{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2016-09-28T03:50:29.715Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2016-09-28T03:50:29.714Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 214, "@type": "newick", "@url": "/curator/download/supporting_files.doc.bbe0c63a89976b8a.5041535445442e747265.tre", "description": {"$": "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": "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"], "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": 603922, "^ot:focalCladeOTTTaxonName": "Sitta", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_828", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1111/j.1474-919x.1998.tb04553.x"}, "^ot:studyPublicationReference": "Pasquet, Eric. 2008. Phylogeny of the nuthatches of the Sitta canadensis group and its evolutionary and biogeographic implications. Ibis 140 (1): 150-156", "^ot:studyYear": 2008, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Parus ater", "^ot:ottId": 746130, "^ot:ottTaxonName": "Periparus ater"}, "otu10": {"^ot:originalLabel": "Sitta europaea", "^ot:ottId": 82242, "^ot:ottTaxonName": "Sitta europaea"}, "otu11": {"^ot:originalLabel": "Sitta carolinensis", "^ot:ottId": 82247, "^ot:ottTaxonName": "Sitta carolinensis"}, "otu12": {"^ot:originalLabel": "Sitta himalayensis", "^ot:ottId": 82248, "^ot:ottTaxonName": "Sitta himalayensis"}, "otu2": {"^ot:originalLabel": "Sylvia melanocephala", "^ot:ottId": 1093905, "^ot:ottTaxonName": "Sylvia melanocephala"}, "otu3": {"^ot:originalLabel": "Sitta frontalis", "^ot:ottId": 82249, "^ot:ottTaxonName": "Sitta frontalis"}, "otu4": {"^ot:originalLabel": "Sitta pygmaea", "^ot:ottId": 82240, "^ot:ottTaxonName": "Sitta pygmaea"}, "otu5": {"^ot:originalLabel": "Sitta canadensis", "^ot:ottId": 603923, "^ot:ottTaxonName": "Sitta canadensis"}, "otu6": {"^ot:originalLabel": "Sitta villosa", "^ot:ottId": 82239, "^ot:ottTaxonName": "Sitta villosa"}, "otu7": {"^ot:originalLabel": "Sitta whiteheadi", "^ot:ottId": 82233, "^ot:ottTaxonName": "Sitta whiteheadi"}, "otu8": {"^ot:originalLabel": "Sitta krueperi", "^ot:ottId": 82237, "^ot:ottTaxonName": "Sitta krueperi"}, "otu9": {"^ot:originalLabel": "Sitta ledanti", "^ot:ottId": 82236, "^ot:ottTaxonName": "Sitta ledanti"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 3", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "node4", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge2": {"@source": "node1", "@target": "node3"}, "edge3": {"@source": "node1", "@target": "node4"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge11": {"@source": "node10", "@target": "node12"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13"}, "edge13": {"@source": "node12", "@target": "node14"}}, "node15": {"edge15": {"@source": "node15", "@target": "node16"}, "edge16": {"@source": "node15", "@target": "node17"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge19": {"@source": "node18", "@target": "node20"}}, "node20": {"edge20": {"@source": "node20", "@target": "node21"}, "edge21": {"@source": "node20", "@target": "node22"}}, "node4": {"edge17": {"@source": "node4", "@target": "node18"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node5": {"edge5": {"@source": "node5", "@target": "node6"}, "edge6": {"@source": "node5", "@target": "node7"}}, "node7": {"edge7": {"@source": "node7", "@target": "node8"}, "edge8": {"@source": "node7", "@target": "node9"}}, "node9": {"edge14": {"@source": "node9", "@target": "node15"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu5"}, "node12": {}, "node13": {"@otu": "otu6"}, "node14": {"@otu": "otu7"}, "node15": {}, "node16": {"@otu": "otu8"}, "node17": {"@otu": "otu9"}, "node18": {}, "node19": {"@otu": "otu10"}, "node2": {"@otu": "otu1"}, "node20": {}, "node21": {"@otu": "otu11"}, "node22": {"@otu": "otu12"}, "node3": {"@otu": "otu2"}, "node4": {}, "node5": {}, "node6": {"@otu": "otu3"}, "node7": {}, "node8": {"@otu": "otu4"}, "node9": {}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "c16ce9b1340e27a520ef2621f6f58bae8ff25420", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 28 Sep 2016 03:53:28 +0000", "date_ISO_8601": "2016-09-28 03:53:28 +0000", "relative_date": "10 years ago", "message_subject": "treeeeeeeeeee", "message_body": "(Update document 'ot_828' via OpenTree API)"}, {"id": "b7598761cdaabf9b265f5c4cdf45edf9598ae967", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 28 Sep 2016 03:51:34 +0000", "date_ISO_8601": "2016-09-28 03:51:34 +0000", "relative_date": "10 years ago", "message_subject": "init", "message_body": "(Update document 'ot_828' via OpenTree API)"}, {"id": "93283d3b64afc4e42620a71537e39e5fcb521a07", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 28 Sep 2016 03:50:28 +0000", "date_ISO_8601": "2016-09-28 03:50:28 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_828' via OpenTree API"}]}