{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}]}, "^ot:annotationEvents": {"annotation": [{"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu393902", "otu393923"], "@otusID": "otus2629", "@otuID": ["otu393902", "otu393923"]}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu393902", "otu393923"], "refersTo": {"@top": "otus", "@idref": "otus2629", "@otusID": "otus2629"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:dataDeposit"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6162"], "^ot:curatorName": "Chris Owen", "^ot:focalClade": 1062253, "^ot:focalCladeOTTTaxonName": "Insecta", "^ot:messages": {"message": []}, "^ot:otusElementOrder": ["otus2629"], "^ot:studyId": "pg_2629", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1111/syen.12028"}, "^ot:studyPublicationReference": "Letsch, H. and S. Simon. 2013. Insect phylogenomics: new insights on the relationships of lower neopteran orders (Polyneoptera). Systematic Entomology 38 (4): 783-793.", "^ot:studyYear": 2013, "^ot:tag": [], "^ot:treesElementOrder": ["trees2629"], "otusById": {"otus2629": {"otuById": {"otu393885": {"^ot:originalLabel": "Triops cancriformis", "^ot:ottId": 176180, "^ot:ottTaxonName": "Triops cancriformis"}, "otu393886": {"^ot:originalLabel": "Daphnia pulex", "^ot:ottId": 59086, "^ot:ottTaxonName": "Daphnia pulex"}, "otu393887": {"^ot:originalLabel": "Daphnia magna", "^ot:ottId": 668392, "^ot:ottTaxonName": "Daphnia magna"}, "otu393888": {"^ot:originalLabel": "Folsomia candida", "^ot:ottId": 861693, "^ot:ottTaxonName": "Folsomia candida"}, "otu393889": {"^ot:originalLabel": "Onychiurus arcticus", "^ot:ottId": 799602, "^ot:ottTaxonName": "Megaphorura arctica"}, "otu393890": {"^ot:originalLabel": "Anurida maritima", "^ot:ottId": 84744, "^ot:ottTaxonName": "Anurida maritima"}, "otu393891": {"^ot:originalLabel": "Campodea cf. fragilis", "^ot:ottId": 527583, "^ot:ottTaxonName": "Campodea fragilis"}, "otu393892": {"^ot:originalLabel": "Lepismachilis y signata", "^ot:ottId": 700453, "^ot:ottTaxonName": "Lepismachilis y-signata"}, "otu393893": {"^ot:originalLabel": "Ischnura elegans", "^ot:ottId": 253311, "^ot:ottTaxonName": "Ischnura elegans"}, "otu393894": {"^ot:originalLabel": "Baetis sp", "^ot:ottId": 796327, "^ot:ottTaxonName": "Baetis sp. AB-2009"}, "otu393895": {"^ot:originalLabel": "Zoraptera gurneyi", "^ot:ottId": 423782, "^ot:ottTaxonName": "Zorotypus gurneyi"}, "otu393896": {"^ot:originalLabel": "Nemurella pictetii", "^ot:ottId": 362169, "^ot:ottTaxonName": "Nemurella pictetii"}, "otu393897": {"^ot:originalLabel": "Forficula auricularia", "^ot:ottId": 673084, "^ot:ottTaxonName": "Forficula auricularia"}, "otu393898": {"^ot:originalLabel": "Locusta migratoria", "^ot:ottId": 178934, "^ot:ottTaxonName": "Locusta migratoria"}, "otu393899": {"^ot:originalLabel": "Gryllus bimaculatus", "^ot:ottId": 1077624, "^ot:ottTaxonName": "Gryllus bimaculatus"}, "otu393900": {"^ot:originalLabel": "Laupala kohalensis", "^ot:ottId": 55726, "^ot:ottTaxonName": "Laupala kohalensis"}, "otu393901": {"^ot:originalLabel": "Phyllium phillipinicum", "^ot:ottId": 156711, "^ot:ottTaxonName": "Phyllium philippinicum"}, "otu393902": {"^ot:originalLabel": "Embioptera gen"}, "otu393903": {"^ot:originalLabel": "Reticulitermes flavipes", "^ot:ottId": 991735, "^ot:ottTaxonName": "Reticulitermes flavipes"}, "otu393904": {"^ot:originalLabel": "Periplaneta americana", "^ot:ottId": 48288, "^ot:ottTaxonName": "Periplaneta americana"}, "otu393905": {"^ot:originalLabel": "Blattella germanica", "^ot:ottId": 48282, "^ot:ottTaxonName": "Blattella germanica"}, "otu393906": {"^ot:originalLabel": "Hodotermopsis sjoestedti", "^ot:ottId": 944978, "^ot:ottTaxonName": "Hodotermopsis sjostedti"}, "otu393907": {"^ot:originalLabel": "Lysiphlebus testaceipes", "^ot:ottId": 68346, "^ot:ottTaxonName": "Lysiphlebus testaceipes"}, "otu393908": {"^ot:originalLabel": "Nasonia vitripennis", "^ot:ottId": 729593, "^ot:ottTaxonName": "Nasonia vitripennis"}, "otu393909": {"^ot:originalLabel": "Dendroctonus ponderosae", "^ot:ottId": 1017374, "^ot:ottTaxonName": "Dendroctonus ponderosae"}, "otu393910": {"^ot:originalLabel": "Tribolium castaneum", "^ot:ottId": 148904, "^ot:ottTaxonName": "Tribolium castaneum"}, "otu393911": {"^ot:originalLabel": "Onthophagus taurus", "^ot:ottId": 262810, "^ot:ottTaxonName": "Onthophagus taurus"}, "otu393912": {"^ot:originalLabel": "Ctenocephalides felis", "^ot:ottId": 81976, "^ot:ottTaxonName": "Ctenocephalides felis"}, "otu393913": {"^ot:originalLabel": "Phlebotomus papatasi", "^ot:ottId": 1008039, "^ot:ottTaxonName": "Phlebotomus papatasi"}, "otu393914": {"^ot:originalLabel": "Anopheles stephensi", "^ot:ottId": 116726, "^ot:ottTaxonName": "Anopheles stephensi"}, "otu393915": {"^ot:originalLabel": "Antheraea assama", "^ot:ottId": 738629, "^ot:ottTaxonName": "Antheraea assama"}, "otu393916": {"^ot:originalLabel": "Bombyx mori", "^ot:ottId": 440274, "^ot:ottTaxonName": "Bombyx mori"}, "otu393917": {"^ot:originalLabel": "Heliothis virescens", "^ot:ottId": 742356, "^ot:ottTaxonName": "Heliothis virescens"}, "otu393918": {"^ot:originalLabel": "Bicyclus anynana", "^ot:ottId": 559934, "^ot:ottTaxonName": "Bicyclus anynana"}, "otu393919": {"^ot:originalLabel": "Rhodnius prolixus", "^ot:ottId": 958469, "^ot:ottTaxonName": "Rhodnius prolixus"}, "otu393920": {"^ot:originalLabel": "Nilaparvata lugens", "^ot:ottId": 876508, "^ot:ottTaxonName": "Nilaparvata lugens"}, "otu393921": {"^ot:originalLabel": "Peregrinus maidis", "^ot:ottId": 291011, "^ot:ottTaxonName": "Peregrinus maidis"}, "otu393922": {"^ot:originalLabel": "Graphocephala atropunctata", "^ot:ottId": 739003, "^ot:ottTaxonName": "Graphocephala atropunctata"}, "otu393923": {"^ot:originalLabel": "Homalodisca coagulata"}, "otu393924": {"^ot:originalLabel": "Oncometopia nigricans", "^ot:ottId": 295519, "^ot:ottTaxonName": "Oncometopia nigricans"}, "otu393925": {"^ot:originalLabel": "Bemisia tabaci", "^ot:ottId": 290577, "^ot:ottTaxonName": "Bemisia tabaci"}, "otu393926": {"^ot:originalLabel": "Diaphorina citri", "^ot:ottId": 624956, "^ot:ottTaxonName": "Diaphorina citri"}, "otu393927": {"^ot:originalLabel": "Pachypsylla venusta", "^ot:ottId": 265329, "^ot:ottTaxonName": "Pachypsylla venusta"}, "otu393928": {"^ot:originalLabel": "Maconellicoccus hirsutus", "^ot:ottId": 197458, "^ot:ottTaxonName": "Maconellicoccus hirsutus"}, "otu393929": {"^ot:originalLabel": "Aphis gossypii", "^ot:ottId": 1026471, "^ot:ottTaxonName": "Aphis gossypii"}, "otu393930": {"^ot:originalLabel": "Toxoptera citricida", "^ot:ottId": 34342, "^ot:ottTaxonName": "Toxoptera citricida"}, "otu393931": {"^ot:originalLabel": "Myzus persicae", "^ot:ottId": 785522, "^ot:ottTaxonName": "Myzus persicae"}, "otu393932": {"^ot:originalLabel": "Acyrthosiphon pisum", "^ot:ottId": 814484, "^ot:ottTaxonName": "Acyrthosiphon pisum"}}}}, "treesById": {"trees2629": {"@otus": "otus2629", "^ot:treeElementOrder": ["tree6162"], "treeById": {"tree6162": {"@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "50% maj-rule ML", "^ot:inGroupClade": "node1052666", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1052660", "^ot:specifiedRoot": "node1052660", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1052660": {"edge1052661": {"@source": "node1052660", "@target": "node1052661"}, "edge1052666": {"@source": "node1052660", "@target": "node1052666"}}, "node1052661": {"edge1052662": {"@source": "node1052661", "@target": "node1052662"}, "edge1052663": {"@source": "node1052661", "@target": "node1052663"}}, "node1052663": {"edge1052664": {"@source": "node1052663", "@target": "node1052664"}, "edge1052665": {"@source": "node1052663", "@target": "node1052665"}}, "node1052666": {"edge1052667": {"@source": "node1052666", "@target": "node1052667"}, "edge1052672": {"@source": "node1052666", "@target": "node1052672"}}, "node1052667": {"edge1052668": {"@source": "node1052667", "@target": "node1052668"}, "edge1052669": {"@source": "node1052667", "@target": "node1052669"}}, "node1052669": {"edge1052670": {"@source": "node1052669", "@target": "node1052670"}, "edge1052671": {"@source": "node1052669", "@target": "node1052671"}}, "node1052672": {"edge1052673": {"@source": "node1052672", "@target": "node1052673"}, "edge1052674": {"@source": "node1052672", "@target": "node1052674"}}, "node1052674": {"edge1052675": {"@source": "node1052674", "@target": "node1052675"}, "edge1052676": {"@source": "node1052674", "@target": "node1052676"}}, "node1052676": {"edge1052677": {"@source": "node1052676", "@target": "node1052677"}, "edge1052678": {"@source": "node1052676", "@target": "node1052678"}}, "node1052678": {"edge1052679": {"@source": "node1052678", "@target": "node1052679"}, "edge1052680": {"@source": "node1052678", "@target": "node1052680"}}, "node1052680": {"edge1052681": {"@source": "node1052680", "@target": "node1052681"}, "edge1052704": {"@source": "node1052680", "@target": "node1052704"}}, "node1052681": {"edge1052682": {"@source": "node1052681", "@target": "node1052682"}, "edge1052683": {"@source": "node1052681", "@target": "node1052683"}}, "node1052683": {"edge1052684": {"@source": "node1052683", "@target": "node1052684"}, "edge1052687": {"@source": "node1052683", "@target": "node1052687"}}, "node1052684": {"edge1052685": {"@source": "node1052684", "@target": "node1052685"}, "edge1052686": {"@source": "node1052684", "@target": "node1052686"}}, "node1052687": {"edge1052688": {"@source": "node1052687", "@target": "node1052688"}, "edge1052693": {"@source": "node1052687", "@target": "node1052693"}}, "node1052688": {"edge1052689": {"@source": "node1052688", "@target": "node1052689"}, "edge1052690": {"@source": "node1052688", "@target": "node1052690"}}, "node1052690": {"edge1052691": {"@source": "node1052690", "@target": "node1052691"}, "edge1052692": {"@source": "node1052690", "@target": "node1052692"}}, "node1052693": {"edge1052694": {"@source": "node1052693", "@target": "node1052694"}, "edge1052697": {"@source": "node1052693", "@target": "node1052697"}}, "node1052694": {"edge1052695": {"@source": "node1052694", "@target": "node1052695"}, "edge1052696": {"@source": "node1052694", "@target": "node1052696"}}, "node1052697": {"edge1052698": {"@source": "node1052697", "@target": "node1052698"}, "edge1052699": {"@source": "node1052697", "@target": "node1052699"}}, "node1052699": {"edge1052700": {"@source": "node1052699", "@target": "node1052700"}, "edge1052701": {"@source": "node1052699", "@target": "node1052701"}}, "node1052701": {"edge1052702": {"@source": "node1052701", "@target": "node1052702"}, "edge1052703": {"@source": "node1052701", "@target": "node1052703"}}, "node1052704": {"edge1052705": {"@source": "node1052704", "@target": "node1052705"}, "edge1052728": {"@source": "node1052704", "@target": "node1052728"}}, "node1052705": {"edge1052706": {"@source": "node1052705", "@target": "node1052706"}, "edge1052709": {"@source": "node1052705", "@target": "node1052709"}}, "node1052706": {"edge1052707": {"@source": "node1052706", "@target": "node1052707"}, "edge1052708": {"@source": "node1052706", "@target": "node1052708"}}, "node1052709": {"edge1052710": {"@source": "node1052709", "@target": "node1052710"}, "edge1052715": {"@source": "node1052709", "@target": "node1052715"}}, "node1052710": {"edge1052711": {"@source": "node1052710", "@target": "node1052711"}, "edge1052712": {"@source": "node1052710", "@target": "node1052712"}}, "node1052712": {"edge1052713": {"@source": "node1052712", "@target": "node1052713"}, "edge1052714": {"@source": "node1052712", "@target": "node1052714"}}, "node1052715": {"edge1052716": {"@source": "node1052715", "@target": "node1052716"}, "edge1052717": {"@source": "node1052715", "@target": "node1052717"}}, "node1052717": {"edge1052718": {"@source": "node1052717", "@target": "node1052718"}, "edge1052721": {"@source": "node1052717", "@target": "node1052721"}}, "node1052718": {"edge1052719": {"@source": "node1052718", "@target": "node1052719"}, "edge1052720": {"@source": "node1052718", "@target": "node1052720"}}, "node1052721": {"edge1052722": {"@source": "node1052721", "@target": "node1052722"}, "edge1052723": {"@source": "node1052721", "@target": "node1052723"}}, "node1052723": {"edge1052724": {"@source": "node1052723", "@target": "node1052724"}, "edge1052725": {"@source": "node1052723", "@target": "node1052725"}}, "node1052725": {"edge1052726": {"@source": "node1052725", "@target": "node1052726"}, "edge1052727": {"@source": "node1052725", "@target": "node1052727"}}, "node1052728": {"edge1052729": {"@source": "node1052728", "@target": "node1052729"}, "edge1052740": {"@source": "node1052728", "@target": "node1052740"}}, "node1052729": {"edge1052730": {"@source": "node1052729", "@target": "node1052730"}, "edge1052731": {"@source": "node1052729", "@target": "node1052731"}}, "node1052731": {"edge1052732": {"@source": "node1052731", "@target": "node1052732"}, "edge1052735": {"@source": "node1052731", "@target": "node1052735"}}, "node1052732": {"edge1052733": {"@source": "node1052732", "@target": "node1052733"}, "edge1052734": {"@source": "node1052732", "@target": "node1052734"}}, "node1052735": {"edge1052736": {"@source": "node1052735", "@target": "node1052736"}, "edge1052737": {"@source": "node1052735", "@target": "node1052737"}}, "node1052737": {"edge1052738": {"@source": "node1052737", "@target": "node1052738"}, "edge1052739": {"@source": "node1052737", "@target": "node1052739"}}, "node1052740": {"edge1052741": {"@source": "node1052740", "@target": "node1052741"}, "edge1052746": {"@source": "node1052740", "@target": "node1052746"}}, "node1052741": {"edge1052742": {"@source": "node1052741", "@target": "node1052742"}, "edge1052743": {"@source": "node1052741", "@target": "node1052743"}}, "node1052743": {"edge1052744": {"@source": "node1052743", "@target": "node1052744"}, "edge1052745": {"@source": "node1052743", "@target": "node1052745"}}, "node1052746": {"edge1052747": {"@source": "node1052746", "@target": "node1052747"}, "edge1052748": {"@source": "node1052746", "@target": "node1052748"}}, "node1052748": {"edge1052749": {"@source": "node1052748", "@target": "node1052749"}, "edge1052750": {"@source": "node1052748", "@target": "node1052750"}}, "node1052750": {"edge1052751": {"@source": "node1052750", "@target": "node1052751"}, "edge1052752": {"@source": "node1052750", "@target": "node1052752"}}, "node1052752": {"edge1052753": {"@source": "node1052752", "@target": "node1052753"}, "edge1052754": {"@source": "node1052752", "@target": "node1052754"}}}, "nodeById": {"node1052660": {"@root": true}, "node1052661": {}, "node1052662": {"@otu": "otu393885"}, "node1052663": {}, "node1052664": {"@otu": "otu393886"}, "node1052665": {"@otu": "otu393887"}, "node1052666": {}, "node1052667": {}, "node1052668": {"@otu": "otu393888"}, "node1052669": {}, "node1052670": {"@otu": "otu393889"}, "node1052671": {"@otu": "otu393890"}, "node1052672": {}, "node1052673": {"@otu": "otu393891"}, "node1052674": {}, "node1052675": {"@otu": "otu393892"}, "node1052676": {}, "node1052677": {"@otu": "otu393893"}, "node1052678": {}, "node1052679": {"@otu": "otu393894"}, "node1052680": {}, "node1052681": {}, "node1052682": {"@otu": "otu393895"}, "node1052683": {}, "node1052684": {}, "node1052685": {"@otu": "otu393896"}, "node1052686": {"@otu": "otu393897"}, "node1052687": {}, "node1052688": {}, "node1052689": {"@otu": "otu393898"}, "node1052690": {}, "node1052691": {"@otu": "otu393899"}, "node1052692": {"@otu": "otu393900"}, "node1052693": {}, "node1052694": {}, "node1052695": {"@otu": "otu393901"}, "node1052696": {"@otu": "otu393902"}, "node1052697": {}, "node1052698": {"@otu": "otu393903"}, "node1052699": {}, "node1052700": {"@otu": "otu393904"}, "node1052701": {}, "node1052702": {"@otu": "otu393905"}, "node1052703": {"@otu": "otu393906"}, "node1052704": {}, "node1052705": {}, "node1052706": {}, "node1052707": {"@otu": "otu393907"}, "node1052708": {"@otu": "otu393908"}, "node1052709": {}, "node1052710": {}, "node1052711": {"@otu": "otu393909"}, "node1052712": {}, "node1052713": {"@otu": "otu393910"}, "node1052714": {"@otu": "otu393911"}, "node1052715": {}, "node1052716": {"@otu": "otu393912"}, "node1052717": {}, "node1052718": {}, "node1052719": {"@otu": "otu393913"}, "node1052720": {"@otu": "otu393914"}, "node1052721": {}, "node1052722": {"@otu": "otu393915"}, "node1052723": {}, "node1052724": {"@otu": "otu393916"}, "node1052725": {}, "node1052726": {"@otu": "otu393917"}, "node1052727": {"@otu": "otu393918"}, "node1052728": {}, "node1052729": {}, "node1052730": {"@otu": "otu393919"}, "node1052731": {}, "node1052732": {}, "node1052733": {"@otu": "otu393920"}, "node1052734": {"@otu": "otu393921"}, "node1052735": {}, "node1052736": {"@otu": "otu393922"}, "node1052737": {}, "node1052738": {"@otu": "otu393923"}, "node1052739": {"@otu": "otu393924"}, "node1052740": {}, "node1052741": {}, "node1052742": {"@otu": "otu393925"}, "node1052743": {}, "node1052744": {"@otu": "otu393926"}, "node1052745": {"@otu": "otu393927"}, "node1052746": {}, "node1052747": {"@otu": "otu393928"}, "node1052748": {}, "node1052749": {"@otu": "otu393929"}, "node1052750": {}, "node1052751": {"@otu": "otu393930"}, "node1052752": {}, "node1052753": {"@otu": "otu393931"}, "node1052754": {"@otu": "otu393932"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "d33fb39501605772a074dffc82affa5344ea9a94", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Wed, 11 Jun 2014 22:18:34 -0500", "date_ISO_8601": "2014-06-11 22:18:34 -0500", "relative_date": "12 years ago", "message_subject": "corrected study ids"}, {"id": "f8a738aeda20a73750847484e110a85c7a3e0a12", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 10 Jun 2014 23:36:42 -0500", "date_ISO_8601": "2014-06-10 23:36:42 -0500", "relative_date": "12 years ago", "message_subject": "Migrating info from gcmdr to nexsons", "message_body": "using peyotl d69c8b180fce7703c7203a0b51712eab57e2988c\ndev/decorate_pg_studies_with_gcmdr_info.py\nto set:\n  ^ot:candidateTreeForSynthesis\n  ^ot:specifiedRoot, and\n  ^ot:unrootedTree\nproperties based on the use of the trees for synthesis study\nlists in gcmdr commit 35bf307e72bed4f59724762dde4a12965abcea92"}, {"id": "593d6fbab385716dc0a12f3fc95133e8b7479b37", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 29 Apr 2014 20:05:19 -0500", "date_ISO_8601": "2014-04-29 20:05:19 -0500", "relative_date": "12 years ago", "message_subject": "initial commit with phylografter files from 29 Apr, 2014"}]}