{"sha": "6bed60428352c04d00341ad513a8efb9442e4d8a", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-07-30T15:53:46.382Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-07-30T15:53:46.382Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "Penaeus_sl Bayesian consensus_con_edited.tre", "@size": "", "@type": "newick", "@url": "", "description": {"$": "MrBayes 50% majority consensus tree"}, "sourceForTree": [{"$": "tree1"}]}]}}, "refersTo": {"@top": {"$": "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": ["otu10", "otu14", "otu15"], "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"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu10", "otu14", "otu15"], "@otusID": "otus1", "@otuID": ["otu10", "otu14", "otu15"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1"], "^ot:comment": "", "^ot:curatorName": ["chris-owen"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 212711, "^ot:focalCladeOTTTaxonName": "Penaeidae", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_114", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1111/j.1463-6409.2011.00483.x"}, "^ot:studyPublicationReference": "Ka Yan Ma, Tin-Yam Chan, Ka Hou Chu, 2011, 'Refuting the six-genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes', Zoologica Scripta, vol. 40, no. 5, pp. 498-508", "^ot:studyYear": 2011, "^ot:tag": ["Penaeus"], "^ot:treesElementOrder": ["trees1"], "^xhtml:license": {"@href": "http://creativecommons.org/publicdomain/zero/1.0/"}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Fenneropenaeus merguiensis", "^ot:ottId": 119131, "^ot:ottTaxonName": "Fenneropenaeus merguiensis"}, "otu10": {"^ot:originalLabel": "Penaeus vannamei"}, "otu11": {"^ot:originalLabel": "Melicertus hathor", "^ot:ottId": 16339, "^ot:ottTaxonName": "Melicertus hathor"}, "otu12": {"^ot:originalLabel": "Melicertus latisulcatus", "^ot:ottId": 796549, "^ot:ottTaxonName": "Melicertus latisulcatus"}, "otu13": {"^ot:originalLabel": "Melicertus plebejus", "^ot:ottId": 796547, "^ot:ottTaxonName": "Melicertus plebejus"}, "otu14": {"^ot:originalLabel": "Marsupenaeus japonicus varI"}, "otu15": {"^ot:originalLabel": "Marsupenaeus japonicus varII"}, "otu16": {"^ot:originalLabel": "Melicertus canaliculatus", "^ot:ottId": 163889, "^ot:ottTaxonName": "Melicertus canaliculatus"}, "otu17": {"^ot:originalLabel": "Melicertus longistylus", "^ot:ottId": 769324, "^ot:ottTaxonName": "Melicertus longistylus"}, "otu18": {"^ot:originalLabel": "Melicertus marginatus", "^ot:ottId": 769326, "^ot:ottTaxonName": "Melicertus marginatus"}, "otu19": {"^ot:originalLabel": "Melicertus kerathurus", "^ot:ottId": 119143, "^ot:ottTaxonName": "Melicertus kerathurus"}, "otu2": {"^ot:originalLabel": "Fenneropenaeus silasi", "^ot:ottId": 347049, "^ot:ottTaxonName": "Fenneropenaeus silasi"}, "otu20": {"^ot:originalLabel": "Funchalia sp", "^ot:ottId": 285757, "^ot:ottTaxonName": "Funchalia"}, "otu21": {"^ot:originalLabel": "Pelagopenaeus balboae", "^ot:ottId": 879530, "^ot:ottTaxonName": "Pelagopenaeus balboae"}, "otu22": {"^ot:originalLabel": "Heteropenaeus longimanus", "^ot:ottId": 506846, "^ot:ottTaxonName": "Heteropenaeus longimanus"}, "otu23": {"^ot:originalLabel": "Megokris pescadoreensis", "^ot:ottId": 607304, "^ot:ottTaxonName": "Megokris pescadoreensis"}, "otu24": {"^ot:originalLabel": "Trachysalambria starobogatovi", "^ot:ottId": 499908, "^ot:ottTaxonName": "Trachysalambria starobogatovi"}, "otu25": {"^ot:originalLabel": "Parapenaeopsis cornuta", "^ot:ottId": 138030, "^ot:ottTaxonName": "Parapenaeopsis cornuta"}, "otu26": {"^ot:originalLabel": "Metapenaeus ensis", "^ot:ottId": 680008, "^ot:ottTaxonName": "Metapenaeus ensis"}, "otu27": {"^ot:originalLabel": "Sicyonia lancifer", "^ot:ottId": 449924, "^ot:ottTaxonName": "Sicyonia lancifer"}, "otu28": {"^ot:originalLabel": "Metapenaeopsis provocatoria", "^ot:ottId": 376941, "^ot:ottTaxonName": "Metapenaeopsis provocatoria"}, "otu29": {"^ot:originalLabel": "Metapenaeopsis palmensis", "^ot:ottId": 376940, "^ot:ottTaxonName": "Metapenaeopsis palmensis"}, "otu3": {"^ot:originalLabel": "Fenneropenaeus chinensis", "^ot:ottId": 976415, "^ot:ottTaxonName": "Fenneropenaeus chinensis"}, "otu30": {"^ot:originalLabel": "Penaeopsis eduardoi", "^ot:ottId": 1009542, "^ot:ottTaxonName": "Penaeopsis eduardoi"}, "otu31": {"^ot:originalLabel": "Parapenaeus sextuberculatus", "^ot:ottId": 1083408, "^ot:ottTaxonName": "Parapenaeus sextuberculatus"}, "otu32": {"^ot:originalLabel": "Aristeus virilis", "^ot:ottId": 1026333, "^ot:ottTaxonName": "Aristeus virilis"}, "otu33": {"^ot:originalLabel": "Solenocera crassicornis", "^ot:ottId": 100840, "^ot:ottTaxonName": "Solenocera crassicornis"}, "otu4": {"^ot:originalLabel": "Penaeus esculentus", "^ot:ottId": 796554, "^ot:ottTaxonName": "Penaeus esculentus"}, "otu5": {"^ot:originalLabel": "Penaeus semiculatus", "^ot:ottId": 2971265, "^ot:ottTaxonName": "Penaeus semisculcatus"}, "otu6": {"^ot:originalLabel": "Penaeus monodon", "^ot:ottId": 212713, "^ot:ottTaxonName": "Penaeus monodon"}, "otu7": {"^ot:originalLabel": "Farfantepenaeus aztecus", "^ot:ottId": 736322, "^ot:ottTaxonName": "Farfantepenaeus aztecus"}, "otu8": {"^ot:originalLabel": "Farfantepenaeus duorarum", "^ot:ottId": 163894, "^ot:ottTaxonName": "Farfantepenaeus duorarum"}, "otu9": {"^ot:originalLabel": "Litopenaeus setiferus", "^ot:ottId": 163881, "^ot:ottTaxonName": "Litopenaeus setiferus"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "MrBayes 50% maj-rule con tree", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:substitutionCount", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node2", "^ot:messages": {"message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@id": "messageu885e99dc-2b61-47d4-b73b-b555027f4589", "@severity": "INFO", "@wasGeneratedBy": "opentree.2nexml", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "Penaeus_sl Bayesian consensus_con_edited.tre", "@size": 1993, "@sourceForTree": "tree1", "@type": "newick", "@url": "/curator/default/to_nexson?output=input&uploadid=u885e99dc-2b61-47d4-b73b-b555027f4589", "description": {"$": "Source data for tree 'tree1'"}}]}}}]}, "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": ["MrBayes", "MrBayes", "NaK", "MrBayes", "NaK", "PEPCK", "MrBayes", "NaK", "PEPCK", "Enolase", "MrBayes", "NaK", "PEPCK", "Enolase", "16S", "MrBayes", "NaK", "PEPCK", "Enolase", "16S", "12S"], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@length": 0.102701, "@source": "node1", "@target": "node2"}, "edge44": {"@length": 0.051351, "@source": "node1", "@target": "node45"}}, "node13": {"edge13": {"@length": 0.044856, "@source": "node13", "@target": "node14"}, "edge14": {"@length": 0.040039, "@source": "node13", "@target": "node15"}}, "node17": {"edge17": {"@length": 0.017175, "@source": "node17", "@target": "node18"}, "edge20": {"@length": 0.02714, "@source": "node17", "@target": "node21"}}, "node18": {"edge18": {"@length": 0.032704, "@source": "node18", "@target": "node19"}, "edge19": {"@length": 0.052336, "@source": "node18", "@target": "node20"}}, "node2": {"edge2": {"@length": 0.018738, "@source": "node2", "@target": "node3"}, "edge43": {"@length": 0.150747, "@source": "node2", "@target": "node44"}}, "node21": {"edge21": {"@length": 0.050401, "@source": "node21", "@target": "node22"}, "edge22": {"@length": 0.018679, "@source": "node21", "@target": "node23"}}, "node24": {"edge24": {"@length": 0.008962, "@source": "node24", "@target": "node25"}, "edge39": {"@length": 0.064255, "@source": "node24", "@target": "node40"}}, "node25": {"edge25": {"@length": 0.005107, "@source": "node25", "@target": "node26"}, "edge38": {"@length": 0.051668, "@source": "node25", "@target": "node39"}}, "node26": {"edge26": {"@length": 0.004536, "@source": "node26", "@target": "node27"}, "edge37": {"@length": 0.020354, "@source": "node26", "@target": "node38"}}, "node27": {"edge27": {"@length": 0.005719, "@source": "node27", "@target": "node28"}, "edge32": {"@length": 0.009072, "@source": "node27", "@target": "node33"}}, "node28": {"edge28": {"@length": 0.01041, "@source": "node28", "@target": "node29"}, "edge31": {"@length": 0.015247, "@source": "node28", "@target": "node32"}}, "node29": {"edge29": {"@length": 0.016054, "@source": "node29", "@target": "node30"}, "edge30": {"@length": 0.011847, "@source": "node29", "@target": "node31"}}, "node3": {"edge3": {"@length": 0.020015, "@source": "node3", "@target": "node4"}, "edge40": {"@length": 0.129661, "@source": "node3", "@target": "node41"}}, "node33": {"edge33": {"@length": 0.011901, "@source": "node33", "@target": "node34"}, "edge36": {"@length": 0.038641, "@source": "node33", "@target": "node37"}}, "node34": {"edge34": {"@length": 0.008535, "@source": "node34", "@target": "node35"}, "edge35": {"@length": 0.007686, "@source": "node34", "@target": "node36"}}, "node4": {"edge23": {"@length": 0.0475, "@source": "node4", "@target": "node24"}, "edge4": {"@length": 0.049584, "@source": "node4", "@target": "node5"}}, "node41": {"edge41": {"@length": 0.068653, "@source": "node41", "@target": "node42"}, "edge42": {"@length": 0.062183, "@source": "node41", "@target": "node43"}}, "node45": {"edge45": {"@length": 0.055994, "@source": "node45", "@target": "node46"}, "edge62": {"@length": 0.078612, "@source": "node45", "@target": "node63"}}, "node46": {"edge46": {"@length": 0.059991, "@source": "node46", "@target": "node47"}, "edge55": {"@length": 0.042167, "@source": "node46", "@target": "node56"}}, "node47": {"edge47": {"@length": 0.047178, "@source": "node47", "@target": "node48"}, "edge54": {"@length": 0.290249, "@source": "node47", "@target": "node55"}}, "node48": {"edge48": {"@length": 0.108466, "@source": "node48", "@target": "node49"}, "edge53": {"@length": 0.186739, "@source": "node48", "@target": "node54"}}, "node49": {"edge49": {"@length": 0.052255, "@source": "node49", "@target": "node50"}, "edge52": {"@length": 0.111629, "@source": "node49", "@target": "node53"}}, "node5": {"edge16": {"@length": 0.033747, "@source": "node5", "@target": "node17"}, "edge5": {"@length": 0.026262, "@source": "node5", "@target": "node6"}}, "node50": {"edge50": {"@length": 0.060841, "@source": "node50", "@target": "node51"}, "edge51": {"@length": 0.114327, "@source": "node50", "@target": "node52"}}, "node56": {"edge56": {"@length": 0.075161, "@source": "node56", "@target": "node57"}, "edge59": {"@length": 0.025968, "@source": "node56", "@target": "node60"}}, "node57": {"edge57": {"@length": 0.06588, "@source": "node57", "@target": "node58"}, "edge58": {"@length": 0.067275, "@source": "node57", "@target": "node59"}}, "node6": {"edge15": {"@length": 0.062689, "@source": "node6", "@target": "node16"}, "edge6": {"@length": 0.008432, "@source": "node6", "@target": "node7"}}, "node60": {"edge60": {"@length": 0.061209, "@source": "node60", "@target": "node61"}, "edge61": {"@length": 0.066869, "@source": "node60", "@target": "node62"}}, "node63": {"edge63": {"@length": 0.253536, "@source": "node63", "@target": "node64"}, "edge64": {"@length": 0.274457, "@source": "node63", "@target": "node65"}}, "node7": {"edge12": {"@length": 0.014483, "@source": "node7", "@target": "node13"}, "edge7": {"@length": 0.031784, "@source": "node7", "@target": "node8"}}, "node8": {"edge11": {"@length": 0.021578, "@source": "node8", "@target": "node12"}, "edge8": {"@length": 0.021782, "@source": "node8", "@target": "node9"}}, "node9": {"edge10": {"@length": 0.006796, "@source": "node9", "@target": "node11"}, "edge9": {"@length": 0.006769, "@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {"@otu": "otu1"}, "node11": {"@otu": "otu2"}, "node12": {"@otu": "otu3"}, "node13": {}, "node14": {"@otu": "otu4"}, "node15": {"@otu": "otu5"}, "node16": {"@otu": "otu6"}, "node17": {}, "node18": {}, "node19": {"@otu": "otu7"}, "node2": {}, "node20": {"@otu": "otu8"}, "node21": {}, "node22": {"@otu": "otu9"}, "node23": {"@otu": "otu10"}, "node24": {}, "node25": {}, "node26": {}, "node27": {}, "node28": {}, "node29": {}, "node3": {}, "node30": {"@otu": "otu11"}, "node31": {"@otu": "otu12"}, "node32": {"@otu": "otu13"}, "node33": {}, "node34": {}, "node35": {"@otu": "otu14"}, "node36": {"@otu": "otu15"}, "node37": {"@otu": "otu16"}, "node38": {"@otu": "otu17"}, "node39": {"@otu": "otu18"}, "node4": {}, "node40": {"@otu": "otu19"}, "node41": {}, "node42": {"@otu": "otu20"}, "node43": {"@otu": "otu21"}, "node44": {"@otu": "otu22"}, "node45": {}, "node46": {}, "node47": {}, "node48": {}, "node49": {}, "node5": {}, "node50": {}, "node51": {"@otu": "otu23"}, "node52": {"@otu": "otu24"}, "node53": {"@otu": "otu25"}, "node54": {"@otu": "otu26"}, "node55": {"@otu": "otu27"}, "node56": {}, "node57": {}, "node58": {"@otu": "otu28"}, "node59": {"@otu": "otu29"}, "node6": {}, "node60": {}, "node61": {"@otu": "otu30"}, "node62": {"@otu": "otu31"}, "node63": {}, "node64": {"@otu": "otu32"}, "node65": {"@otu": "otu33"}, "node7": {}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "6bed60428352c04d00341ad513a8efb9442e4d8a"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "eeacea98f0c905122d3bf06801c67f3754ecca76", "author_name": "chris-owen", "author_email": "EMAIL_NOT_PROVIDED", "date": "Wed, 30 Jul 2014 16:09:48 +0000", "date_ISO_8601": "2014-07-30 16:09:48 +0000", "relative_date": "12 years ago", "message_subject": "ingroups added, rooted, 3 terminals not mapping", "message_body": "Checked the three terminals in WoRMS and the valid names are not in the current version of the OTT taxonomy.\n\n(Update Study #ot_114 via OpenTree API)"}, {"id": "f91c1b343c4d0c09cf36042da06b3a04e0430133", "author_name": "chris-owen", "author_email": "EMAIL_NOT_PROVIDED", "date": "Wed, 30 Jul 2014 16:06:52 +0000", "date_ISO_8601": "2014-07-30 16:06:52 +0000", "relative_date": "12 years ago", "message_subject": "ingroups added, rooted, 3 terminals not mapping", "message_body": "Checked the three terminals in WoRMS and the valid names are not in the current version of the OTT taxonomy.\n\n(Update Study #ot_114 via OpenTree API)"}, {"id": "17a4c21aca880ef7d99efca83b9c4bd408fcc890", "author_name": "chris-owen", "author_email": "EMAIL_NOT_PROVIDED", "date": "Wed, 30 Jul 2014 15:53:44 +0000", "date_ISO_8601": "2014-07-30 15:53:44 +0000", "relative_date": "12 years ago", "message_subject": "Update Study #ot_114 via OpenTree API"}]}