{"sha": "2aa180baef3c5e313da1e7f09c83ce2c0467b457", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2018-07-10T21:26:11.462Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2018-07-10T21:26:11.462Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "complete_dataset2_clean_RAxML10k.nex", "@size": 6662, "@type": "nexus", "@url": "/curator/download/supporting_files.doc.8b0534ac764b6af8.636f6d706c6574655f64617461736574325f636c65616e5f5241784d4c31306b2e6e6578.nex", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["Pietro de Mello"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 639666, "^ot:focalCladeOTTTaxonName": "Testudines", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_1490", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2014.10.021"}, "^ot:studyPublicationReference": "Nicholas G. Crawford, James F. Parham, Anna B. Sellas, Brant C. Faircloth, Travis C. Glenn, Theodore J. Papenfuss, James B. Henderson, Madison H. Hansen, W. Brian Simison, 2015, 'A phylogenomic analysis of turtles', Molecular Phylogenetics and Evolution, vol. 83, pp. 250-257", "^ot:studyYear": 2015, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Sphenodon punctatus", "^ot:ottId": 35890, "^ot:ottTaxonName": "Sphenodon punctatus"}, "otu10": {"^ot:originalLabel": "Phrynops sp", "^ot:ottId": 66456, "^ot:ottTaxonName": "Phrynops"}, "otu11": {"^ot:originalLabel": "Platemys platycephala", "^ot:ottId": 709464, "^ot:ottTaxonName": "Platemys platycephala"}, "otu12": {"^ot:originalLabel": "Carettochelys insculpta", "^ot:ottId": 810244, "^ot:ottTaxonName": "Carettochelys insculpta"}, "otu13": {"^ot:originalLabel": "Lissemys punctata", "^ot:ottId": 619852, "^ot:ottTaxonName": "Lissemys punctata"}, "otu14": {"^ot:originalLabel": "Apalone ferox", "^ot:ottId": 378502, "^ot:ottTaxonName": "Apalone ferox"}, "otu15": {"^ot:originalLabel": "Pelodiscus sinensis", "^ot:ottId": 143391, "^ot:ottTaxonName": "Pelodiscus sinensis"}, "otu16": {"^ot:originalLabel": "Nilssonia formosa", "^ot:ottId": 623211, "^ot:ottTaxonName": "Nilssonia formosa"}, "otu17": {"^ot:originalLabel": "Chelonia mydas", "^ot:ottId": 559133, "^ot:ottTaxonName": "Chelonia mydas"}, "otu18": {"^ot:originalLabel": "Lepidochelys olivacea", "^ot:ottId": 430320, "^ot:ottTaxonName": "Lepidochelys olivacea"}, "otu19": {"^ot:originalLabel": "Dermochelys coriacea", "^ot:ottId": 243403, "^ot:ottTaxonName": "Dermochelys coriacea"}, "otu2": {"^ot:originalLabel": "Anolis carolinensis", "^ot:ottId": 705356, "^ot:ottTaxonName": "Anolis carolinensis"}, "otu20": {"^ot:originalLabel": "Chelydra sp", "^ot:ottId": 587316, "^ot:ottTaxonName": "Chelydra"}, "otu21": {"^ot:originalLabel": "Dermatemys sp", "^ot:ottId": 619851, "^ot:ottTaxonName": "Dermatemys"}, "otu22": {"^ot:originalLabel": "Kinosternon flavescens", "^ot:ottId": 487667, "^ot:ottTaxonName": "Kinosternon flavescens"}, "otu23": {"^ot:originalLabel": "Sternotherus minor", "^ot:ottId": 828705, "^ot:ottTaxonName": "Sternotherus minor"}, "otu24": {"^ot:originalLabel": "Staurotypus triporcatus", "^ot:ottId": 149793, "^ot:ottTaxonName": "Staurotypus triporcatus"}, "otu25": {"^ot:originalLabel": "Platysternon megacephalum", "^ot:ottId": 619860, "^ot:ottTaxonName": "Platysternon megacephalum"}, "otu26": {"^ot:originalLabel": "Chrysemys picta", "^ot:ottId": 587300, "^ot:ottTaxonName": "Chrysemys picta"}, "otu27": {"^ot:originalLabel": "Graptemys pseudogeographica", "^ot:ottId": 1092200, "^ot:ottTaxonName": "Graptemys pseudogeographica"}, "otu28": {"^ot:originalLabel": "Trachemys scripta", "^ot:ottId": 725741, "^ot:ottTaxonName": "Trachemys scripta"}, "otu29": {"^ot:originalLabel": "Deirochelys reticularia", "^ot:ottId": 848781, "^ot:ottTaxonName": "Deirochelys reticularia"}, "otu3": {"^ot:originalLabel": "Python molurus", "^ot:ottId": 737826, "^ot:ottTaxonName": "Python molurus"}, "otu30": {"^ot:originalLabel": "Terrapene ornata", "^ot:ottId": 1013359, "^ot:ottTaxonName": "Terrapene ornata"}, "otu31": {"^ot:originalLabel": "Clemmys marmorata", "^ot:ottId": 743507, "^ot:ottTaxonName": "Actinemys marmorata"}, "otu32": {"^ot:originalLabel": "Gopherus berlandieri", "^ot:ottId": 1041231, "^ot:ottTaxonName": "Gopherus berlandieri"}, "otu33": {"^ot:originalLabel": "Testudo horsfieldii", "^ot:ottId": 809861, "^ot:ottTaxonName": "Testudo horsfieldii"}, "otu34": {"^ot:originalLabel": "Geochelone pardalis", "^ot:ottId": 776504, "^ot:ottTaxonName": "Stigmochelys pardalis"}, "otu35": {"^ot:originalLabel": "Cyclemys dentata", "^ot:ottId": 54221, "^ot:ottTaxonName": "Cyclemys dentata"}, "otu36": {"^ot:originalLabel": "Geoemyda spengleri", "^ot:ottId": 105478, "^ot:ottTaxonName": "Geoemyda spengleri"}, "otu37": {"^ot:originalLabel": "Rhinoclemmys punctularia", "^ot:ottId": 203555, "^ot:ottTaxonName": "Rhinoclemmys punctularia"}, "otu38": {"^ot:originalLabel": "Homo sapiens19", "^ot:ottId": 770315, "^ot:ottTaxonName": "Homo sapiens"}, "otu4": {"^ot:originalLabel": "Crocodylus porosus", "^ot:ottId": 35872, "^ot:ottTaxonName": "Crocodylus porosus"}, "otu5": {"^ot:originalLabel": "Gallus gallus", "^ot:ottId": 153563, "^ot:ottTaxonName": "Gallus gallus"}, "otu6": {"^ot:originalLabel": "Erymnochelys madagascariensis", "^ot:ottId": 775068, "^ot:ottTaxonName": "Erymnochelys madagascariensis"}, "otu7": {"^ot:originalLabel": "Podocnemis erythracephala", "^ot:ottId": 674543, "^ot:ottTaxonName": "Podocnemis erythrocephala"}, "otu8": {"^ot:originalLabel": "Pelusios castaneus", "^ot:ottId": 394412, "^ot:ottTaxonName": "Pelusios castaneus"}, "otu9": {"^ot:originalLabel": "Pelomedusa subrufa1", "^ot:ottId": 775044, "^ot:ottTaxonName": "Pelomedusa subrufa"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Raxml", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node8", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@length": 0.055913, "@source": "node1", "@target": "node2"}, "edge74": {"@length": 0.055913, "@source": "node1", "@target": "node75"}}, "node12": {"edge12": {"@length": 0.007518, "@source": "node12", "@target": "node13"}, "edge23": {"@length": 0.003631, "@source": "node12", "@target": "node24"}}, "node13": {"edge13": {"@length": 0.006712, "@source": "node13", "@target": "node14"}, "edge20": {"@length": 0.012102, "@source": "node13", "@target": "node21"}}, "node14": {"edge14": {"@length": 0.007772, "@source": "node14", "@target": "node15"}, "edge17": {"@length": 0.01344, "@source": "node14", "@target": "node18"}}, "node15": {"edge15": {"@length": 0.016889, "@source": "node15", "@target": "node16"}, "edge16": {"@length": 0.014658, "@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@length": 0.004184, "@source": "node18", "@target": "node19"}, "edge19": {"@length": 0.004228, "@source": "node18", "@target": "node20"}}, "node2": {"edge2": {"@length": 0.006787, "@source": "node2", "@target": "node3"}, "edge7": {"@length": 0.004176, "@source": "node2", "@target": "node8"}}, "node21": {"edge21": {"@length": 0.003964, "@source": "node21", "@target": "node22"}, "edge22": {"@length": 0.004705, "@source": "node21", "@target": "node23"}}, "node24": {"edge24": {"@length": 0.00651, "@source": "node24", "@target": "node25"}, "edge33": {"@length": 0.00456, "@source": "node24", "@target": "node34"}}, "node25": {"edge25": {"@length": 0.034977, "@source": "node25", "@target": "node26"}, "edge26": {"@length": 0.01578, "@source": "node25", "@target": "node27"}}, "node27": {"edge27": {"@length": 0.0238, "@source": "node27", "@target": "node28"}, "edge28": {"@length": 0.003641, "@source": "node27", "@target": "node29"}}, "node29": {"edge29": {"@length": 0.005354, "@source": "node29", "@target": "node30"}, "edge30": {"@length": 0.001588, "@source": "node29", "@target": "node31"}}, "node3": {"edge3": {"@length": 0.027118, "@source": "node3", "@target": "node4"}, "edge4": {"@length": 0.070174, "@source": "node3", "@target": "node5"}}, "node31": {"edge31": {"@length": 0.003867, "@source": "node31", "@target": "node32"}, "edge32": {"@length": 0.003653, "@source": "node31", "@target": "node33"}}, "node34": {"edge34": {"@length": 0.000483, "@source": "node34", "@target": "node35"}, "edge49": {"@length": 0.002494, "@source": "node34", "@target": "node50"}}, "node35": {"edge35": {"@length": 0.005796, "@source": "node35", "@target": "node36"}, "edge40": {"@length": 0.000678, "@source": "node35", "@target": "node41"}}, "node36": {"edge36": {"@length": 0.002758, "@source": "node36", "@target": "node37"}, "edge39": {"@length": 0.010034, "@source": "node36", "@target": "node40"}}, "node37": {"edge37": {"@length": 0.002228, "@source": "node37", "@target": "node38"}, "edge38": {"@length": 0.004352, "@source": "node37", "@target": "node39"}}, "node41": {"edge41": {"@length": 0.007686, "@source": "node41", "@target": "node42"}, "edge42": {"@length": 0.005081, "@source": "node41", "@target": "node43"}}, "node43": {"edge43": {"@length": 0.011015, "@source": "node43", "@target": "node44"}, "edge44": {"@length": 0.004668, "@source": "node43", "@target": "node45"}}, "node45": {"edge45": {"@length": 0.003008, "@source": "node45", "@target": "node46"}, "edge48": {"@length": 0.007534, "@source": "node45", "@target": "node49"}}, "node46": {"edge46": {"@length": 0.002403, "@source": "node46", "@target": "node47"}, "edge47": {"@length": 0.001864, "@source": "node46", "@target": "node48"}}, "node5": {"edge5": {"@length": 0.053678, "@source": "node5", "@target": "node6"}, "edge6": {"@length": 0.087573, "@source": "node5", "@target": "node7"}}, "node50": {"edge50": {"@length": 0.000366, "@source": "node50", "@target": "node51"}, "edge63": {"@length": 0.003453, "@source": "node50", "@target": "node64"}}, "node51": {"edge51": {"@length": 0.003806, "@source": "node51", "@target": "node52"}, "edge52": {"@length": 0.001797, "@source": "node51", "@target": "node53"}}, "node53": {"edge53": {"@length": 0.001981, "@source": "node53", "@target": "node54"}, "edge60": {"@length": 0.000917, "@source": "node53", "@target": "node61"}}, "node54": {"edge54": {"@length": 0.000364, "@source": "node54", "@target": "node55"}, "edge59": {"@length": 0.002094, "@source": "node54", "@target": "node60"}}, "node55": {"edge55": {"@length": 0.001321, "@source": "node55", "@target": "node56"}, "edge56": {"@length": 0.000432, "@source": "node55", "@target": "node57"}}, "node57": {"edge57": {"@length": 0.001274, "@source": "node57", "@target": "node58"}, "edge58": {"@length": 0.000676, "@source": "node57", "@target": "node59"}}, "node61": {"edge61": {"@length": 0.002184, "@source": "node61", "@target": "node62"}, "edge62": {"@length": 0.001587, "@source": "node61", "@target": "node63"}}, "node64": {"edge64": {"@length": 0.002942, "@source": "node64", "@target": "node65"}, "edge69": {"@length": 0.001286, "@source": "node64", "@target": "node70"}}, "node65": {"edge65": {"@length": 0.007006, "@source": "node65", "@target": "node66"}, "edge66": {"@length": 0.002047, "@source": "node65", "@target": "node67"}}, "node67": {"edge67": {"@length": 0.005377, "@source": "node67", "@target": "node68"}, "edge68": {"@length": 0.007127, "@source": "node67", "@target": "node69"}}, "node70": {"edge70": {"@length": 0.00033, "@source": "node70", "@target": "node71"}, "edge73": {"@length": 0.007202, "@source": "node70", "@target": "node74"}}, "node71": {"edge71": {"@length": 0.003664, "@source": "node71", "@target": "node72"}, "edge72": {"@length": 0.003653, "@source": "node71", "@target": "node73"}}, "node8": {"edge11": {"@length": 0.016173, "@source": "node8", "@target": "node12"}, "edge8": {"@length": 0.00529, "@source": "node8", "@target": "node9"}}, "node9": {"edge10": {"@length": 0.047644, "@source": "node9", "@target": "node11"}, "edge9": {"@length": 0.025683, "@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu4"}, "node11": {"@otu": "otu5"}, "node12": {}, "node13": {}, "node14": {}, "node15": {}, "node16": {"@otu": "otu6"}, "node17": {"@otu": "otu7"}, "node18": {}, "node19": {"@otu": "otu8"}, "node2": {}, "node20": {"@otu": "otu9"}, "node21": {}, "node22": {"@otu": "otu10"}, "node23": {"@otu": "otu11"}, "node24": {}, "node25": {}, "node26": {"@otu": "otu12"}, "node27": {}, "node28": {"@otu": "otu13"}, "node29": {}, "node3": {}, "node30": {"@otu": "otu14"}, "node31": {}, "node32": {"@otu": "otu15"}, "node33": {"@otu": "otu16"}, "node34": {}, "node35": {}, "node36": {}, "node37": {}, "node38": {"@otu": "otu17"}, "node39": {"@otu": "otu18"}, "node4": {"@otu": "otu1"}, "node40": {"@otu": "otu19"}, "node41": {}, "node42": {"@otu": "otu20"}, "node43": {}, "node44": {"@otu": "otu21"}, "node45": {}, "node46": {}, "node47": {"@otu": "otu22"}, "node48": {"@otu": "otu23"}, "node49": {"@otu": "otu24"}, "node5": {}, "node50": {}, "node51": {}, "node52": {"@otu": "otu25"}, "node53": {}, "node54": {}, "node55": {}, "node56": {"@otu": "otu26"}, "node57": {}, "node58": {"@otu": "otu27"}, "node59": {"@otu": "otu28"}, "node6": {"@otu": "otu2"}, "node60": {"@otu": "otu29"}, "node61": {}, "node62": {"@otu": "otu30"}, "node63": {"@otu": "otu31"}, "node64": {}, "node65": {}, "node66": {"@otu": "otu32"}, "node67": {}, "node68": {"@otu": "otu33"}, "node69": {"@otu": "otu34"}, "node7": {"@otu": "otu3"}, "node70": {}, "node71": {}, "node72": {"@otu": "otu35"}, "node73": {"@otu": "otu36"}, "node74": {"@otu": "otu37"}, "node75": {"@otu": "otu38"}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "2aa180baef3c5e313da1e7f09c83ce2c0467b457"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "9f77dd22eadc8a81504952540c295208ec54eb07", "author_name": "Pietro de Mello", "author_email": "ANONYMOUS", "date": "Tue, 10 Jul 2018 21:30:03 +0000", "date_ISO_8601": "2018-07-10 21:30:03 +0000", "relative_date": "8 years ago", "message_subject": "Minor correction in species names, add metadata.", "message_body": "(Update document 'ot_1490' via OpenTree API)"}, {"id": "f0173c876cc4b05609af334ddb8bcd27a9c7bacd", "author_name": "Pietro de Mello", "author_email": "ANONYMOUS", "date": "Tue, 10 Jul 2018 21:26:18 +0000", "date_ISO_8601": "2018-07-10 21:26:18 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_1490' via OpenTree API"}]}