Monday, February 02, 2009

Thoughts on the Wellcome Interactive Tree of Life

Last night BBC One aired David Attenborough's Charles Darwin and the Tree of Life, which featured a lovely "fly through" the tree of life:



In conjunction with the TV show, the Wellcome Trust has launched the Interactive Tree of Life, a Flash-based view of the tree of life. There's also a blog about the project. Here's a demo of the tree:



The tree looks very nice, and a lot of work has gone into it, but I am somewhat underwhelmed. The tree itself is tiny, and does a poor job of conveying the relative diversity of life (e.g., no plants, bacteria, few arthropods, etc.). It displays the tree on a 2D plane, and the user can move relative to that plane. I'm not convinced this is the best way to display large trees. Something modelled on Perceptive Pixel's demo might be more useful. I blogged about this last year, but the video host service has disappeared. You can see the tree display 50 seconds in to the video below:



There also seems to be some confusion over the license used. The disclaimer states that it is Creative Commons Attribution-Noncommercial 2.5 Generic, but the link is to Attribution-Noncommercial-No Derivative Works 3.0. There's a big difference. The disclaimer encourages us to remix it, the linked license says that we cannot.

Out of curiosity I grabbed the code from the web site (a 1.5Gb file) and had a quick look. The bulk of the files are media, such as images, movies, and 3D Maya models. There's some nice stuff here. The actual tree itself is there in New Hampshire eXtended format. Here it is displayed in TreeView X:



Here's the NHX tree itself.


((((((((((((((((((((((((((((((Antelope:25.38857142856932 [&&NHX:id=51129:tol=Y ], Sheep:25.38857142856932 [&&NHX:id=51093:tol=Y ]):4.231428571428751 [&&NHX:id=51154 ], Cow:29.619999999998072 [&&NHX:id=51150 ])Bovidae:33.26333333333336 [&&NHX:id=50878:tol=Y ], Pig:62.883333333331485 [&&NHX:id=51287:tol=Y ]):0.978333333333334, Hippopotamus:63.86166666666491 [&&NHX:id=30366 ]):2.445833333333335, Camel:66.30749999999811 [&&NHX:id=30350:tol=Y ])Artiodactyla:7.337500000000006 [&&NHX:id=15976:tol=Y ], Humpback_whale:73.64499999999816 [&&NHX:id=16054 ]):9.663854166666676 [&&NHX:id=15975 ], (((Horse:72.14374999999836 [&&NHX:id=16255 ], Rhino:72.14374999999836 [&&NHX:id=16262 ])Perissodactyla:5.153125000000017 [&&NHX:id=15980:tol=Y ], Elephant:77.29687499999827 [&&NHX:id=22667:tol=Y ]):4.294270833333347 [&&NHX:id=15979 ], Aardvark:81.59114583333152 [&&NHX:id=16881 ]):1.717708333333339):15.761701388888907 [&&NHX:id=15974 ], ((((Brown_bear:40.2599999999984 [&&NHX:id=123666:tol=Y ], Polar_bear:40.2599999999984 [&&NHX:id=123667:tol=Y ])Ursidae:11.18333333333332 [&&NHX:id=16015:tol=Y ], Seal:51.443333333331715 [&&NHX:id=16020 ]):4.473333333333327, Dog:55.91666666666514 [&&NHX:id=16013 ])Caniformia:11.18333333333332 [&&NHX:id=16011 ], (Cat:40.259999999998215 [&&NHX:id=123531:tol=Y ], Lion:40.259999999998215 [&&NHX:id=123566:tol=Y ])Felidae:26.839999999999964 [&&NHX:id=16006:tol=Y ])Carnivora:31.9705555555556 [&&NHX:id=15971:tol=Y ]):0.15222222222222132, ((Mole:86.06453703703531 [&&NHX:id=16213 ], Shrew:86.06453703703531 [&&NHX:id=16223 ]):3.759497354497354, Hedgehog:89.82403439153265 [&&NHX:id=16211 ])Insectivora:9.398743386243385 [&&NHX:id=15968:tol=Y ]):0.3805555555555533, (((Chimpanzee:9.143333333331611 [&&NHX:id=26565 ], Human:9.143333333331611 [&&NHX:id=16421:tol=Y ]):82.69666666666664 [&&NHX:id=16412 ], Tree_shrew:91.83999999999833 [&&NHX:id=50808 ]):4.1099999999999755 [&&NHX:id=15962 ], Fruit_bat:95.94999999999834 [&&NHX:id=16076 ]):3.6533333333333116 [&&NHX:id=15961 ]):1.14166666666666, ((Hamster:56.967999999998256 [&&NHX:id=16546 ], Rat:56.96799999999821 [&&NHX:id=50732 ])Eumuroida:33.211999999999804 [&&NHX:id=16528 ], Rabbit:90.17999999999788 [&&NHX:id=16227 ])Glires:10.565000000000104 [&&NHX:id=15957 ]):16.484999999999623 [&&NHX:id=15955 ], Kangaroo:117.22999999999797 [&&NHX:id=16248 ]):31.38499999999999 [&&NHX:id=15993 ], Platypus:148.61499999999816 [&&NHX:id=16253:tol=Y ]):39.50999999999999 [&&NHX:id=15990 ], Megazostrodon:4.0625 [&&NHX:id=15032:nsz=2:ncol=red:ext=Y ])Cynodontia:32.5 [&&NHX:id=15030 ], Dimetrodon:4.0625 [&&NHX:id=14972:nsz=2:ncol=red:ext=Y ])Sphenacodontoidea:73.125 [&&NHX:id=14971 ], (((((((((((((Flamingo:106.30859375000043 [&&NHX:id=89474:tol=Y ], Toucan:106.3085937500002 [&&NHX:id=93330:tol=Y ]):1.4296874999999905, Penguin:107.73828125000037 [&&NHX:id=57223:tol=Y ])Neoaves:3.5742187499999765 [&&NHX:id=26305:tol=Y ], Duck:111.31250000000024 [&&NHX:id=89298:tol=Y ])Neognathae:4.289062499999972 [&&NHX:id=26291 ], Ostrich:115.60156250000016 [&&NHX:id=26289:tol=Y ])Neornithes:4.289062499999972 [&&NHX:id=15834:tol=Y ], Ichthyornis:4.386242378048764 [&&NHX:id=15833:nsz=2:ncol=red:ext=Y ])Euornithes_true_birds:12.867187499999915 [&&NHX:id=15829 ], Archaeopteryx:2.144531249999986 [&&NHX:id=15824:nsz=2:ncol=red:ext=Y ])Aves:12.867187499999915 [&&NHX:id=15721:tol=Y ], Tyrannosaurus_Rex:79.47061157226744 [&&NHX:id=15889:nsz=2:ncol=red:ext=Y ]):74.99999999999773 [&&NHX:id=15713 ], Diplodocus:157.62263488769486 [&&NHX:id=15756:nsz=2:ncol=red:ext=Y ])Saurischia:9.374999999999716 [&&NHX:id=15724 ], Iguanadon:165.44959259033112 [&&NHX:id=15740:nsz=2:ncol=red:ext=Y ])Dinosauria:20.400000000000002 [&&NHX:id=14883:tol=Y ], Crocodile:250.39999999999782 [&&NHX:id=14868 ])Archosauria:22.950000000000003 [&&NHX:id=14900:tol=Y ], Snake:273.34999999999803 [&&NHX:id=17563 ])Sauria:12.75 [&&NHX:id=14913 ], Brouffia:1.275 [&&NHX:id=14865:nsz=2:ncol=red:ext=Y ]):5.1 [&&NHX:id=14864 ], Tortoise:291.1999999999979 [&&NHX:id=17631 ])Reptilia:2.55 [&&NHX:id=14846 ])Amniota:56.25000000000091 [&&NHX:id=14990:tol=Y ], (Amphibians:317.3333333333312 [&&NHX:id=14940 ], Newt:317.3333333333311 [&&NHX:id=82771 ])Living_amphibians:32.66666666666758 [&&NHX:id=14997:tol=Y ])Tetrapoda:9.00000000000009 [&&NHX:id=14987 ], Seymouriamorpha:14.610465116279109 [&&NHX:id=17554:nsz=2:ncol=red:ext=Y ]):40.87500000000041 [&&NHX:id=14985 ], (Acanthostega:1.8750000000000189 [&&NHX:id=15016:tol=Y:nsz=2:ncol=red:ext=Y ], Icthyostega:1.8750000000000189 [&&NHX:id=15015:tol=Y:nsz=2:ncol=red:ext=Y ]):0.7500000000000075):13.125000000000131 [&&NHX:id=14976 ], Panderichthys:2.2500000000000226 [&&NHX:id=14951:nsz=2:ncol=red:ext=Y ]):4.500000000000045 [&&NHX:id=14950 ], Eusthenopteron:2.2500000000000226 [&&NHX:id=14949:nsz=2:ncol=red:ext=Y ]):9.00000000000009 [&&NHX:id=14948 ], ((Paddle_fish:363.6363636363626 [&&NHX:id=68750 ], Sturgeon:363.6363636363626 [&&NHX:id=68749 ])Acipenseriformes:24.242424242424242 [&&NHX:id=68726:tol=Y ], Clown_fish:387.8787878787866 [&&NHX:id=52149 ]):38.621212121213034 [&&NHX:id=68709 ])Osteichthyes:9.00000000000009 [&&NHX:id=14921 ], Shark:435.5 [&&NHX:id=14925 ])Node_1:13.944444444444489 [&&NHX:id=14919 ], Cephalaspidida:19.261904761904795 [&&NHX:id=16894:nsz=2:ncol=red:ext=Y ])Node_3:28.333333333333336 [&&NHX:id=14840 ], Pteraspis:46.45061728395067 [&&NHX:id=16929:nsz=2:ncol=red:ext=Y ])Node_1:9.444444444444445 [&&NHX:id=14833 ], Lamprey:487.22222222222223 [&&NHX:id=15919 ])Vertebrata:18.88888888888889 [&&NHX:id=14829:tol=Y ], Pikaia:506.1111111111113 [&&NHX:id=14824 ]):158.00000000000003 [&&NHX:id=14822 ], ((((((((Fruit_fly:339.4285714285717 [&&NHX:id=10610 ], Peacock_butterfly:339.42857142857144 [&&NHX:id=94054 ]):7.071428571428555 [&&NHX:id=8224 ], Wasp:346.5000000000002 [&&NHX:id=11244 ]):28.28571428571422 [&&NHX:id=8223 ], Cockroach:374.7857142857142 [&&NHX:id=8544 ])Neoptera:7.071428571428555 [&&NHX:id=8267:tol=Y ], Giant_dragonfly:10.607142857142833 [&&NHX:id=13265:nsz=2:ncol=red:ext=Y ])Pterygota:98.80952380952378 [&&NHX:id=8210:tol=Y ], Brine_shrimp:480.6666666666665 [&&NHX:id=6387 ]):43.81073446327684 [&&NHX:id=2527 ], ((((Harevest_mite:496.40677966101725 [&&NHX:id=2612 ], Spider:496.4067796610171 [&&NHX:id=2788:tol=Y ]):8.864406779661008 [&&NHX:id=2542 ], Harvestman:505.27118644067804 [&&NHX:id=2556 ])Arachnida:8.864406779661008 [&&NHX:id=2536:tol=Y ], Sea_Scorpion:39.88983050847454 [&&NHX:id=8174:nsz=2:ncol=red:ext=Y ])Chelicerata:7.387005649717507 [&&NHX:id=2535 ], Millipede:521.5225988700563 [&&NHX:id=52849 ]):2.954802259887003)Arthropoda:40.855932203389834 [&&NHX:id=2469:tol=Y ], (Opabinia:555.9111111111108 [&&NHX:id=20357 ], Velvet_worm:555.9111111111108 [&&NHX:id=20356 ])Onychophora:9.422222222222217 [&&NHX:id=2470:tol=Y ]):70.55555555555556 [&&NHX:id=2468 ], Acoel:635.8888888888889 [&&NHX:id=20383 ]):28.222222222222225)Bilateria:85.88888888888889 [&&NHX:id=2459:tol=Y ], Sponge:750.0 [&&NHX:id=20438 ])Animals:2250.0 [&&NHX:id=2374:tol=Y ], E._coli:3000.0 [&&NHX:id=2306 ])Life_on_earth;


It's great to see creative people tackling the challenge of displaying the tree of life. I just not convinced that this is the best way to do it.

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