{"sha": "9f142662c80384add868f25e83f5aa64c86e050f", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2016-02-23T14:13:49.345Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2016-02-23T14:13:49.345Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 122, "@type": "newick", "@url": "/curator/download/supporting_files.doc.b9f71de7a8b04fdd.5041535445442e747265.tre", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": "otu6", "@otusID": "otus1", "@otuID": "otu6"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "Tree reconstructed manually from PDF in publication", "^ot:curatorName": ["Christine Ewers-Saucedo"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 363891, "^ot:focalCladeOTTTaxonName": "Acrothoracica", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_646", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.11646/zootaxa.3694.3.3"}, "^ot:studyPublicationReference": "Benny K.K. CHAN, Chi Chiu CHEANG, I-Han CHEN, Gregory A. KOLBASOV, 2013, '<p><strong>Acrothoracican barnacles (Lithoglyptida) in Taiwan, including the taxonomic status of <em>Balanodytes</em> <em>taiwanus</em> Utinomi, 1950 and cryptic diversity of <em>Auritoglyptes bicornis</em> (Aurivillius, 1892)</strong></p>', Zootaxa, vol. 3694, no. 3, p. 221", "^ot:studyYear": 2013, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Trypetesa habei", "^ot:ottId": 749408, "^ot:ottTaxonName": "Trypetesa habei"}, "otu2": {"^ot:originalLabel": "Balanodytes taiwanus", "^ot:ottId": 749375, "^ot:ottTaxonName": "Armatoglyptes habei"}, "otu3": {"^ot:originalLabel": "Berndtia purpurea", "^ot:ottId": 6739, "^ot:ottTaxonName": "Berndtia purpurea"}, "otu4": {"^ot:originalLabel": "Auritoglyptes bicornis", "^ot:ottId": 325117, "^ot:ottTaxonName": "Auritoglyptes bicornis"}, "otu5": {"^ot:originalLabel": "Kochlorine hamata", "^ot:ottId": 749401, "^ot:ottTaxonName": "Kochlorine hamata"}, "otu6": {"^ot:originalLabel": "Lithoglyptes sp"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 7A (16S rDNA)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node3", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@source": "node1", "@target": "node2"}, "edge2": {"@source": "node1", "@target": "node3"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge4": {"@source": "node3", "@target": "node5"}}, "node5": {"edge5": {"@source": "node5", "@target": "node6"}, "edge6": {"@source": "node5", "@target": "node7"}}, "node7": {"edge7": {"@source": "node7", "@target": "node8"}, "edge8": {"@source": "node7", "@target": "node9"}}, "node9": {"edge10": {"@source": "node9", "@target": "node11"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu5"}, "node11": {"@otu": "otu6"}, "node2": {"@otu": "otu1"}, "node3": {}, "node4": {"@otu": "otu2"}, "node5": {}, "node6": {"@otu": "otu3"}, "node7": {}, "node8": {"@otu": "otu4"}, "node9": {}}}}}}}}, "branch2sha": {"master": "9f142662c80384add868f25e83f5aa64c86e050f"}, "commentHTML": "<p>Tree reconstructed manually from PDF in publication</p>", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "94fa20254ac1820adb276357a50b6556110fa83f", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Thu, 31 Mar 2016 19:05:12 +0000", "date_ISO_8601": "2016-03-31 19:05:12 +0000", "relative_date": "10 years ago", "message_subject": "Unmapped undetermined species names", "message_body": "(Update document 'ot_646' via OpenTree API)"}, {"id": "46e68ecbf317a875722e92ab01d485ced0a62b53", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Tue, 23 Feb 2016 14:17:42 +0000", "date_ISO_8601": "2016-02-23 14:17:42 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_646' via OpenTree API"}, {"id": "10740605d3a1f1623a1051f5fc98d386c678cc16", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Tue, 23 Feb 2016 14:13:47 +0000", "date_ISO_8601": "2016-02-23 14:13:47 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_646' via OpenTree API"}]}