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.
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?)
The problem with rolling up 2.2 million species into 7 kingdoms is it surfaces data quality issues loudly. Ranking photos by popularity means one node mismatch in millions due to a homonym will send that up from 10 levels deep. As I find these, I'm trying to squash them.
Very cool. Perhaps you've seen OneZoom[0] already which is purely based on phylogenetic data sourced from Open Tree of Life. OTOL has been around for a long time. The project aggregates phylogenetic data from thousands of studies and creates a massive synthetic tree.[1] It's neat because anyone can contribute. If you find a study not represented in there you can contribute the newick tree/annotation for it.
OneZoom is a great museum piece. Very engaging visualization that invites large touchscreen interaction. Impressive code behind it too for pruning offscreen vectors so the zoom stays smooth. On desktop however, perhaps due to my age, it gives me a bit of gorilla arm.
Thanks to open data, I offer the same node hierarchy of OTT, among 10 other backbones, but present it with 3 different (perhaps less dazzling) viewing mechanics switchable at the top: Icicle, which packs hierarchy into a fixed vertical height while allowing depth to stay horizontally reachable. Chronogram is the opposite, showing structure even 10 levels deep in a compact horizontal region, but at the expense of large vertical expansion. And Tree, the default, which is a compromise that can also show multiple winding paths simultaneously by folding them against the gutter.
I also focus less on the tree itself and more on trait overlay and rolling up thousands or even millions of species into compact segments so you can get a feel for how many chordates lay eggs or how many spiders are carnivorous in a glance.
https://ptree.org/#OTT
Yes I saw the OTT tab after I left my comment. Mostly I wanted to take the opportunity to sing the praises of the OTT project
It's a very cool project! I'm a believer in the idea of mixing phylogenetic trees and trait tables. In tomato breeding, there is a lot of attention paid to closely related species as they hybridize quite readily. Being able to represent the phylogenetic relationships alongside their traits, habitats, etc is an extremely useful data visualization strategy. I actually made a tool to automate making charts like these but I don't think it's mature enough to share yet
Love this. Also love that this is coming from someone with expertise who, based on comments below, takes quality seriously. Particularly cool when juxtaposed against one the other day “Any Human Ever” which was at first enthralling and joy-inducing, but upon deeper inspection was just a slop factory spreading misinformation across the internet.
This is the highest compliment, and I see why no other projects have tried to join all the different trees of life together or attach and reconcile traits. This was the majority of the project.
However, the unique "roll-up" visualization of traits brought in an interesting method of self-correction. For example, if any other phyla than the obvious 4 showed up with a single egg-laying species, I went back to the drawing board to find out where that incorrect join introduced the error.
Neat potentially. But in "species or group" I typed homo sapiens and it loaded up that whole tree. I noticed that a sibling of human is "cumshot man." I searched this on Google and expectedly got porn results. Not sure why that shows up.
Thank you for sharing this. It's such a great example of how fun learning and the internet can be. It's downright refreshing when things don't have the same exact design as the rest of the universe, and take the time to teach something.
23 comments
[ 0.24 ms ] story [ 4.7 ms ] threadAcross 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.
Discussed a few times over the years!
Interactive Periodic Table - https://news.ycombinator.com/item?id=27650576 - June 2021 (22 comments)
Dynamic Periodic Table (2017) - https://news.ycombinator.com/item?id=20495105 - July 2019 (21 comments)
Worlds Best Periodic Table - https://news.ycombinator.com/item?id=4378346 - Aug 2012 (5 comments)
Dynamic Periodic Table - https://news.ycombinator.com/item?id=3199922 - Nov 2011 (20 comments)
Dynamic/Interactive Periodic Table - https://news.ycombinator.com/item?id=1193431 - March 2010 (2 comments)
[0] https://www.onezoom.org/
[1] https://tree.opentreeoflife.org/opentree/argus/ottol@378964/...
Thanks to open data, I offer the same node hierarchy of OTT, among 10 other backbones, but present it with 3 different (perhaps less dazzling) viewing mechanics switchable at the top: Icicle, which packs hierarchy into a fixed vertical height while allowing depth to stay horizontally reachable. Chronogram is the opposite, showing structure even 10 levels deep in a compact horizontal region, but at the expense of large vertical expansion. And Tree, the default, which is a compromise that can also show multiple winding paths simultaneously by folding them against the gutter.
I also focus less on the tree itself and more on trait overlay and rolling up thousands or even millions of species into compact segments so you can get a feel for how many chordates lay eggs or how many spiders are carnivorous in a glance. https://ptree.org/#OTT
It's a very cool project! I'm a believer in the idea of mixing phylogenetic trees and trait tables. In tomato breeding, there is a lot of attention paid to closely related species as they hybridize quite readily. Being able to represent the phylogenetic relationships alongside their traits, habitats, etc is an extremely useful data visualization strategy. I actually made a tool to automate making charts like these but I don't think it's mature enough to share yet
Anyhow really great work on the project
However, the unique "roll-up" visualization of traits brought in an interesting method of self-correction. For example, if any other phyla than the obvious 4 showed up with a single egg-laying species, I went back to the drawing board to find out where that incorrect join introduced the error.
https://www.inaturalist.org/photos/660443931
https://www.researchgate.net/publication/37538009_mSpace_Exp...