{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-08-06T17:44:17.296Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Birds"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}, {"@active": true, "@valid": true, "new": {"$": ""}, "old": {"$": "\\b\\s+(\\w*)$"}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-08-06T17:44:17.296Z", "@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": "<content provided as a string in a \"content\" rather than a file upload>", "@size": "", "@type": "newick", "@url": "", "description": {"$": ""}, "sourceForTree": [{"$": "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:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node12", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node12"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node13", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node13"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node14", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node14"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node15", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node15"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node16", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node16"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node38", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node38"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node39", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node39"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node41", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node41"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node42", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node42"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu1", "otu2"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu10", "otu11", "otu13"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu12", "otu16"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu15", "otu17"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu18", "otu19"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu20", "otu21"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu3", "otu4", "otu5"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu6", "otu9"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu7", "otu8"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:messages", "^ot:nearestTaxonMRCAName", "^ot:nearestTaxonMRCAOttId"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu7", "otu8"], "@otusID": "otus1", "@otuID": ["otu7", "otu8"]}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthMode"], "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": 815707, "^ot:focalCladeOTTTaxonName": "Capito", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_151", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1650/0010-5422(2005)107[0527:gvimds]2.0.co;2"}, "^ot:studyPublicationReference": "Armenta, Jessica K., Jason D. Weckstein, Daniel F. Lane. 2005. Geographic variation in mitochondrial DNA sequences of an Amazonian nonpasserine: The Black-spotted Barbet complex. The Condor 107 (3): 527-536.", "^ot:studyYear": 2005, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Capito auratus aurantiicinctus M45737", "^ot:ottId": 977875, "^ot:ottTaxonName": "Capito auratus aurantiicinctus"}, "otu10": {"^ot:originalLabel": "Capito auratus auratus B6947", "^ot:ottId": 977867, "^ot:ottTaxonName": "Capito auratus auratus"}, "otu11": {"^ot:originalLabel": "Capito auratus auratus B6969", "^ot:ottId": 977867, "^ot:ottTaxonName": "Capito auratus auratus"}, "otu12": {"^ot:originalLabel": "Capito auratus orosae B25503", "^ot:ottId": 977876, "^ot:ottTaxonName": "Capito auratus orosae"}, "otu13": {"^ot:originalLabel": "Capito auratus auratus B4805", "^ot:ottId": 977867, "^ot:ottTaxonName": "Capito auratus auratus"}, "otu14": {"^ot:originalLabel": "Capito auratus amazonicus M49882", "^ot:ottId": 977868, "^ot:ottTaxonName": "Capito auratus amazonicus"}, "otu15": {"^ot:originalLabel": "Capito auratus insperatus B6798", "^ot:ottId": 977877, "^ot:ottTaxonName": "Capito auratus insperatus"}, "otu16": {"^ot:originalLabel": "Capito auratus orosae B35719", "^ot:ottId": 977876, "^ot:ottTaxonName": "Capito auratus orosae"}, "otu17": {"^ot:originalLabel": "Capito auratus insperatus B11206", "^ot:ottId": 977877, "^ot:ottTaxonName": "Capito auratus insperatus"}, "otu18": {"^ot:originalLabel": "Capito brunneipectus B25499", "^ot:ottId": 965757, "^ot:ottTaxonName": "Capito brunneipectus"}, "otu19": {"^ot:originalLabel": "Capito brunneipectus B35612", "^ot:ottId": 965757, "^ot:ottTaxonName": "Capito brunneipectus"}, "otu2": {"^ot:originalLabel": "Capito auratus aurantiicinctus M49289", "^ot:ottId": 977875, "^ot:ottTaxonName": "Capito auratus aurantiicinctus"}, "otu20": {"^ot:originalLabel": "Capito niger B09373", "^ot:ottId": 1068254, "^ot:ottTaxonName": "Capito niger"}, "otu21": {"^ot:originalLabel": "Capito niger B10393", "^ot:ottId": 1068254, "^ot:ottTaxonName": "Capito niger"}, "otu22": {"^ot:originalLabel": "Capito maculicoronatus maculicoronatus B28524", "^ot:ottId": 977869, "^ot:ottTaxonName": "Capito maculicoronatus maculicoronatus"}, "otu23": {"^ot:originalLabel": "Capito maculicoronatus rubrilateralis B2178", "^ot:ottId": 370836, "^ot:ottTaxonName": "Capito maculicoronatus rubrilateralis"}, "otu24": {"^ot:originalLabel": "Capito squamatus B7738", "^ot:ottId": 712005, "^ot:ottTaxonName": "Capito squamatus"}, "otu25": {"^ot:originalLabel": "Capito wallacei B27757", "^ot:ottId": 712006, "^ot:ottTaxonName": "Capito wallacei"}, "otu26": {"^ot:originalLabel": "Capito quinticolor B29985", "^ot:ottId": 712004, "^ot:ottTaxonName": "Capito quinticolor"}, "otu27": {"^ot:originalLabel": "Capito dayi B18305", "^ot:ottId": 815708, "^ot:ottTaxonName": "Capito dayi"}, "otu28": {"^ot:originalLabel": "Capito aurovirens B7344", "^ot:ottId": 712007, "^ot:ottTaxonName": "Capito aurovirens"}, "otu3": {"^ot:originalLabel": "Capito auratus transilens B7567", "^ot:ottId": 977865, "^ot:ottTaxonName": "Capito auratus transilens"}, "otu4": {"^ot:originalLabel": "Capito auratus transilens B25572", "^ot:ottId": 977865, "^ot:ottTaxonName": "Capito auratus transilens"}, "otu5": {"^ot:originalLabel": "Capito auratus transilens B7549", "^ot:ottId": 977865, "^ot:ottTaxonName": "Capito auratus transilens"}, "otu6": {"^ot:originalLabel": "Capito auratus punctatus B27403", "^ot:ottId": 977874, "^ot:ottTaxonName": "Capito auratus punctatus"}, "otu7": {"^ot:originalLabel": "Capito auratus auratus/punctatus intergrade B4448"}, "otu8": {"^ot:originalLabel": "Capito auratus auratus/punctatus intergrade B4430"}, "otu9": {"^ot:originalLabel": "Capito auratus punctatus B27553", "^ot:ottId": 977874, "^ot:ottTaxonName": "Capito auratus punctatus"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 3", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node1", "^ot:messages": {"message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@id": "messageu1e4fe535-98d2-408d-af75-904d673bfe82", "@severity": "INFO", "@wasGeneratedBy": "opentree.2nexml", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "<content provided as a string in a \"content\" rather than a file upload>", "@size": 929, "@sourceForTree": "tree1", "@type": "newick", "@url": "/curator/default/to_nexson?output=input&uploadid=u1e4fe535-98d2-408d-af75-904d673bfe82", "description": {"$": "Source data for tree 'tree1'"}}]}}}]}, "^ot:nearestTaxonMRCAName": "Capito (genus in family Ramphastidae)", "^ot:nearestTaxonMRCAOttId": "815707", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge51": {"@source": "node1", "@target": "node52"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge16": {"@source": "node10", "@target": "node17"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge12": {"@source": "node11", "@target": "node13"}, "edge13": {"@source": "node11", "@target": "node14"}, "edge14": {"@source": "node11", "@target": "node15"}, "edge15": {"@source": "node11", "@target": "node16"}}, "node17": {"edge17": {"@source": "node17", "@target": "node18"}, "edge20": {"@source": "node17", "@target": "node21"}}, "node18": {"edge18": {"@source": "node18", "@target": "node19"}, "edge19": {"@source": "node18", "@target": "node20"}}, "node2": {"edge2": {"@source": "node2", "@target": "node3"}, "edge48": {"@source": "node2", "@target": "node49"}}, "node23": {"edge23": {"@source": "node23", "@target": "node24"}, "edge24": {"@source": "node23", "@target": "node25"}}, "node26": {"edge26": {"@source": "node26", "@target": "node27"}, "edge35": {"@source": "node26", "@target": "node36"}}, "node27": {"edge27": {"@source": "node27", "@target": "node28"}, "edge34": {"@source": "node27", "@target": "node35"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge33": {"@source": "node28", "@target": "node34"}}, "node29": {"edge29": {"@source": "node29", "@target": "node30"}, "edge32": {"@source": "node29", "@target": "node33"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge47": {"@source": "node3", "@target": "node48"}}, "node30": {"edge30": {"@source": "node30", "@target": "node31"}, "edge31": {"@source": "node30", "@target": "node32"}}, "node37": {"edge37": {"@source": "node37", "@target": "node38"}, "edge38": {"@source": "node37", "@target": "node39"}}, "node4": {"edge4": {"@source": "node4", "@target": "node5"}, "edge42": {"@source": "node4", "@target": "node43"}}, "node40": {"edge40": {"@source": "node40", "@target": "node41"}, "edge41": {"@source": "node40", "@target": "node42"}}, "node43": {"edge43": {"@source": "node43", "@target": "node44"}, "edge46": {"@source": "node43", "@target": "node47"}}, "node44": {"edge44": {"@source": "node44", "@target": "node45"}, "edge45": {"@source": "node44", "@target": "node46"}}, "node49": {"edge49": {"@source": "node49", "@target": "node50"}, "edge50": {"@source": "node49", "@target": "node51"}}, "node5": {"edge39": {"@source": "node5", "@target": "node40"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node6": {"edge36": {"@source": "node6", "@target": "node37"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node7": {"edge25": {"@source": "node7", "@target": "node26"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge22": {"@source": "node8", "@target": "node23"}, "edge8": {"@source": "node8", "@target": "node9"}}, "node9": {"edge21": {"@source": "node9", "@target": "node22"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {}, "node12": {"@otu": "otu1", "^ot:isTaxonExemplar": true}, "node13": {"@otu": "otu2", "^ot:isTaxonExemplar": false}, "node14": {"@otu": "otu3", "^ot:isTaxonExemplar": true}, "node15": {"@otu": "otu4", "^ot:isTaxonExemplar": false}, "node16": {"@otu": "otu5", "^ot:isTaxonExemplar": false}, "node17": {}, "node18": {}, "node19": {"@otu": "otu6"}, "node2": {}, "node20": {"@otu": "otu7"}, "node21": {"@otu": "otu8"}, "node22": {"@otu": "otu9"}, "node23": {}, "node24": {"@otu": "otu10"}, "node25": {"@otu": "otu11"}, "node26": {}, "node27": {}, "node28": {}, "node29": {}, "node3": {}, "node30": {}, "node31": {"@otu": "otu12"}, "node32": {"@otu": "otu13"}, "node33": {"@otu": "otu14"}, "node34": {"@otu": "otu15"}, "node35": {"@otu": "otu16"}, "node36": {"@otu": "otu17"}, "node37": {}, "node38": {"@otu": "otu18", "^ot:isTaxonExemplar": true}, "node39": {"@otu": "otu19", "^ot:isTaxonExemplar": false}, "node4": {}, "node40": {}, "node41": {"@otu": "otu20", "^ot:isTaxonExemplar": true}, "node42": {"@otu": "otu21", "^ot:isTaxonExemplar": false}, "node43": {}, "node44": {}, "node45": {"@otu": "otu22"}, "node46": {"@otu": "otu23"}, "node47": {"@otu": "otu24"}, "node48": {"@otu": "otu25"}, "node49": {}, "node5": {}, "node50": {"@otu": "otu26"}, "node51": {"@otu": "otu27"}, "node52": {"@otu": "otu28"}, "node6": {}, "node7": {}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "d1d10a16086181061e3cbea73d90efa54a179ad2", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 6 Aug 2014 17:47:34 +0000", "date_ISO_8601": "2014-08-06 17:47:34 +0000", "relative_date": "12 years ago", "message_subject": "Capito", "message_body": "(Update Study #ot_151 via OpenTree API)"}, {"id": "5146823376707793bb8309ee9ffb4af136908a4c", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 6 Aug 2014 17:44:16 +0000", "date_ISO_8601": "2014-08-06 17:44:16 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #ot_151 via OpenTree API"}]}