{"sha": "3f7bd72a0486fba3f756bbb61fabda2acf6c259f", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-07-01T16:50:21.638Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-07-01T16:50:21.638Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "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": ["otu427164", "otu427165", "otu427166"], "refersTo": {"@top": "otus", "@idref": "otus2875", "@otusID": "otus2875"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu427181", "otu427182"], "refersTo": {"@top": "otus", "@idref": "otus2875", "@otusID": "otus2875"}, "@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": "tree6668", "@treesID": "trees2875", "@treeID": "tree6668"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6668"], "^ot:comment": "", "^ot:curatorName": ["Joseph Brown", "Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 631323, "^ot:focalCladeOTTTaxonName": "Oriolus", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus2875"], "^ot:studyId": "pg_2875", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1111/j.1600-0587.2010.06167.x"}, "^ot:studyPublicationReference": "J\u00f8nsson, Knud A., Rauri C. K. Bowie, Robert G. Moyle, Martin Irestedt, Les Christidis, Janette A. Norman, Jon Fjelds\u00e5. 2010. Phylogeny and biogeography of Oriolidae (Aves: Passeriformes). Ecography 33 (2): 232-241.", "^ot:studyYear": 2010, "^ot:tag": [], "^ot:treesElementOrder": ["trees2875"], "otusById": {"otus2875": {"otuById": {"otu427160": {"^ot:originalLabel": "Oriolus percivali", "^ot:ottId": 667454, "^ot:ottTaxonName": "Oriolus percivali"}, "otu427161": {"^ot:originalLabel": "Oriolus nigripennis", "^ot:ottId": 667450, "^ot:ottTaxonName": "Oriolus nigripennis"}, "otu427162": {"^ot:originalLabel": "Oriolus larvatus", "^ot:ottId": 433927, "^ot:ottTaxonName": "Oriolus larvatus"}, "otu427163": {"^ot:originalLabel": "Oriolus monacha", "^ot:ottId": 144733, "^ot:ottTaxonName": "Oriolus monacha"}, "otu427164": {"^ot:originalLabel": "Oriolus chinensis diffusus China", "^ot:ottId": 636501, "^ot:ottTaxonName": "Oriolus chinensis diffusus"}, "otu427165": {"^ot:originalLabel": "Oriolus chinensis diffusus Vietnam", "^ot:ottId": 636501, "^ot:ottTaxonName": "Oriolus chinensis diffusus"}, "otu427166": {"^ot:originalLabel": "Oriolus chinensis diffusus Korea", "^ot:ottId": 636501, "^ot:ottTaxonName": "Oriolus chinensis diffusus"}, "otu427167": {"^ot:originalLabel": "Oriolus kundoo", "^ot:ottId": 114674, "^ot:ottTaxonName": "Oriolus kundoo"}, "otu427168": {"^ot:originalLabel": "Oriolus oriolus", "^ot:ottId": 299687, "^ot:ottTaxonName": "Oriolus oriolus"}, "otu427169": {"^ot:originalLabel": "Oriolus chinensis chinensis", "^ot:ottId": 524117, "^ot:ottTaxonName": "Oriolus chinensis chinensis"}, "otu427170": {"^ot:originalLabel": "Oriolus chinensis melanisticus", "^ot:ottId": 636495, "^ot:ottTaxonName": "Oriolus chinensis melanisticus"}, "otu427171": {"^ot:originalLabel": "Oriolus auratus", "^ot:ottId": 1013348, "^ot:ottTaxonName": "Oriolus auratus"}, "otu427172": {"^ot:originalLabel": "Oriolus brachyrhynchus", "^ot:ottId": 675806, "^ot:ottTaxonName": "Oriolus brachyrhynchus"}, "otu427173": {"^ot:originalLabel": "Oriolus chlorocephalus", "^ot:ottId": 636499, "^ot:ottTaxonName": "Oriolus chlorocephalus"}, "otu427174": {"^ot:originalLabel": "Oriolus xanthornus", "^ot:ottId": 583087, "^ot:ottTaxonName": "Oriolus xanthornus"}, "otu427175": {"^ot:originalLabel": "Oriolus hosii", "^ot:ottId": 636490, "^ot:ottTaxonName": "Oriolus hosii"}, "otu427176": {"^ot:originalLabel": "Oriolus cruentus", "^ot:ottId": 639778, "^ot:ottTaxonName": "Oriolus cruentus"}, "otu427177": {"^ot:originalLabel": "Oriolus trailli", "^ot:ottId": 667447, "^ot:ottTaxonName": "Oriolus traillii"}, "otu427178": {"^ot:originalLabel": "Oriolus mellianus", "^ot:ottId": 144735, "^ot:ottTaxonName": "Oriolus mellianus"}, "otu427179": {"^ot:originalLabel": "Oriolus isabellae", "^ot:ottId": 114668, "^ot:ottTaxonName": "Oriolus isabellae"}, "otu427180": {"^ot:originalLabel": "Oriolus albiloris", "^ot:ottId": 63088, "^ot:ottTaxonName": "Oriolus albiloris"}, "otu427181": {"^ot:originalLabel": "Oriolus steerei Negros", "^ot:ottId": 667444, "^ot:ottTaxonName": "Oriolus steerii"}, "otu427182": {"^ot:originalLabel": "Oriolus steerei Mindago", "^ot:ottId": 667444, "^ot:ottTaxonName": "Oriolus steerii"}, "otu427183": {"^ot:originalLabel": "Oriolus xanthonotus", "^ot:ottId": 353511, "^ot:ottTaxonName": "Oriolus xanthonotus"}, "otu427184": {"^ot:originalLabel": "Oriolus flavocinctus", "^ot:ottId": 55849, "^ot:ottTaxonName": "Oriolus flavocinctus"}, "otu427185": {"^ot:originalLabel": "Oriolus melanotis", "^ot:ottId": 144737, "^ot:ottTaxonName": "Oriolus melanotis"}, "otu427186": {"^ot:originalLabel": "Oriolus szalayi", "^ot:ottId": 667442, "^ot:ottTaxonName": "Oriolus szalayi"}, "otu427187": {"^ot:originalLabel": "Oriolus bouroensis", "^ot:ottId": 63086, "^ot:ottTaxonName": "Oriolus bouroensis"}, "otu427188": {"^ot:originalLabel": "Oriolus forsteni", "^ot:ottId": 636488, "^ot:ottTaxonName": "Oriolus forsteni"}, "otu427189": {"^ot:originalLabel": "Oriolus phaeochromus", "^ot:ottId": 667452, "^ot:ottTaxonName": "Oriolus phaeochromus"}, "otu427190": {"^ot:originalLabel": "Oriolus sagittatus", "^ot:ottId": 293726, "^ot:ottTaxonName": "Oriolus sagittatus"}, "otu427191": {"^ot:originalLabel": "Pitohui dichrous", "^ot:ottId": 749722, "^ot:ottTaxonName": "Pitohui dichrous"}, "otu427192": {"^ot:originalLabel": "Pitohui kirhocephalus", "^ot:ottId": 95988, "^ot:ottTaxonName": "Pitohui kirhocephalus"}, "otu427193": {"^ot:originalLabel": "Sphecotheres vielloti", "^ot:ottId": 319134, "^ot:ottTaxonName": "Sphecotheres vieilloti"}, "otu427194": {"^ot:originalLabel": "Hylophilus ochraceiceps", "^ot:ottId": 669572, "^ot:ottTaxonName": "Hylophilus ochraceiceps"}, "otu427195": {"^ot:originalLabel": "Vireo olivaceus", "^ot:ottId": 604019, "^ot:ottTaxonName": "Vireo olivaceus"}, "otu427196": {"^ot:originalLabel": "Cyclarhis gujanensis", "^ot:ottId": 621721, "^ot:ottTaxonName": "Cyclarhis gujanensis"}}}}, "treesById": {"trees2875": {"@otus": "otus2875", "^ot:treeElementOrder": ["tree6668"], "treeById": {"tree6668": {"@label": "Fig. 3 Bayesian (topology)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node1162203", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1162202", "^ot:specifiedRoot": "node1162202", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1162202": {"edge1162203": {"@source": "node1162202", "@target": "node1162203"}, "edge1162270": {"@source": "node1162202", "@target": "node1162270"}}, "node1162203": {"edge1162204": {"@source": "node1162203", "@target": "node1162204"}, "edge1162265": {"@source": "node1162203", "@target": "node1162265"}}, "node1162204": {"edge1162205": {"@source": "node1162204", "@target": "node1162205"}, "edge1162252": {"@source": "node1162204", "@target": "node1162252"}}, "node1162205": {"edge1162206": {"@source": "node1162205", "@target": "node1162206"}, "edge1162243": {"@source": "node1162205", "@target": "node1162243"}}, "node1162206": {"edge1162207": {"@source": "node1162206", "@target": "node1162207"}, "edge1162236": {"@source": "node1162206", "@target": "node1162236"}}, "node1162207": {"edge1162208": {"@source": "node1162207", "@target": "node1162208"}, "edge1162231": {"@source": "node1162207", "@target": "node1162231"}}, "node1162208": {"edge1162209": {"@source": "node1162208", "@target": "node1162209"}, "edge1162216": {"@source": "node1162208", "@target": "node1162216"}}, "node1162209": {"edge1162210": {"@source": "node1162209", "@target": "node1162210"}, "edge1162215": {"@source": "node1162209", "@target": "node1162215"}}, "node1162210": {"edge1162211": {"@source": "node1162210", "@target": "node1162211"}, "edge1162214": {"@source": "node1162210", "@target": "node1162214"}}, "node1162211": {"edge1162212": {"@source": "node1162211", "@target": "node1162212"}, "edge1162213": {"@source": "node1162211", "@target": "node1162213"}}, "node1162216": {"edge1162217": {"@source": "node1162216", "@target": "node1162217"}, "edge1162230": {"@source": "node1162216", "@target": "node1162230"}}, "node1162217": {"edge1162218": {"@source": "node1162217", "@target": "node1162218"}, "edge1162223": {"@source": "node1162217", "@target": "node1162223"}}, "node1162218": {"edge1162219": {"@source": "node1162218", "@target": "node1162219"}, "edge1162222": {"@source": "node1162218", "@target": "node1162222"}}, "node1162219": {"edge1162220": {"@source": "node1162219", "@target": "node1162220"}, "edge1162221": {"@source": "node1162219", "@target": "node1162221"}}, "node1162223": {"edge1162224": {"@source": "node1162223", "@target": "node1162224"}, "edge1162227": {"@source": "node1162223", "@target": "node1162227"}}, "node1162224": {"edge1162225": {"@source": "node1162224", "@target": "node1162225"}, "edge1162226": {"@source": "node1162224", "@target": "node1162226"}}, "node1162227": {"edge1162228": {"@source": "node1162227", "@target": "node1162228"}, "edge1162229": {"@source": "node1162227", "@target": "node1162229"}}, "node1162231": {"edge1162232": {"@source": "node1162231", "@target": "node1162232"}, "edge1162235": {"@source": "node1162231", "@target": "node1162235"}}, "node1162232": {"edge1162233": {"@source": "node1162232", "@target": "node1162233"}, "edge1162234": {"@source": "node1162232", "@target": "node1162234"}}, "node1162236": {"edge1162237": {"@source": "node1162236", "@target": "node1162237"}, "edge1162240": {"@source": "node1162236", "@target": "node1162240"}}, "node1162237": {"edge1162238": {"@source": "node1162237", "@target": "node1162238"}, "edge1162239": {"@source": "node1162237", "@target": "node1162239"}}, "node1162240": {"edge1162241": {"@source": "node1162240", "@target": "node1162241"}, "edge1162242": {"@source": "node1162240", "@target": "node1162242"}}, "node1162243": {"edge1162244": {"@source": "node1162243", "@target": "node1162244"}, "edge1162251": {"@source": "node1162243", "@target": "node1162251"}}, "node1162244": {"edge1162245": {"@source": "node1162244", "@target": "node1162245"}, "edge1162250": {"@source": "node1162244", "@target": "node1162250"}}, "node1162245": {"edge1162246": {"@source": "node1162245", "@target": "node1162246"}, "edge1162249": {"@source": "node1162245", "@target": "node1162249"}}, "node1162246": {"edge1162247": {"@source": "node1162246", "@target": "node1162247"}, "edge1162248": {"@source": "node1162246", "@target": "node1162248"}}, "node1162252": {"edge1162253": {"@source": "node1162252", "@target": "node1162253"}, "edge1162258": {"@source": "node1162252", "@target": "node1162258"}}, "node1162253": {"edge1162254": {"@source": "node1162253", "@target": "node1162254"}, "edge1162257": {"@source": "node1162253", "@target": "node1162257"}}, "node1162254": {"edge1162255": {"@source": "node1162254", "@target": "node1162255"}, "edge1162256": {"@source": "node1162254", "@target": "node1162256"}}, "node1162258": {"edge1162259": {"@source": "node1162258", "@target": "node1162259"}, "edge1162264": {"@source": "node1162258", "@target": "node1162264"}}, "node1162259": {"edge1162260": {"@source": "node1162259", "@target": "node1162260"}, "edge1162263": {"@source": "node1162259", "@target": "node1162263"}}, "node1162260": {"edge1162261": {"@source": "node1162260", "@target": "node1162261"}, "edge1162262": {"@source": "node1162260", "@target": "node1162262"}}, "node1162265": {"edge1162266": {"@source": "node1162265", "@target": "node1162266"}, "edge1162269": {"@source": "node1162265", "@target": "node1162269"}}, "node1162266": {"edge1162267": {"@source": "node1162266", "@target": "node1162267"}, "edge1162268": {"@source": "node1162266", "@target": "node1162268"}}, "node1162270": {"edge1162271": {"@source": "node1162270", "@target": "node1162271"}, "edge1162274": {"@source": "node1162270", "@target": "node1162274"}}, "node1162271": {"edge1162272": {"@source": "node1162271", "@target": "node1162272"}, "edge1162273": {"@source": "node1162271", "@target": "node1162273"}}}, "nodeById": {"node1162202": {"@root": true}, "node1162203": {}, "node1162204": {}, "node1162205": {}, "node1162206": {}, "node1162207": {}, "node1162208": {}, "node1162209": {}, "node1162210": {}, "node1162211": {}, "node1162212": {"@otu": "otu427160"}, "node1162213": {"@otu": "otu427161"}, "node1162214": {"@otu": "otu427162"}, "node1162215": {"@otu": "otu427163"}, "node1162216": {}, "node1162217": {}, "node1162218": {}, "node1162219": {}, "node1162220": {"@otu": "otu427164"}, "node1162221": {"@otu": "otu427165"}, "node1162222": {"@otu": "otu427166"}, "node1162223": {}, "node1162224": {}, "node1162225": {"@otu": "otu427167"}, "node1162226": {"@otu": "otu427168"}, "node1162227": {}, "node1162228": {"@otu": "otu427169"}, "node1162229": {"@otu": "otu427170"}, "node1162230": {"@otu": "otu427171"}, "node1162231": {}, "node1162232": {}, "node1162233": {"@otu": "otu427172"}, "node1162234": {"@otu": "otu427173"}, "node1162235": {"@otu": "otu427174"}, "node1162236": {}, "node1162237": {}, "node1162238": {"@otu": "otu427175"}, "node1162239": {"@otu": "otu427176"}, "node1162240": {}, "node1162241": {"@otu": "otu427177"}, "node1162242": {"@otu": "otu427178"}, "node1162243": {}, "node1162244": {}, "node1162245": {}, "node1162246": {}, "node1162247": {"@otu": "otu427179"}, "node1162248": {"@otu": "otu427180"}, "node1162249": {"@otu": "otu427181"}, "node1162250": {"@otu": "otu427182"}, "node1162251": {"@otu": "otu427183"}, "node1162252": {}, "node1162253": {}, "node1162254": {}, "node1162255": {"@otu": "otu427184"}, "node1162256": {"@otu": "otu427185"}, "node1162257": {"@otu": "otu427186"}, "node1162258": {}, "node1162259": {}, "node1162260": {}, "node1162261": {"@otu": "otu427187"}, "node1162262": {"@otu": "otu427188"}, "node1162263": {"@otu": "otu427189"}, "node1162264": {"@otu": "otu427190"}, "node1162265": {}, "node1162266": {}, "node1162267": {"@otu": "otu427191"}, "node1162268": {"@otu": "otu427192"}, "node1162269": {"@otu": "otu427193"}, "node1162270": {}, "node1162271": {}, "node1162272": {"@otu": "otu427194"}, "node1162273": {"@otu": "otu427195"}, "node1162274": {"@otu": "otu427196"}}}}}}}}, "branch2sha": {"master": "3f7bd72a0486fba3f756bbb61fabda2acf6c259f"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "98b56c0443cdc709a11b4fdc30cdd582748002c2", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Tue, 1 Jul 2014 17:50:58 +0100", "date_ISO_8601": "2014-07-01 17:50:58 +0100", "relative_date": "12 years ago", "message_subject": "fix tree name", "message_body": "(Update Study #pg_2875 via OpenTree API)"}, {"id": "d33fb39501605772a074dffc82affa5344ea9a94", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Wed, 11 Jun 2014 22:18:34 -0500", "date_ISO_8601": "2014-06-11 22:18:34 -0500", "relative_date": "12 years ago", "message_subject": "corrected study ids"}, {"id": "f8a738aeda20a73750847484e110a85c7a3e0a12", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 10 Jun 2014 23:36:42 -0500", "date_ISO_8601": "2014-06-10 23:36:42 -0500", "relative_date": "12 years ago", "message_subject": "Migrating info from gcmdr to nexsons", "message_body": "using peyotl d69c8b180fce7703c7203a0b51712eab57e2988c\ndev/decorate_pg_studies_with_gcmdr_info.py\nto set:\n  ^ot:candidateTreeForSynthesis\n  ^ot:specifiedRoot, and\n  ^ot:unrootedTree\nproperties based on the use of the trees for synthesis study\nlists in gcmdr commit 35bf307e72bed4f59724762dde4a12965abcea92"}, {"id": "593d6fbab385716dc0a12f3fc95133e8b7479b37", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 29 Apr 2014 20:05:19 -0500", "date_ISO_8601": "2014-04-29 20:05:19 -0500", "relative_date": "12 years ago", "message_subject": "initial commit with phylografter files from 29 Apr, 2014"}]}