9feb1b6e1b4bedc62cc78a12770731dc56af7137 hiram Sat Aug 5 21:50:34 2017 -0700 adding Hep B virus, HPV, Staphylococcus aureus bacteria refs #19937 diff --git src/hg/js/dbDbTaxonomy.js src/hg/js/dbDbTaxonomy.js index de2feb2..69d6887 100644 --- src/hg/js/dbDbTaxonomy.js +++ src/hg/js/dbDbTaxonomy.js @@ -596,53 +596,54 @@ [ ["Chrysemys picta", 8479, null, [ ["Painted turtle", 8478, "Chrysemys picta bellii" ] ] ] ] ] ] ] ] ] ] ], ["Trionychia", 1579275, null, [ ["Trionychidae", 34907, null, [ ["Apalone", 55533, null, [ ["Spiny softshell turtle", 55534, "Apalone spinifera" ] ] ], ["Pelodiscus", 204969, null, [ ["Chinese softshell turtle", 13735, "Pelodiscus sinensis" ] ] ] ] ] ] ] ] ] ] ] ] ], ["Lepidosauria", 8504, null, [ ["Squamata", 8509, null, [ ["Bifurcata", 1329961, null, [ ["Unidentata", 1329950, null, [ ["Episquamata", 1329912, null, [ ["Toxicofera", 1329911, null, [ ["Iguania", 8511, null, - [ ["Iguanidae", 8515, null, - [ ["Polychrotinae", 81957, null, + [ ["Dactyloidae", 2024747, null, [ ["Anolis", 28376, null, - [ ["Lizard", 28377, "Anolis carolinensis" ] ] ] ] ] ] ] ] ], + [ ["Lizard", 28377, "Anolis carolinensis" ] ] ] ] ] ] ], ["Serpentes", 8570, null, [ ["Colubroidea", 34989, null, [ ["Colubridae", 8578, null, [ ["Natricinae", 169862, null, [ ["Thamnophis", 34999, null, [ ["Garter snake", 35019, "Thamnophis sirtalis" ] ] ] ] ] ] ] ] ], ["Henophidia", 34979, null, [ ["Pythonidae", 34984, null, [ ["Python", 37579, null, [ ["Burmese python", 176946, "Python bivittatus" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Amphibia", 8292, null, [ ["Batrachia", 41666, null, [ ["Anura", 8342, null, [ ["Pipoidea", 30319, null, [ ["Pipidae", 8352, null, [ ["Xenopodinae", 8360, null, [ ["Xenopus", 8353, null, [ ["Silurana", 8363, null, - [ ["X. tropicalis", 8364, "Xenopus tropicalis" ] ] ] ] ] ] ] ] ] ] ], + [ ["X. tropicalis", 8364, "Xenopus tropicalis" ] ] ], + ["Xenopus", 262014, null, + [ ["African clawed frog", 8355, "Xenopus laevis" ] ] ] ] ] ] ] ] ] ] ], ["Neobatrachia", 8416, null, [ ["Ranoidea", 30352, null, [ ["Dicroglossidae", 685122, null, [ ["Dicroglossinae", 1191378, null, [ ["Nanorana", 120497, null, [ ["Tibetan frog", 125878, "Nanorana parkeri" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Coelacanthimorpha", 118072, null, [ ["Coelacanthiformes", 7894, null, [ ["Coelacanthidae", 7895, null, [ ["Latimeria", 7896, null, [ ["Coelacanth", 7897, "Latimeria chalumnae" ] ] ] ] ] ] ] ] ] ] ], ["Actinopterygii", 7898, null, [ ["Actinopteri", 186623, null, [ ["Neopterygii", 41665, null, [ ["Teleostei", 32443, null, @@ -1028,68 +1029,85 @@ [ ["Hexacorallia", 6102, null, [ ["Actiniaria", 6103, null, [ ["Edwardsiidae", 45349, null, [ ["Nematostella", 45350, null, [ ["Starlet sea anemone", 45351, "Nematostella vectensis" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Fungi", 4751, null, [ ["Dikarya", 451864, null, [ ["Ascomycota", 4890, null, [ ["saccharomyceta", 716545, null, [ ["Saccharomycotina", 147537, null, [ ["Saccharomycetes", 4891, null, [ ["Saccharomycetales", 4892, null, [ ["Saccharomycetaceae", 4893, null, [ ["Saccharomyces", 4930, null, [ ["S. cerevisiae", 4932, "Saccharomyces cerevisiae", - [ ["S. cerevisiae", 559292, "Saccharomyces cerevisiae S288c" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], + [ ["S. cerevisiae", 559292, "Saccharomyces cerevisiae S288C" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Alveolata", 33630, null, [ ["Apicomplexa", 5794, null, [ ["Aconoidasida", 422676, null, [ ["Haemosporida", 5819, null, [ ["Plasmodiidae", 1639119, null, [ ["Plasmodium", 5820, null, [ ["Plasmodium (Laverania)", 418107, null, [ ["P. falciparum", 5833, "Plasmodium falciparum", [ ["Plasmodium falciparum 3d7", 36329, "Plasmodium falciparum 3D7" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Ciliophora", 5878, null, [ ["Intramacronucleata", 431838, null, [ ["Spirotrichea", 33829, null, [ ["Stichotrichia", 194286, null, [ ["Sporadotrichida", 693921, null, [ ["Oxytrichidae", 57506, null, [ ["Oxytrichinae", 1001750, null, [ ["Oxytricha", 5943, null, [ ["Oxytricha trifallax", 1172189, "Oxytricha trifallax" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Bacteria", 2, null, [ ["Proteobacteria", 1224, null, [ ["Gammaproteobacteria", 1236, null, [ ["Pseudomonadales", 72274, null, [ ["Moraxellaceae", 468, null, [ ["Acinetobacter", 469, null, [ ["Acinetobacter calcoaceticus/baumannii complex", 909768, null, [ ["Acinetobacter baumannii", 470, null, - [ ["Acinetobacter baumannii", 1100841, "Acinetobacter baumannii TYTH-1" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], + [ ["Acinetobacter baumannii", 1100841, "Acinetobacter baumannii TYTH-1" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], + ["Terrabacteria group", 1783272, null, + [ ["Firmicutes", 1239, null, + [ ["Bacilli", 91061, null, + [ ["Bacillales", 1385, null, + [ ["Staphylococcaceae", 90964, null, + [ ["Staphylococcus", 1279, null, + [ ["Staphylococcus aureus", 1280, null, + [ ["Staphylococcus aureus subsp. aureus", 46170, null, + [ ["Staph", 93061, "Staphylococcus aureus subsp. aureus NCTC 8325" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Viruses", 10239, null, [ ["ssRNA viruses", 439488, null, [ ["ssRNA negative-strand viruses", 35301, null, [ ["Mononegavirales", 11157, null, [ ["Filoviridae", 11266, null, [ ["Ebolavirus", 186536, null, [ ["Ebola virus", 186538, "Zaire ebolavirus" ], ["Bundibugyo ebolavirus", 565995, "Bundibugyo ebolavirus" ], ["Reston ebolavirus", 186539, "Reston ebolavirus" ], ["Sudan ebolavirus", 186540, "Sudan ebolavirus" ], ["Tai forest ebolavirus", 186541, "Tai Forest ebolavirus" ] ] ], ["Marburgvirus", 186537, null, [ ["Marburg virus", 11269, "Marburg marburgvirus" ] ] ] ] ] ] ] ] ], ["ssRNA positive-strand viruses, no DNA stage", 35278, null, [ ["Nidovirales", 76804, null, [ ["Coronaviridae", 11118, null, [ ["Coronavirinae", 693995, null, [ ["Betacoronavirus", 694002, null, - [ ["Severe acute respiratory syndrome-related coronavirus", 694009, null, + [ ["SARS-related coronavirus", 694009, null, [ ["SARS coronavirus", 227859, "SARS coronavirus" ] ] ] ] ] ] ] ] ] ] ] ] ] ] ], ["Retro-transcribing viruses", 35268, null, - [ ["Retroviridae", 11632, null, + [ ["Hepadnaviridae", 10404, null, + [ ["Orthohepadnavirus", 10405, null, + [ ["Hbv", 10407, "Hepatitis B virus" ] ] ] ] ], + ["Retroviridae", 11632, null, [ ["Orthoretrovirinae", 327045, null, [ ["Betaretrovirus", 140052, null, - [ ["MMTV", 11757, "Mouse mammary tumor virus" ] ] ] ] ] ] ] ] ] ] ] ] ]; + [ ["MMTV", 11757, "Mouse mammary tumor virus" ] ] ] ] ] ] ] ] ], + ["dsDNA viruses, no RNA stage", 35237, null, + [ ["Papillomaviridae", 151340, null, + [ ["Alphapapillomavirus", 333750, null, + [ ["Alphapapillomavirus 14", 931244, null, + [ ["Hpv", 333769, "Human papillomavirus type 90" ] ] ] ] ] ] ] ] ] ] ] ] ];