy moved from eight levels to nine, and companion databases for ribosomal operons, mixoplankton and mitochondrial COI have been linked in.
◆Where it's heading
The database is becoming a hub rather than a single file. Each recent release integrates something maintained elsewhere, with the ROD, EukRibo, Mixoplankton and now eKOI databases reachable through the same interface, while the SSU flat files themselves change little between versions. Curation continues underneath, clade by clade, at a pace set by which specialist contributed that cycle.
◆Prediction
Expect the next release to integrate or refresh another linked database while the SSU files see routine curation, following the pattern of the last three.

◆Recent moves

  1. 9mo ago

    eKOI mitochondrial COI database reachable from the interface

    Version 1.0 of the eKOI database, covering the eukaryotic mitochondrial COI gene, becomes available through the web interface. The release is candid that the SSU flat files barely changed and that 5.1.0 remains usable, so the addition sits alongside the database rather than inside it.

    View source ↗
  2. 1y ago

    Ribosomal Operon Database 1.2 integrated; ten clades curated

    Integrates version 1.2 of the Ribosomal Operon Database and lands curation across ten clades from Apicomplexa to Foraminifera, including a new class for Pseudoscourfieldia and Pycnococcus. Ten named contributors, several from a EukRef workshop, which is how most of this database's content arrives.

    View source ↗
  3. 2y ago

    Taxonomy restructured from eight levels to nine

    ⚡ SPARK

    The taxonomy gains a level, moving from kingdom-to-species in eight ranks to domain-to-species in nine with a new subdivision rank, following Burki et al.'s tree of eukaryotes. Nearly 18,000 sequences have their taxonomy updated, a new supergroup is added, and artificial ciliate groups are collapsed back into real families.

    View source ↗
  4. 3y ago

    New web interface at app.pr2-database.org

    A new web application for browsing the database, with the underlying data unchanged and users pointed at 4.14.0 for the text files. Access rather than content.

    View source ↗
  5. 4y ago

    One SSU database for nuclear, organelle and bacterial sequences

    ⚡ SPARK

    Collapses the separate references into a single SSU database holding 18S from nucleus and nucleomorph, 16S from plastid, apicoplast, chromatophore and mitochondrion, and a selection of bacteria, with organelle origin encoded as a taxonomy suffix so assignment software can still tell them apart.

    View source ↗
  6. 5y ago

    2,966 sequences added and 3,817 removed across four clades

    A curation release: 2,966 sequences added, 933 updated and 3,817 removed, with Suessiales, Thalassiosirales, Pelagophyceae and Chrysophyceae revised against recent literature. This is the baseline activity the structural releases sit on top of.

    View source ↗