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rhaps0dy 1 days ago [-]
Super cool! I just learned about 'incertae sedis' from here—though I think these things should at least be in their kingdom (e.g. Naldaviricetes are clearly viruses no?)
Lucent 1 days ago [-]
Absolutely agree with the underlying UX point. "Incertae sedis" shouldn't leave you unable to tell what broad kind of organism you're looking at.
I do filter structural junk per backbone, but only from evidence that backbone itself supplies: synonym/accepted status, "not-a-taxon", environmental, hidden, unplaced flags. I also insert neutral buckets such as "classes (no phylum)" where ranks are skipped, so thousands of taxa don't spill into one flat level.
What I deliberately don't do is move a taxon to the parent that I think makes more biological sense. Ptree (Ptable gets the same kind of requests to classify metalloids) is downstream of academic taxonomic authorities operating under something like Wikipedia's "no original research" policy. It can expose disagreement among authorities, but it shouldn't quietly become another undocumented taxonomy.
Naldaviricetes is a good example. It is unquestionably a class of viruses, but "Viruses" is not necessarily its formal kingdom. ICTV currently leaves it unassigned to a realm, kingdom, or phylum so Ptree's ICTV backbone places it directly beneath a display root called Viruses. NCBI places it beneath "Viruses incertae sedis," while GBIF supplies it without that viral higher lineage, producing the confusing placement you found.
Lucent 2 days ago [-]
Ptree consolidates of 11 taxonomic trees, both categorical like we used in school (plant, animalia) and phylogenetic (evolutionary descent), with instant crosswalk between them.
Across those trees it overlays 41 visual properties (categorical and numerical) assembled from hundreds of biological traits and sources. Color the tree by habitat, nutrition, size, longevity, even see vertical range of birds and depth of fish visually.
The backend is 800 GB of raw data distilled through a 9-step build process that reconciles and links all 11 trees along with hundreds of traits so every node in every tree gets all the properties. Every color and number presented retains and shows its provenance: original wording, citation, and license.
The frontend uses a custom Miller column implementation with fold-away gutter, all composited animation (no frameworks, pure DOM mutation). Use +'s to try to confuse it by expanding many branches and it will fold them away and route edges around them.
Made by the creator of ptable.com, a popular interactive periodic table website around since 1997.
takomora 2 days ago [-]
Great design, very snappy. Fun to browse and learn about species I didn't know exist and see how species are related to each other.
I do filter structural junk per backbone, but only from evidence that backbone itself supplies: synonym/accepted status, "not-a-taxon", environmental, hidden, unplaced flags. I also insert neutral buckets such as "classes (no phylum)" where ranks are skipped, so thousands of taxa don't spill into one flat level.
What I deliberately don't do is move a taxon to the parent that I think makes more biological sense. Ptree (Ptable gets the same kind of requests to classify metalloids) is downstream of academic taxonomic authorities operating under something like Wikipedia's "no original research" policy. It can expose disagreement among authorities, but it shouldn't quietly become another undocumented taxonomy.
Naldaviricetes is a good example. It is unquestionably a class of viruses, but "Viruses" is not necessarily its formal kingdom. ICTV currently leaves it unassigned to a realm, kingdom, or phylum so Ptree's ICTV backbone places it directly beneath a display root called Viruses. NCBI places it beneath "Viruses incertae sedis," while GBIF supplies it without that viral higher lineage, producing the confusing placement you found.
Across those trees it overlays 41 visual properties (categorical and numerical) assembled from hundreds of biological traits and sources. Color the tree by habitat, nutrition, size, longevity, even see vertical range of birds and depth of fish visually.
The backend is 800 GB of raw data distilled through a 9-step build process that reconciles and links all 11 trees along with hundreds of traits so every node in every tree gets all the properties. Every color and number presented retains and shows its provenance: original wording, citation, and license.
The frontend uses a custom Miller column implementation with fold-away gutter, all composited animation (no frameworks, pure DOM mutation). Use +'s to try to confuse it by expanding many branches and it will fold them away and route edges around them.
Made by the creator of ptable.com, a popular interactive periodic table website around since 1997.