{"sha": "1bbbe21bdd9a32ef81abeb3f038a977fdc0e8e7b", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-08-06T05:54:05.735Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-08-06T05:54:05.735Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": "", "@type": "newick", "@url": "", "description": {"$": ""}, "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:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node38", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node38"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node39", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node39"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node52", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node52"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node53", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node53"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node63", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node63"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node64", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node64"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu14", "otu15"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu22", "otu23"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu31", "otu32"], "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:branchLengthMode"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:messages", "^ot:nearestTaxonMRCAName", "^ot:nearestTaxonMRCAOttId"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "", "^ot:curatorName": ["Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 815968, "^ot:focalCladeOTTTaxonName": "Meropidae", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_148", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2007.07.004"}, "^ot:studyPublicationReference": "Marks, Ben D., Jason D. Weckstein, Robert G. Moyle. 2007. Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution 45 (1): 23-32.", "^ot:studyYear": 2007, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Actenoides concretus", "^ot:ottId": 571609, "^ot:ottTaxonName": "Actenoides concretus"}, "otu10": {"^ot:originalLabel": "Merops gularis gularis", "^ot:ottId": 150515, "^ot:ottTaxonName": "Merops gularis gularis"}, "otu11": {"^ot:originalLabel": "Merops muelleri mentalis", "^ot:ottId": 724983, "^ot:ottTaxonName": "Merops muelleri mentalis"}, "otu12": {"^ot:originalLabel": "Merops muelleri muelleri", "^ot:ottId": 150518, "^ot:ottTaxonName": "Merops muelleri muelleri"}, "otu13": {"^ot:originalLabel": "Merops boehmi", "^ot:ottId": 423285, "^ot:ottTaxonName": "Merops boehmi"}, "otu14": {"^ot:originalLabel": "Merops apiaster 1", "^ot:ottId": 755107, "^ot:ottTaxonName": "Merops apiaster"}, "otu15": {"^ot:originalLabel": "Merops apiaster 2", "^ot:ottId": 755107, "^ot:ottTaxonName": "Merops apiaster"}, "otu16": {"^ot:originalLabel": "Merops ornatus", "^ot:ottId": 614658, "^ot:ottTaxonName": "Merops ornatus"}, "otu17": {"^ot:originalLabel": "Merops persicus", "^ot:ottId": 898071, "^ot:ottTaxonName": "Merops persicus"}, "otu18": {"^ot:originalLabel": "Merops superciliosus", "^ot:ottId": 898073, "^ot:ottTaxonName": "Merops superciliosus"}, "otu19": {"^ot:originalLabel": "Merops philippinus", "^ot:ottId": 372777, "^ot:ottTaxonName": "Merops philippinus"}, "otu2": {"^ot:originalLabel": "Todus angustirostris", "^ot:ottId": 986892, "^ot:ottTaxonName": "Todus angustirostris"}, "otu20": {"^ot:originalLabel": "Merops viridis viridis", "^ot:ottId": 372775, "^ot:ottTaxonName": "Merops viridis viridis"}, "otu21": {"^ot:originalLabel": "Merops viridis americanus", "^ot:ottId": 372774, "^ot:ottTaxonName": "Merops viridis americanus"}, "otu22": {"^ot:originalLabel": "Merops leschenaulti 115", "^ot:ottId": 372778, "^ot:ottTaxonName": "Merops leschenaulti"}, "otu23": {"^ot:originalLabel": "Merops leschenaulti 286", "^ot:ottId": 372778, "^ot:ottTaxonName": "Merops leschenaulti"}, "otu24": {"^ot:originalLabel": "Merops orientalis", "^ot:ottId": 423282, "^ot:ottTaxonName": "Merops orientalis"}, "otu25": {"^ot:originalLabel": "Merops nubicus", "^ot:ottId": 989087, "^ot:ottTaxonName": "Merops nubicus"}, "otu26": {"^ot:originalLabel": "Merops malimbicus", "^ot:ottId": 1050190, "^ot:ottTaxonName": "Merops malimbicus"}, "otu27": {"^ot:originalLabel": "Merops albicollis", "^ot:ottId": 423284, "^ot:ottTaxonName": "Merops albicollis"}, "otu28": {"^ot:originalLabel": "Merops breweri", "^ot:ottId": 724987, "^ot:ottTaxonName": "Merops breweri"}, "otu29": {"^ot:originalLabel": "Merops bulocki", "^ot:ottId": 704136, "^ot:ottTaxonName": "Merops bulocki"}, "otu3": {"^ot:originalLabel": "Momotus momota", "^ot:ottId": 989081, "^ot:ottTaxonName": "Momotus momota"}, "otu30": {"^ot:originalLabel": "Merops bullockoides", "^ot:ottId": 423281, "^ot:ottTaxonName": "Merops bullockoides"}, "otu31": {"^ot:originalLabel": "Meropogon forsteni 315", "^ot:ottId": 1050191, "^ot:ottTaxonName": "Meropogon forsteni"}, "otu32": {"^ot:originalLabel": "Meropogon forsteni 316", "^ot:ottId": 1050191, "^ot:ottTaxonName": "Meropogon forsteni"}, "otu33": {"^ot:originalLabel": "Nyctyornis amictus", "^ot:ottId": 524018, "^ot:ottTaxonName": "Nyctyornis amictus"}, "otu4": {"^ot:originalLabel": "Merops pusillus pusillus", "^ot:ottId": 948869, "^ot:ottTaxonName": "Merops pusillus pusillus"}, "otu5": {"^ot:originalLabel": "Merops pusillus meridionalis", "^ot:ottId": 948865, "^ot:ottTaxonName": "Merops pusillus meridionalis"}, "otu6": {"^ot:originalLabel": "Merops variegatus loringi", "^ot:ottId": 948874, "^ot:ottTaxonName": "Merops variegatus loringi"}, "otu7": {"^ot:originalLabel": "Merops hirundineus", "^ot:ottId": 150514, "^ot:ottTaxonName": "Merops hirundineus"}, "otu8": {"^ot:originalLabel": "Merops oreobates", "^ot:ottId": 948862, "^ot:ottTaxonName": "Merops oreobates"}, "otu9": {"^ot:originalLabel": "Merops gularis australis", "^ot:ottId": 150516, "^ot:ottTaxonName": "Merops gularis australis"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 2b", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node7", "^ot:messages": {"message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@id": "messageu5f4f44f1-202d-4ef5-9b09-eb16f20043d8", "@severity": "INFO", "@wasGeneratedBy": "opentree.2nexml", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": 737, "@sourceForTree": "tree1", "@type": "newick", "@url": "/curator/default/to_nexson?output=input&uploadid=u5f4f44f1-202d-4ef5-9b09-eb16f20043d8", "description": {"$": "Source data for tree 'tree1'"}}]}}}]}, "^ot:nearestTaxonMRCAName": "Meropidae", "^ot:nearestTaxonMRCAOttId": "815968", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge6": {"@source": "node1", "@target": "node7"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge57": {"@source": "node10", "@target": "node58"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge30": {"@source": "node11", "@target": "node31"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge29": {"@source": "node12", "@target": "node30"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14"}, "edge22": {"@source": "node13", "@target": "node23"}}, "node14": {"edge14": {"@source": "node14", "@target": "node15"}, "edge19": {"@source": "node14", "@target": "node20"}}, "node15": {"edge15": {"@source": "node15", "@target": "node16"}, "edge18": {"@source": "node15", "@target": "node19"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge17": {"@source": "node16", "@target": "node18"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge5": {"@source": "node2", "@target": "node6"}}, "node20": {"edge20": {"@source": "node20", "@target": "node21"}, "edge21": {"@source": "node20", "@target": "node22"}}, "node23": {"edge23": {"@source": "node23", "@target": "node24"}, "edge26": {"@source": "node23", "@target": "node27"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge25": {"@source": "node24", "@target": "node26"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge28": {"@source": "node27", "@target": "node29"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge4": {"@source": "node3", "@target": "node5"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge56": {"@source": "node31", "@target": "node57"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge55": {"@source": "node32", "@target": "node56"}}, "node33": {"edge33": {"@source": "node33", "@target": "node34"}, "edge54": {"@source": "node33", "@target": "node55"}}, "node34": {"edge34": {"@source": "node34", "@target": "node35"}, "edge45": {"@source": "node34", "@target": "node46"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge40": {"@source": "node35", "@target": "node41"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge39": {"@source": "node36", "@target": "node40"}}, "node37": {"edge37": {"@source": "node37", "@target": "node38"}, "edge38": {"@source": "node37", "@target": "node39"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge44": {"@source": "node41", "@target": "node45"}}, "node42": {"edge42": {"@source": "node42", "@target": "node43"}, "edge43": {"@source": "node42", "@target": "node44"}}, "node46": {"edge46": {"@source": "node46", "@target": "node47"}, "edge53": {"@source": "node46", "@target": "node54"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge50": {"@source": "node47", "@target": "node51"}}, "node48": {"edge48": {"@source": "node48", "@target": "node49"}, "edge49": {"@source": "node48", "@target": "node50"}}, "node51": {"edge51": {"@source": "node51", "@target": "node52"}, "edge52": {"@source": "node51", "@target": "node53"}}, "node59": {"edge59": {"@source": "node59", "@target": "node60"}, "edge60": {"@source": "node59", "@target": "node61"}}, "node62": {"edge62": {"@source": "node62", "@target": "node63"}, "edge63": {"@source": "node62", "@target": "node64"}}, "node7": {"edge64": {"@source": "node7", "@target": "node65"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge61": {"@source": "node8", "@target": "node62"}, "edge8": {"@source": "node8", "@target": "node9"}}, "node9": {"edge58": {"@source": "node9", "@target": "node59"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {}, "node12": {}, "node13": {}, "node14": {}, "node15": {}, "node16": {}, "node17": {"@otu": "otu4"}, "node18": {"@otu": "otu5"}, "node19": {"@otu": "otu6"}, "node2": {}, "node20": {}, "node21": {"@otu": "otu7"}, "node22": {"@otu": "otu8"}, "node23": {}, "node24": {}, "node25": {"@otu": "otu9"}, "node26": {"@otu": "otu10"}, "node27": {}, "node28": {"@otu": "otu11"}, "node29": {"@otu": "otu12"}, "node3": {}, "node30": {"@otu": "otu13"}, "node31": {}, "node32": {}, "node33": {}, "node34": {}, "node35": {}, "node36": {}, "node37": {}, "node38": {"@otu": "otu14", "^ot:isTaxonExemplar": true}, "node39": {"@otu": "otu15", "^ot:isTaxonExemplar": false}, "node4": {"@otu": "otu1"}, "node40": {"@otu": "otu16"}, "node41": {}, "node42": {}, "node43": {"@otu": "otu17"}, "node44": {"@otu": "otu18"}, "node45": {"@otu": "otu19"}, "node46": {}, "node47": {}, "node48": {}, "node49": {"@otu": "otu20"}, "node5": {"@otu": "otu2"}, "node50": {"@otu": "otu21"}, "node51": {}, "node52": {"@otu": "otu22", "^ot:isTaxonExemplar": true}, "node53": {"@otu": "otu23", "^ot:isTaxonExemplar": false}, "node54": {"@otu": "otu24"}, "node55": {"@otu": "otu25"}, "node56": {"@otu": "otu26"}, "node57": {"@otu": "otu27"}, "node58": {"@otu": "otu28"}, "node59": {}, "node6": {"@otu": "otu3"}, "node60": {"@otu": "otu29"}, "node61": {"@otu": "otu30"}, "node62": {}, "node63": {"@otu": "otu31", "^ot:isTaxonExemplar": true}, "node64": {"@otu": "otu32", "^ot:isTaxonExemplar": false}, "node65": {"@otu": "otu33"}, "node7": {}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "1bbbe21bdd9a32ef81abeb3f038a977fdc0e8e7b"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "cc85d806b15d26f237277c822c7438a3db36204d", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 6 Aug 2014 05:57:15 +0000", "date_ISO_8601": "2014-08-06 05:57:15 +0000", "relative_date": "12 years ago", "message_subject": "Meropidae", "message_body": "(Update Study #ot_148 via OpenTree API)"}, {"id": "8f772c7dca2c11651e78c7f0bd251d5c5ef68688", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 6 Aug 2014 05:54:03 +0000", "date_ISO_8601": "2014-08-06 05:54:03 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #ot_148 via OpenTree API"}]}