{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "0.0.0", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "otus": {"@id": "otus1", "otu": [{"@id": "otu1", "@about": "#otu1", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Megalaima asiatica"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 6154888}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Psilopogon asiaticus"}]}, {"@id": "otu2", "@about": "#otu2", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Megalaima chrysopogon"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 6154891}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Psilopogon chrysopogon"}]}, {"@id": "otu3", "@about": "#otu3", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Megalaima franklinii"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 6154899}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Psilopogon franklinii"}]}, {"@id": "otu4", "@about": "#otu4", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Megalaima haemacephala"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 738739}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Megalaima haemacephala"}]}, {"@id": "otu5", "@about": "#otu5", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Trachyphonus erythrocephalus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 266067}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Trachyphonus erythrocephalus"}]}, {"@id": "otu6", "@about": "#otu6", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Tricholaema hirsuta"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 214989}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Tricholaema hirsuta"}]}, {"@id": "otu7", "@about": "#otu7", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Megalaima mystacophanos"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 6154908}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Psilopogon mystacophanos"}]}, {"@id": "otu8", "@about": "#otu8", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Psilopogon pyrolophus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 291641}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Psilopogon pyrolophus"}]}, {"@id": "otu9", "@about": "#otu9", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Megalaima oorti"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 738735}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Megalaima oorti"}]}], "@about": "#otus1"}, "trees": {"@otus": "otus1", "@id": "trees1", "tree": [{"@label": "Untitled (tree1)", "@xsi:type": "nex:FloatTree", "node": [{"@root": true, "@id": "tree1_ROOT", "@about": "#tree1_ROOT"}, {"@id": "node10", "@about": "#node10"}, {"@otu": "otu5", "@id": "node11", "@about": "#node11", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu6", "@id": "node12", "@about": "#node12", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node8", "@about": "#node8"}, {"@id": "node7", "@about": "#node7"}, {"@id": "node13", "@about": "#node13"}, {"@otu": "otu7", "@id": "node14", "@about": "#node14", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu8", "@id": "node15", "@about": "#node15", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node5", "@about": "#node5"}, {"@id": "node3", "@about": "#node3"}, {"@id": "node1", "@about": "#node1"}, {"@otu": "otu1", "@id": "node2", "@about": "#node2", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu9", "@id": "node16", "@about": "#node16", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu2", "@id": "node4", "@about": "#node4", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu3", "@id": "node6", "@about": "#node6", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu4", "@id": "node9", "@about": "#node9", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}], "edge": [{"@source": "tree1_ROOT", "@target": "node10", "@id": "edge9", "@about": "#edge9"}, {"@source": "node10", "@target": "node11", "@id": "edge10", "@about": "#edge10"}, {"@source": "node10", "@target": "node12", "@id": "edge11", "@about": "#edge11"}, {"@source": "tree1_ROOT", "@target": "node8", "@id": "tree1_ROOT_EDGE", "@about": "#tree1_ROOT_EDGE"}, {"@source": "node8", "@target": "node7", "@id": "edge7", "@about": "#edge7"}, {"@source": "node7", "@target": "node13", "@id": "edge12", "@about": "#edge12"}, {"@source": "node13", "@target": "node14", "@id": "edge13", "@about": "#edge13"}, {"@source": "node13", "@target": "node15", "@id": "edge14", "@about": "#edge14"}, {"@source": "node7", "@target": "node5", "@id": "edge6", "@about": "#edge6"}, {"@source": "node5", "@target": "node3", "@id": "edge4", "@about": "#edge4"}, {"@source": "node3", "@target": "node1", "@id": "edge2", "@about": "#edge2"}, {"@source": "node1", "@target": "node2", "@id": "edge1", "@about": "#edge1"}, {"@source": "node1", "@target": "node16", "@id": "edge15", "@about": "#edge15"}, {"@source": "node3", "@target": "node4", "@id": "edge3", "@about": "#edge3"}, {"@source": "node5", "@target": "node6", "@id": "edge5", "@about": "#edge5"}, {"@source": "node8", "@target": "node9", "@id": "edge8", "@about": "#edge8"}], "@id": "tree1", "@about": "#tree1", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthDescription", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthMode", "@datatype": "xsd:string", "$": "ot:undefined"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthTimeUnit", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatedType", "@datatype": "xsd:string", "$": "Maximum parsimony "}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:inGroupClade", "@datatype": "xsd:string", "$": "node8"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:nodeLabelMode", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:nodeLabelTimeUnit", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:outGroupEdge", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:specifiedRoot", "@datatype": "xsd:string", "$": "tree1_ROOT"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:unrootedTree", "@datatype": "xsd:boolean", "$": false}]}], "@about": "#trees1"}, "meta": [{"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}, "@about": "#peyotl-validator"}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0", "@about": "#opentree-curation-webapp"}], "@xsi:type": "nex:LiteralMeta", "@property": "ot:agents"}, {"annotation": [{"@dateCreated": "2016-10-05T20:25:43.375Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": false, "searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}], "@about": "#otu-mapping-hints"}, {"@dateCreated": "2016-10-05T20:25:43.375Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 210, "@type": "newick", "@url": "/curator/download/supporting_files.doc.82017460e98d0d68.5041535445442e747265.tre", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}], "@about": "#supporting-files-metadata"}, {"@dateCreated": "2023-03-30T22:49:34.573Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}], "@about": "#merged-namesets-metadata"}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}], "@about": "#peyotl-validator-event"}], "@xsi:type": "nex:LiteralMeta", "@property": "ot:annotationEvents"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:candidateTreeForSynthesis", "@datatype": "xsd:string", "$": "tree1"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:comment", "@datatype": "xsd:string", "$": "no outgroup was defined in the original study. \ntree from Davis 2014."}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "ningwang83"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "Emily Jane McTavish"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "James Waterford"}, {"@href": "", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:dataDeposit"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalClade", "@datatype": "xsd:int", "$": 291638}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalCladeOTTTaxonName", "@datatype": "xsd:string", "$": "Megalaima"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyId", "@datatype": "xsd:string", "$": "ot_870"}, {"@href": "http://dx.doi.org/10.1111/j.1474-919x.2007.00732.x", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:studyPublication"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyPublicationReference", "@datatype": "xsd:string", "$": "JULIE FEINSTEIN, XIAOJUN YANG, SHOU-HSIEN LI, 2007, 'Molecular systematics and historical biogeography of the Black-browed Barbet species complex (Megalaima oorti)', Ibis, vol. 150, no. 1, pp. 40-49"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyYear", "@datatype": "xsd:int", "$": 2007}]}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "<p>no outgroup was defined in the original study. \ntree from Davis 2014.</p>", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "06b5729e28be6fdbef9795d0cbec910f857efb06", "author_name": "James Waterford", "author_email": "jwaterford@ucsd.edu", "date": "Tue, 18 Jul 2023 19:37:48 +0000", "date_ISO_8601": "2023-07-18 19:37:48 +0000", "relative_date": "2 years, 9 months ago", "message_subject": "Mapped tips to CLO Taxa", "message_body": "(Update document 'ot_870' via OpenTree API)"}, {"id": "13bba0c5cc55b3b285fcb26b7b2330c4a83e76ae", "author_name": "Emily Jane McTavish", "author_email": "ejmctavish@ucmerced.edu", "date": "Thu, 30 Mar 2023 22:51:04 +0000", "date_ISO_8601": "2023-03-30 22:51:04 +0000", "relative_date": "3 years, 1 month ago", "message_subject": "Update mapping to align with eBird", "message_body": "(Update document 'ot_870' via OpenTree API)"}, {"id": "12f773e03b45ce997d1fa00b928e093ca9c643ab", "author_name": "ningwang83", "author_email": "ANONYMOUS", "date": "Wed, 5 Oct 2016 20:34:57 +0000", "date_ISO_8601": "2016-10-05 20:34:57 +0000", "relative_date": "10 years ago", "message_subject": "make comments", "message_body": "(Update document 'ot_870' via OpenTree API)"}, {"id": "22b3eea05a945cba3c1fefa388cf3867155bd6f2", "author_name": "ningwang83", "author_email": "ANONYMOUS", "date": "Wed, 5 Oct 2016 20:34:20 +0000", "date_ISO_8601": "2016-10-05 20:34:20 +0000", "relative_date": "10 years ago", "message_subject": "map OTU, set up trees", "message_body": "(Update document 'ot_870' via OpenTree API)"}, {"id": "0722a39f36953ee0b23510d8b89ada763a6486d9", "author_name": "ningwang83", "author_email": "ANONYMOUS", "date": "Wed, 5 Oct 2016 20:27:19 +0000", "date_ISO_8601": "2016-10-05 20:27:19 +0000", "relative_date": "10 years ago", "message_subject": "Init", "message_body": "(Update document 'ot_870' via OpenTree API)"}, {"id": "8c6a0a8f55e2aed91baaac0d66d234a1c9f253a5", "author_name": "ningwang83", "author_email": "ANONYMOUS", "date": "Wed, 5 Oct 2016 20:25:42 +0000", "date_ISO_8601": "2016-10-05 20:25:42 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_870' via OpenTree API"}]}