{"sha": "24afc85a444963f10ca51c6e20138fe592a4b525", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2018-07-27T15:09:06.976Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}, {"@active": true, "@valid": true, "new": {"$": ""}, "old": {"$": "\\bcf"}}, {"@active": true, "@valid": true, "new": {"$": ""}, "old": {"$": "\\b\\s+(\\S*)$"}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2018-07-27T15:09:06.976Z", "@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": "RAxML_bestTree.P3_ml_09072014.tre", "@size": 1892, "@type": "newick", "@url": "/curator/download/supporting_files.doc.bd9fccc37164076e.5241784d4c5f62657374547265652e50335f6d6c5f30393037323031342e747265.tre", "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": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu10", "otu11"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu12", "otu13", "otu14", "otu15", "otu16"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu17", "otu18", "otu19", "otu20"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu21", "otu22", "otu23", "otu24", "otu25"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu5", "otu6"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu7", "otu8"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@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"}, {"@code": "UNRECOGNIZED_KEY", "data": ["rootedge"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu5", "otu6"], "@otusID": "otus1", "@otuID": ["otu5", "otu6"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["Pietro de Mello"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 190151, "^ot:focalCladeOTTTaxonName": "Gekkonidae", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_1559", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2014.09.016"}, "^ot:studyPublicationReference": "Ishan Agarwal, K. Praveen Karanth, 2015, 'A phylogeny of the only ground-dwelling radiation of Cyrtodactylus (Squamata, Gekkonidae): diversification of Geckoella across peninsular India and Sri Lanka', Molecular Phylogenetics and Evolution, vol. 82, pp. 193-199", "^ot:studyYear": 2015, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Cyrtodactylus triedrus", "^ot:ottId": 1056674, "^ot:ottTaxonName": "Geckoella triedrus"}, "otu10": {"^ot:originalLabel": "Cyrtodactylus jeyporensis 1356", "^ot:ottId": 4123042, "^ot:ottTaxonName": "Geckoella jeyporensis"}, "otu11": {"^ot:originalLabel": "Cyrtodactylus jeyporensis 1206", "^ot:ottId": 4123042, "^ot:ottTaxonName": "Geckoella jeyporensis"}, "otu12": {"^ot:originalLabel": "Cyrtodactylus cfnebulosus 1351", "^ot:ottId": 4122936, "^ot:ottTaxonName": "Cyrtodactylus nebulosus"}, "otu13": {"^ot:originalLabel": "Cyrtodactylus cfnebulosus 1119", "^ot:ottId": 4122936, "^ot:ottTaxonName": "Cyrtodactylus nebulosus"}, "otu14": {"^ot:originalLabel": "Cyrtodactylus cfnebulosus 1205", "^ot:ottId": 4122936, "^ot:ottTaxonName": "Cyrtodactylus nebulosus"}, "otu15": {"^ot:originalLabel": "Cyrtodactylus cfnebulosus 1374", "^ot:ottId": 4122936, "^ot:ottTaxonName": "Cyrtodactylus nebulosus"}, "otu16": {"^ot:originalLabel": "Cyrtodactylus cfnebulosus 1118", "^ot:ottId": 4122936, "^ot:ottTaxonName": "Cyrtodactylus nebulosus"}, "otu17": {"^ot:originalLabel": "Cyrtodactylus deccanensis 1112", "^ot:ottId": 6156637, "^ot:ottTaxonName": "Cyrtodactylus deccanensis"}, "otu18": {"^ot:originalLabel": "Cyrtodactylus deccanensis 1380", "^ot:ottId": 6156637, "^ot:ottTaxonName": "Cyrtodactylus deccanensis"}, "otu19": {"^ot:originalLabel": "Cyrtodactylus deccanensis 1243", "^ot:ottId": 6156637, "^ot:ottTaxonName": "Cyrtodactylus deccanensis"}, "otu2": {"^ot:originalLabel": "Cyrtodactylus intermedius", "^ot:ottId": 917732, "^ot:ottTaxonName": "Cyrtodactylus intermedius"}, "otu20": {"^ot:originalLabel": "Cyrtodactylus cfdeccanensis 1396", "^ot:ottId": 6156637, "^ot:ottTaxonName": "Cyrtodactylus deccanensis"}, "otu21": {"^ot:originalLabel": "Cyrtodactylus cfalbofasciatus 1391", "^ot:ottId": 4123043, "^ot:ottTaxonName": "Geckoella albofasciatus"}, "otu22": {"^ot:originalLabel": "Cyrtodactylus cfalbofasciatus 1418", "^ot:ottId": 4123043, "^ot:ottTaxonName": "Geckoella albofasciatus"}, "otu23": {"^ot:originalLabel": "Cyrtodactylus cfalbofasciatusJB7", "^ot:ottId": 4123043, "^ot:ottTaxonName": "Geckoella albofasciatus"}, "otu24": {"^ot:originalLabel": "Cyrtodactylus albofasciatus 1117", "^ot:ottId": 4123043, "^ot:ottTaxonName": "Geckoella albofasciatus"}, "otu25": {"^ot:originalLabel": "Cyrtodactylus albofasciatus 1109", "^ot:ottId": 4123043, "^ot:ottTaxonName": "Geckoella albofasciatus"}, "otu3": {"^ot:originalLabel": "Cyrtodactylus loriae", "^ot:ottId": 598411, "^ot:ottTaxonName": "Cyrtodactylus loriae"}, "otu4": {"^ot:originalLabel": "Cyrtodactylus pulchellus", "^ot:ottId": 955881, "^ot:ottTaxonName": "Cyrtodactylus pulchellus"}, "otu5": {"^ot:altLabel": "Geckoella varadgirii", "^ot:originalLabel": "Cyrtodactylus varadgirii 1381"}, "otu6": {"^ot:altLabel": "Geckoella varadgirii", "^ot:originalLabel": "Cyrtodactylus varadgirii 1136"}, "otu7": {"^ot:originalLabel": "Cyrtodactylus cfspeciosus 1249", "^ot:ottId": 6156684, "^ot:ottTaxonName": "Geckoella speciosus"}, "otu8": {"^ot:originalLabel": "Cyrtodactylus speciosus 1405", "^ot:ottId": 6156684, "^ot:ottTaxonName": "Geckoella speciosus"}, "otu9": {"^ot:originalLabel": "Cyrtodactylus collegalensis 1444", "^ot:ottId": 4123044, "^ot:ottTaxonName": "Geckoella collegalensis"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Agarwal & Karanth, 2015 Maximum Likelihood", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "tree1_ROOT", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "tree1_ROOT", "^ot:specifiedRoot": "tree1_ROOT", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge46": {"@length": 0.014728, "@source": "node1", "@target": "node47"}, "edge47": {"@length": 0.01569, "@source": "node1", "@target": "node48"}}, "node12": {"edge12": {"@length": 0.081619, "@source": "node12", "@target": "node13"}, "edge21": {"@length": 0.019156, "@source": "node12", "@target": "node22"}}, "node13": {"edge13": {"@length": 0.038457, "@source": "node13", "@target": "node14"}, "edge16": {"@length": 0.012434, "@source": "node13", "@target": "node17"}}, "node14": {"edge14": {"@length": 0.005534, "@source": "node14", "@target": "node15"}, "edge15": {"@length": 0.003669, "@source": "node14", "@target": "node16"}}, "node17": {"edge17": {"@length": 0.026341, "@source": "node17", "@target": "node18"}, "edge20": {"@length": 0.032991, "@source": "node17", "@target": "node21"}}, "node18": {"edge18": {"@length": 0.016126, "@source": "node18", "@target": "node19"}, "edge19": {"@length": 0.023807, "@source": "node18", "@target": "node20"}}, "node2": {"edge1": {"@length": 0.013239, "@source": "node2", "@target": "node1"}, "edge41": {"@length": 0.01002, "@source": "node2", "@target": "node42"}}, "node22": {"edge22": {"@length": 0.080256, "@source": "node22", "@target": "node23"}, "edge25": {"@length": 0.076059, "@source": "node22", "@target": "node26"}}, "node23": {"edge23": {"@length": 0.007694, "@source": "node23", "@target": "node24"}, "edge24": {"@length": 0.002975, "@source": "node23", "@target": "node25"}}, "node26": {"edge26": {"@length": 0.035932, "@source": "node26", "@target": "node27"}, "edge27": {"@length": 0.012925, "@source": "node26", "@target": "node28"}}, "node28": {"edge28": {"@length": 0.022623, "@source": "node28", "@target": "node29"}, "edge29": {"@length": 0.010924, "@source": "node28", "@target": "node30"}}, "node3": {"edge2": {"@length": 0.014351, "@source": "node3", "@target": "node2"}, "edge34": {"@length": 0.021749, "@source": "node3", "@target": "node35"}}, "node30": {"edge30": {"@length": 0.024474, "@source": "node30", "@target": "node31"}, "edge33": {"@length": 0.040505, "@source": "node30", "@target": "node34"}}, "node31": {"edge31": {"@length": 0.012236, "@source": "node31", "@target": "node32"}, "edge32": {"@length": 0.016019, "@source": "node31", "@target": "node33"}}, "node35": {"edge35": {"@length": 0.012054, "@source": "node35", "@target": "node36"}, "edge40": {"@length": 0.036932, "@source": "node35", "@target": "node41"}}, "node36": {"edge36": {"@length": 0.011578, "@source": "node36", "@target": "node37"}, "edge37": {"@length": 0.01909, "@source": "node36", "@target": "node38"}}, "node38": {"edge38": {"@length": 0.000531, "@source": "node38", "@target": "node39"}, "edge39": {"@length": 0.004499, "@source": "node38", "@target": "node40"}}, "node4": {"edge11": {"@length": 0.05158, "@source": "node4", "@target": "node12"}, "edge3": {"@length": 0.127109, "@source": "node4", "@target": "node3"}}, "node42": {"edge42": {"@length": 0.010193, "@source": "node42", "@target": "node43"}, "edge43": {"@length": 0.010631, "@source": "node42", "@target": "node44"}}, "node44": {"edge44": {"@length": 0.002659, "@source": "node44", "@target": "node45"}, "edge45": {"@length": 0.005333, "@source": "node44", "@target": "node46"}}, "node5": {"edge4": {"@length": 0.021519, "@source": "node5", "@target": "node4"}, "edge6": {"@length": 0.018658, "@source": "node5", "@target": "node7"}}, "node7": {"edge7": {"@length": 0.174117, "@source": "node7", "@target": "node8"}, "edge8": {"@length": 0.009315, "@source": "node7", "@target": "node9"}}, "node9": {"edge10": {"@length": 0.15777, "@source": "node9", "@target": "node11"}, "edge9": {"@length": 0.132269, "@source": "node9", "@target": "node10"}}, "tree1_ROOT": {"edge5": {"@length": 0.151396, "@source": "tree1_ROOT", "@target": "node6"}, "tree1_ROOT_EDGE": {"@source": "tree1_ROOT", "@target": "node5"}}}, "nodeById": {"node1": {}, "node10": {"@otu": "otu3"}, "node11": {"@otu": "otu4"}, "node12": {}, "node13": {}, "node14": {}, "node15": {"@otu": "otu5"}, "node16": {"@otu": "otu6"}, "node17": {}, "node18": {}, "node19": {"@otu": "otu7"}, "node2": {}, "node20": {"@otu": "otu8"}, "node21": {"@otu": "otu9"}, "node22": {}, "node23": {}, "node24": {"@otu": "otu10"}, "node25": {"@otu": "otu11"}, "node26": {}, "node27": {"@otu": "otu12"}, "node28": {}, "node29": {"@otu": "otu13"}, "node3": {}, "node30": {}, "node31": {}, "node32": {"@otu": "otu14"}, "node33": {"@otu": "otu15"}, "node34": {"@otu": "otu16"}, "node35": {}, "node36": {}, "node37": {"@otu": "otu17"}, "node38": {}, "node39": {"@otu": "otu18"}, "node4": {}, "node40": {"@otu": "otu19"}, "node41": {"@otu": "otu20"}, "node42": {}, "node43": {"@otu": "otu21"}, "node44": {}, "node45": {"@otu": "otu22"}, "node46": {"@otu": "otu23"}, "node47": {"@otu": "otu24"}, "node48": {"@otu": "otu25"}, "node5": {}, "node6": {"@otu": "otu1"}, "node7": {}, "node8": {"@otu": "otu2"}, "node9": {}, "tree1_ROOT": {"@root": true}}, "rootedge": [{"@id": "enode1", "@length": "0.0", "@target": "node1"}]}}}}}}, "branch2sha": {"master": "24afc85a444963f10ca51c6e20138fe592a4b525"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "bd47f01e730e47478187232caab2acf17e28c8a9", "author_name": "Pietro de Mello", "author_email": "ANONYMOUS", "date": "Fri, 27 Jul 2018 15:19:45 +0000", "date_ISO_8601": "2018-07-27 15:19:45 +0000", "relative_date": "8 years ago", "message_subject": "Minor correction in species names, add metadata.", "message_body": "(Update document 'ot_1559' via OpenTree API)"}, {"id": "ac57c74d509ab190dd1720e19a1c463fcc8d4c7c", "author_name": "Pietro de Mello", "author_email": "ANONYMOUS", "date": "Fri, 27 Jul 2018 15:09:08 +0000", "date_ISO_8601": "2018-07-27 15:09:08 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_1559' via OpenTree API"}]}