{"sha": "24afc85a444963f10ca51c6e20138fe592a4b525", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2016-10-06T19:37:45.809Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": false, "searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2016-10-06T19:37:45.809Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 283, "@type": "newick", "@url": "/curator/download/supporting_files.doc.811a1ba577301174.5041535445442e747265.tre", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2023-06-05T20:46:11.699Z", "@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"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge10", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge10"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge11", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge11"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge12", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge12"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge13", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge13"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge2", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge2"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge3", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge3"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge6", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge6"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge7", "@treesID": "trees1", "@treeID": "tree1", "@edgeID": "edge7"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelDescription", "^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "", "^ot:curatorName": ["Joseph W. Brown", "jwaterford"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 168297, "^ot:focalCladeOTTTaxonName": "Stercorariidae", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_873", "^ot:studyPublication": {"@href": "http://www.uni-heidelberg.de/institute/fak14/ipmb/phazb/pubwink/1993/1.%201993.pdf"}, "^ot:studyPublicationReference": "Blechschmidt, Karin, Hans-Ulrich Peter, Jacobus De Korte, Michael Wink, Ingrid Seibold, Andreas J. Helbig. 1993. Investigations on the molecular systematics of skuas (Stercorariidae). Zool. Jb. Syst. 120: 379-387.", "^ot:studyYear": 1993, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Stercorarius parasiticus", "^ot:ottId": 742640, "^ot:ottTaxonName": "Stercorarius parasiticus"}, "otu10": {"^ot:originalLabel": "Larus canus", "^ot:ottId": 855472, "^ot:ottTaxonName": "Larus canus"}, "otu11": {"^ot:originalLabel": "Gallus gallus", "^ot:ottId": 153563, "^ot:ottTaxonName": "Gallus gallus"}, "otu2": {"^ot:originalLabel": "Stercorarius longicaudus", "^ot:ottId": 742641, "^ot:ottTaxonName": "Stercorarius longicaudus"}, "otu3": {"^ot:originalLabel": "Stercorarius pomarinus", "^ot:ottId": 219032, "^ot:ottTaxonName": "Stercorarius pomarinus"}, "otu4": {"^ot:originalLabel": "Catharacta skua skua", "^ot:ottId": 742633, "^ot:ottTaxonName": "Stercorarius skua"}, "otu5": {"^ot:originalLabel": "Catharacta skua lonngbergi", "^ot:ottId": 1073505, "^ot:ottTaxonName": "Stercorarius antarcticus"}, "otu6": {"^ot:originalLabel": "Catharacta skua antarctica", "^ot:ottId": 5560028, "^ot:ottTaxonName": "Stercorarius antarcticus"}, "otu7": {"^ot:originalLabel": "Catharacta chilensis", "^ot:ottId": 3597019, "^ot:ottTaxonName": "Stercorarius chilensis"}, "otu8": {"^ot:originalLabel": "Catharacta maccormicki", "^ot:ottId": 494176, "^ot:ottTaxonName": "Stercorarius maccormicki"}, "otu9": {"^ot:originalLabel": "Catharacta skua hamiltoni", "^ot:ottId": 742637, "^ot:ottTaxonName": "Stercorarius antarcticus hamiltoni"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Parsimony bootstrap", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "node3", "^ot:nodeLabelDescription": "", "^ot:nodeLabelMode": "ot:bootstrapValues", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge20": {"@source": "node1", "@target": "node21"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12", "^ot:bootstrapValues": 61}, "edge18": {"@source": "node11", "@target": "node19"}}, "node12": {"edge12": {"@source": "node12", "@target": "node13", "^ot:bootstrapValues": 53}, "edge17": {"@source": "node12", "@target": "node18"}}, "node13": {"edge13": {"@source": "node13", "@target": "node14", "^ot:bootstrapValues": 68}, "edge16": {"@source": "node13", "@target": "node17"}}, "node14": {"edge14": {"@source": "node14", "@target": "node15"}, "edge15": {"@source": "node14", "@target": "node16"}}, "node2": {"edge19": {"@source": "node2", "@target": "node20"}, "edge2": {"@source": "node2", "@target": "node3", "^ot:bootstrapValues": 100}}, "node3": {"edge3": {"@source": "node3", "@target": "node4", "^ot:bootstrapValues": 100}, "edge6": {"@source": "node3", "@target": "node7", "^ot:bootstrapValues": 100}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge5": {"@source": "node4", "@target": "node6"}}, "node7": {"edge10": {"@source": "node7", "@target": "node11", "^ot:bootstrapValues": 63}, "edge7": {"@source": "node7", "@target": "node8", "^ot:bootstrapValues": 97}}, "node8": {"edge8": {"@source": "node8", "@target": "node9"}, "edge9": {"@source": "node8", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu4"}, "node11": {}, "node12": {}, "node13": {}, "node14": {}, "node15": {"@otu": "otu5"}, "node16": {"@otu": "otu6"}, "node17": {"@otu": "otu7"}, "node18": {"@otu": "otu8"}, "node19": {"@otu": "otu9"}, "node2": {}, "node20": {"@otu": "otu10"}, "node21": {"@otu": "otu11"}, "node3": {}, "node4": {}, "node5": {"@otu": "otu1"}, "node6": {"@otu": "otu2"}, "node7": {}, "node8": {}, "node9": {"@otu": "otu3"}}}}}}}}, "branch2sha": {"master": "24afc85a444963f10ca51c6e20138fe592a4b525"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "8bfc74f7b706743e5e0cd1cc6e47ab9829980315", "author_name": "jwaterford", "author_email": "jwaterford@ucsd.edu", "date": "Mon, 5 Jun 2023 20:48:08 +0000", "date_ISO_8601": "2023-06-05 20:48:08 +0000", "relative_date": "3 years ago", "message_subject": "Mapped tips to CLO taxa", "message_body": "(Update document 'ot_873' via OpenTree API)"}, {"id": "8e58aa3716c176d0b44b2258ff1f4fcdeac5c132", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Thu, 6 Oct 2016 19:45:22 +0000", "date_ISO_8601": "2016-10-06 19:45:22 +0000", "relative_date": "10 years ago", "message_subject": "Blechschmidt, 1993", "message_body": "(Update document 'ot_873' via OpenTree API)"}, {"id": "d738512e450897bbc1013d267d5694c61748491f", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Thu, 6 Oct 2016 19:37:44 +0000", "date_ISO_8601": "2016-10-06 19:37:44 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_873' via OpenTree API"}]}