{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-08-07T03:08:53.811Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-08-07T03:08:53.811Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": "", "@type": "newick", "@url": "", "description": {"$": ""}, "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": "node11", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node11"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node12", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node12"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node14", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node14"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node15", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node15"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node23", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node23"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node24", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node24"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node26", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node26"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node27", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node27"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node29", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node29"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node30", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node30"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node33", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node33"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node34", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node34"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node37", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node37"}, "@severity": "WARNING"}, {"@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": "node42", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node42"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node43", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node43"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node45", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node45"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node46", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node46"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node8", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node8"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node9", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node9"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu1", "otu2"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu10", "otu9"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu11", "otu12"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu13", "otu14"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu15", "otu16"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu17", "otu18"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu20", "otu21"], "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": ["otu3", "otu4"], "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": "UNRECOGNIZED_KEY", "data": ["^ot:messages", "^ot:nearestTaxonMRCAName", "^ot:nearestTaxonMRCAOttId"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu7", "otu8"], "@otusID": "otus1", "@otuID": ["otu7", "otu8"]}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthMode"], "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": 724182, "^ot:focalCladeOTTTaxonName": "Celeus", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_157", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2011.05.001"}, "^ot:studyPublicationReference": "Benz, Brett W., Mark B. Robbins. 2011. Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae). Molecular Phylogenetics and Evolution 61 (1): 29-44.", "^ot:studyYear": 2011, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Celeus lugubris 1", "^ot:ottId": 499951, "^ot:ottTaxonName": "Celeus lugubris"}, "otu10": {"^ot:originalLabel": "Celeus undatus 2", "^ot:ottId": 724966, "^ot:ottTaxonName": "Celeus undatus"}, "otu11": {"^ot:originalLabel": "Celeus grammicus 1", "^ot:ottId": 499964, "^ot:ottTaxonName": "Celeus grammicus"}, "otu12": {"^ot:originalLabel": "Celeus grammicus 2", "^ot:ottId": 499964, "^ot:ottTaxonName": "Celeus grammicus"}, "otu13": {"^ot:originalLabel": "Celeus castaneus 1", "^ot:ottId": 724960, "^ot:ottTaxonName": "Celeus castaneus"}, "otu14": {"^ot:originalLabel": "Celeus castaneus 2", "^ot:ottId": 724960, "^ot:ottTaxonName": "Celeus castaneus"}, "otu15": {"^ot:originalLabel": "Celeus flavus 1", "^ot:ottId": 524497, "^ot:ottTaxonName": "Celeus flavus"}, "otu16": {"^ot:originalLabel": "Celeus flavus 2", "^ot:ottId": 524497, "^ot:ottTaxonName": "Celeus flavus"}, "otu17": {"^ot:originalLabel": "Celeus spectabilis 1", "^ot:ottId": 983476, "^ot:ottTaxonName": "Celeus spectabilis"}, "otu18": {"^ot:originalLabel": "Celeus spectabilis 2", "^ot:ottId": 983476, "^ot:ottTaxonName": "Celeus spectabilis"}, "otu19": {"^ot:originalLabel": "Celeus obrieni", "^ot:ottId": 724964, "^ot:ottTaxonName": "Celeus obrieni"}, "otu2": {"^ot:originalLabel": "Celeus lugubris 2", "^ot:ottId": 499951, "^ot:ottTaxonName": "Celeus lugubris"}, "otu20": {"^ot:originalLabel": "Celeus loricatus 1", "^ot:ottId": 704541, "^ot:ottTaxonName": "Celeus loricatus"}, "otu21": {"^ot:originalLabel": "Celeus loricatus 2", "^ot:ottId": 704541, "^ot:ottTaxonName": "Celeus loricatus"}, "otu22": {"^ot:originalLabel": "Celeus torquatus 1", "^ot:ottId": 724968, "^ot:ottTaxonName": "Celeus torquatus"}, "otu23": {"^ot:originalLabel": "Celeus torquatus 2", "^ot:ottId": 724968, "^ot:ottTaxonName": "Celeus torquatus"}, "otu24": {"^ot:originalLabel": "Dryocopus lineatus", "^ot:ottId": 290738, "^ot:ottTaxonName": "Dryocopus lineatus"}, "otu25": {"^ot:originalLabel": "Piculus chrysochloros", "^ot:ottId": 149826, "^ot:ottTaxonName": "Piculus chrysochloros"}, "otu3": {"^ot:originalLabel": "Celeus elegans 1", "^ot:ottId": 724183, "^ot:ottTaxonName": "Celeus elegans"}, "otu4": {"^ot:originalLabel": "Celeus elegans 2", "^ot:ottId": 724183, "^ot:ottTaxonName": "Celeus elegans"}, "otu5": {"^ot:originalLabel": "Celeus flavescens 1", "^ot:ottId": 704537, "^ot:ottTaxonName": "Celeus flavescens"}, "otu6": {"^ot:originalLabel": "Celeus flavescens 2", "^ot:ottId": 704537, "^ot:ottTaxonName": "Celeus flavescens"}, "otu7": {"^ot:originalLabel": "Celeus ochraceus 1"}, "otu8": {"^ot:originalLabel": "Celeus ochraceus 2"}, "otu9": {"^ot:originalLabel": "Celeus undatus 1", "^ot:ottId": 724966, "^ot:ottTaxonName": "Celeus undatus"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 4 (mtDNA+nuDNA)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node2", "^ot:messages": {"message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@id": "messageu820bce3f-dab2-44ba-b98f-8961899189b6", "@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": 512, "@sourceForTree": "tree1", "@type": "newick", "@url": "/curator/default/to_nexson?output=input&uploadid=u820bce3f-dab2-44ba-b98f-8961899189b6", "description": {"$": "Source data for tree 'tree1'"}}]}}}]}, "^ot:nearestTaxonMRCAName": "Celeus", "^ot:nearestTaxonMRCAOttId": "724182", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge46": {"@source": "node1", "@target": "node47"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge11": {"@source": "node10", "@target": "node12"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14"}, "edge14": {"@source": "node13", "@target": "node15"}}, "node16": {"edge16": {"@source": "node16", "@target": "node17"}, "edge17": {"@source": "node16", "@target": "node18"}}, "node19": {"edge19": {"@source": "node19", "@target": "node20"}, "edge30": {"@source": "node19", "@target": "node31"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge39": {"@source": "node2", "@target": "node40"}}, "node20": {"edge20": {"@source": "node20", "@target": "node21"}, "edge27": {"@source": "node20", "@target": "node28"}}, "node21": {"edge21": {"@source": "node21", "@target": "node22"}, "edge24": {"@source": "node21", "@target": "node25"}}, "node22": {"edge22": {"@source": "node22", "@target": "node23"}, "edge23": {"@source": "node22", "@target": "node24"}}, "node25": {"edge25": {"@source": "node25", "@target": "node26"}, "edge26": {"@source": "node25", "@target": "node27"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge18": {"@source": "node3", "@target": "node19"}, "edge3": {"@source": "node3", "@target": "node4"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge34": {"@source": "node31", "@target": "node35"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge33": {"@source": "node32", "@target": "node34"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge38": {"@source": "node35", "@target": "node39"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge37": {"@source": "node36", "@target": "node38"}}, "node4": {"edge15": {"@source": "node4", "@target": "node16"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node40": {"edge40": {"@source": "node40", "@target": "node41"}, "edge43": {"@source": "node40", "@target": "node44"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge42": {"@source": "node41", "@target": "node43"}}, "node44": {"edge44": {"@source": "node44", "@target": "node45"}, "edge45": {"@source": "node44", "@target": "node46"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge48": {"@source": "node47", "@target": "node49"}}, "node5": {"edge12": {"@source": "node5", "@target": "node13"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node6": {"edge6": {"@source": "node6", "@target": "node7"}, "edge9": {"@source": "node6", "@target": "node10"}}, "node7": {"edge7": {"@source": "node7", "@target": "node8"}, "edge8": {"@source": "node7", "@target": "node9"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu3", "^ot:isTaxonExemplar": true}, "node12": {"@otu": "otu4", "^ot:isTaxonExemplar": false}, "node13": {}, "node14": {"@otu": "otu5", "^ot:isTaxonExemplar": true}, "node15": {"@otu": "otu6", "^ot:isTaxonExemplar": false}, "node16": {}, "node17": {"@otu": "otu7"}, "node18": {"@otu": "otu8"}, "node19": {}, "node2": {}, "node20": {}, "node21": {}, "node22": {}, "node23": {"@otu": "otu9", "^ot:isTaxonExemplar": true}, "node24": {"@otu": "otu10", "^ot:isTaxonExemplar": false}, "node25": {}, "node26": {"@otu": "otu11", "^ot:isTaxonExemplar": true}, "node27": {"@otu": "otu12", "^ot:isTaxonExemplar": false}, "node28": {}, "node29": {"@otu": "otu13", "^ot:isTaxonExemplar": true}, "node3": {}, "node30": {"@otu": "otu14", "^ot:isTaxonExemplar": false}, "node31": {}, "node32": {}, "node33": {"@otu": "otu15", "^ot:isTaxonExemplar": true}, "node34": {"@otu": "otu16", "^ot:isTaxonExemplar": false}, "node35": {}, "node36": {}, "node37": {"@otu": "otu17", "^ot:isTaxonExemplar": true}, "node38": {"@otu": "otu18", "^ot:isTaxonExemplar": false}, "node39": {"@otu": "otu19"}, "node4": {}, "node40": {}, "node41": {}, "node42": {"@otu": "otu20", "^ot:isTaxonExemplar": true}, "node43": {"@otu": "otu21", "^ot:isTaxonExemplar": false}, "node44": {}, "node45": {"@otu": "otu22", "^ot:isTaxonExemplar": true}, "node46": {"@otu": "otu23", "^ot:isTaxonExemplar": false}, "node47": {}, "node48": {"@otu": "otu24"}, "node49": {"@otu": "otu25"}, "node5": {}, "node6": {}, "node7": {}, "node8": {"@otu": "otu1", "^ot:isTaxonExemplar": true}, "node9": {"@otu": "otu2", "^ot:isTaxonExemplar": false}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "229e92166614dad0f3217426a6e43279411097ea", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Thu, 7 Aug 2014 03:12:06 +0000", "date_ISO_8601": "2014-08-07 03:12:06 +0000", "relative_date": "12 years ago", "message_subject": "Celeus", "message_body": "(Update Study #ot_157 via OpenTree API)"}, {"id": "4e27a1fd51b55182e84c10beb493768b92e3ba8f", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Thu, 7 Aug 2014 03:08:52 +0000", "date_ISO_8601": "2014-08-07 03:08:52 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #ot_157 via OpenTree API"}]}