{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "otus": {"@id": "otus1", "otu": [{"@id": "otu1", "@about": "#otu1", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Stercorarius parasiticus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 742640}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius parasiticus"}]}, {"@id": "otu10", "@about": "#otu10", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Larus canus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 855472}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Larus canus"}]}, {"@id": "otu11", "@about": "#otu11", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Gallus gallus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 153563}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Gallus gallus"}]}, {"@id": "otu2", "@about": "#otu2", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Stercorarius longicaudus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 742641}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius longicaudus"}]}, {"@id": "otu3", "@about": "#otu3", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Stercorarius pomarinus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 219032}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius pomarinus"}]}, {"@id": "otu4", "@about": "#otu4", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Catharacta skua skua"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 742633}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius skua"}]}, {"@id": "otu5", "@about": "#otu5", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Catharacta skua lonngbergi"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 1073505}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius antarcticus"}]}, {"@id": "otu6", "@about": "#otu6", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Catharacta skua antarctica"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 5560028}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius antarcticus"}]}, {"@id": "otu7", "@about": "#otu7", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Catharacta chilensis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 3597019}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius chilensis"}]}, {"@id": "otu8", "@about": "#otu8", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Catharacta maccormicki"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 494176}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius maccormicki"}]}, {"@id": "otu9", "@about": "#otu9", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Catharacta skua hamiltoni"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 742637}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Stercorarius antarcticus hamiltoni"}]}], "@about": "#otus1"}, "trees": {"@otus": "otus1", "@id": "trees1", "tree": [{"@label": "Parsimony bootstrap", "@xsi:type": "nex:FloatTree", "node": [{"@root": true, "@id": "node1", "@about": "#node1"}, {"@id": "node2", "@about": "#node2"}, {"@otu": "otu10", "@id": "node20", "@about": "#node20", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node3", "@about": "#node3"}, {"@id": "node4", "@about": "#node4"}, {"@otu": "otu1", "@id": "node5", "@about": "#node5", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu2", "@id": "node6", "@about": "#node6", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node7", "@about": "#node7"}, {"@id": "node11", "@about": "#node11"}, {"@id": "node12", "@about": "#node12"}, {"@id": "node13", "@about": "#node13"}, {"@id": "node14", "@about": "#node14"}, {"@otu": "otu5", "@id": "node15", "@about": "#node15", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu6", "@id": "node16", "@about": "#node16", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu7", "@id": "node17", "@about": "#node17", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu8", "@id": "node18", "@about": "#node18", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu9", "@id": "node19", "@about": "#node19", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node8", "@about": "#node8"}, {"@otu": "otu3", "@id": "node9", "@about": "#node9", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu4", "@id": "node10", "@about": "#node10", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu11", "@id": "node21", "@about": "#node21", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}], "edge": [{"@source": "node1", "@target": "node2", "@id": "edge1", "@about": "#edge1"}, {"@source": "node2", "@target": "node20", "@id": "edge19", "@about": "#edge19"}, {"@source": "node2", "@target": "node3", "@id": "edge2", "@about": "#edge2", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 100}]}, {"@source": "node3", "@target": "node4", "@id": "edge3", "@about": "#edge3", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 100}]}, {"@source": "node4", "@target": "node5", "@id": "edge4", "@about": "#edge4"}, {"@source": "node4", "@target": "node6", "@id": "edge5", "@about": "#edge5"}, {"@source": "node3", "@target": "node7", "@id": "edge6", "@about": "#edge6", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 100}]}, {"@source": "node7", "@target": "node11", "@id": "edge10", "@about": "#edge10", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 63}]}, {"@source": "node11", "@target": "node12", "@id": "edge11", "@about": "#edge11", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 61}]}, {"@source": "node12", "@target": "node13", "@id": "edge12", "@about": "#edge12", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 53}]}, {"@source": "node13", "@target": "node14", "@id": "edge13", "@about": "#edge13", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 68}]}, {"@source": "node14", "@target": "node15", "@id": "edge14", "@about": "#edge14"}, {"@source": "node14", "@target": "node16", "@id": "edge15", "@about": "#edge15"}, {"@source": "node13", "@target": "node17", "@id": "edge16", "@about": "#edge16"}, {"@source": "node12", "@target": "node18", "@id": "edge17", "@about": "#edge17"}, {"@source": "node11", "@target": "node19", "@id": "edge18", "@about": "#edge18"}, {"@source": "node7", "@target": "node8", "@id": "edge7", "@about": "#edge7", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:bootstrapValues", "@datatype": "xsd:int", "$": 97}]}, {"@source": "node8", "@target": "node9", "@id": "edge8", "@about": "#edge8"}, {"@source": "node8", "@target": "node10", "@id": "edge9", "@about": "#edge9"}, {"@source": "node1", "@target": "node21", "@id": "edge20", "@about": "#edge20"}], "@id": "tree1", "@about": "#tree1", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthDescription", "@datatype": "xsd:string", "$": ""}, {"@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", "$": "Maximum parsimony "}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:inGroupClade", "@datatype": "xsd:string", "$": "node3"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:nodeLabelDescription", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:nodeLabelMode", "@datatype": "xsd:string", "$": "ot:bootstrapValues"}, {"@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", "$": "node1"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:unrootedTree", "@datatype": "xsd:boolean", "$": 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": "2016-10-06T19:37:45.809Z", "@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"}}}], "@about": "#otu-mapping-hints"}, {"@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": {"$": "meta"}}}], "@about": "#supporting-files-metadata"}, {"@dateCreated": "2023-06-05T20:46:11.699Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": []}}, "refersTo": {"@top": {"$": "meta"}}}], "@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: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"}], "@about": "#peyotl-validator-event"}], "@xsi:type": "nex:LiteralMeta", "@property": "ot:annotationEvents"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:candidateTreeForSynthesis", "@datatype": "xsd:string", "$": "tree1"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:comment", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "Joseph W. Brown"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "jwaterford"}, {"@href": "", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:dataDeposit"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalClade", "@datatype": "xsd:int", "$": 168297}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalCladeOTTTaxonName", "@datatype": "xsd:string", "$": "Stercorariidae"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyId", "@datatype": "xsd:string", "$": "ot_873"}, {"@href": "http://www.uni-heidelberg.de/institute/fak14/ipmb/phazb/pubwink/1993/1.%201993.pdf", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:studyPublication"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyPublicationReference", "@datatype": "xsd:string", "$": "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."}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyYear", "@datatype": "xsd:int", "$": 1993}]}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "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": "2 years, 10 months 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"}]}