{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2016-02-22T17:28:32.108Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2016-02-22T17:28:32.108Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "coral_barnacles-Simon-Blecher-2007.tre", "@size": 667, "@type": "newick", "@url": "/curator/download/supporting_files.doc.8353f083591220ea.636f72616c5f6261726e61636c65732d53696d6f6e2d426c65636865722d323030372e747265.tre", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "coral_barnacles-Simon-Blecher-2007.tre", "@size": 667, "@type": "newick", "@url": "/curator/download/supporting_files.doc.885b309ea4f2374c.636f72616c5f6261726e61636c65732d53696d6f6e2d426c65636865722d323030372e747265.tre", "description": {"$": "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": "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:focalCladeOTTTaxonName": "", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_640", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2007.03.026"}, "^ot:studyPublicationReference": "N. Simon-Blecher, D. Huchon, Y. Achituv, 2007, 'Phylogeny of coral-inhabiting barnacles (Cirripedia; Thoracica; Pyrgomatidae) based on 12S, 16S and 18S rDNA analysis', Molecular Phylogenetics and Evolution, vol. 44, no. 3, pp. 1333-1341", "^ot:studyYear": 2007, "^ot:tag": [], "^ot:treesElementOrder": ["trees1"], "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "Neotrevathana elongatum", "^ot:ottId": 1013019, "^ot:ottTaxonName": "Neotrevathana elongatum"}, "otu10": {"^ot:originalLabel": "Nobia grandis", "^ot:ottId": 472040, "^ot:ottTaxonName": "Nobia grandis"}, "otu11": {"^ot:originalLabel": "Cantellius palidus", "^ot:ottId": 472001, "^ot:ottTaxonName": "Cantellius pallidus"}, "otu12": {"^ot:originalLabel": "Armatobalanus allium", "^ot:ottId": 562531, "^ot:ottTaxonName": "Armatobalanus allium"}, "otu13": {"^ot:originalLabel": "Ceratochoncha domingensis", "^ot:ottId": 1008117, "^ot:ottTaxonName": "Ceratoconcha domingensis"}, "otu14": {"^ot:originalLabel": "Megatrema anglicum", "^ot:ottId": 2958463, "^ot:ottTaxonName": "Adna anglica"}, "otu15": {"^ot:originalLabel": "Menesiniella aquila", "^ot:ottId": 203265, "^ot:ottTaxonName": "Menesiniella aquila"}, "otu16": {"^ot:originalLabel": "Wanella milleporae", "^ot:ottId": 580631, "^ot:ottTaxonName": "Wanella milleporae"}, "otu17": {"^ot:originalLabel": "Balanus perforatus", "^ot:ottId": 142403, "^ot:ottTaxonName": "Perforatus perforatus"}, "otu18": {"^ot:originalLabel": "Balanus balanus", "^ot:ottId": 323642, "^ot:ottTaxonName": "Balanus balanus"}, "otu19": {"^ot:originalLabel": "Balanus crenatus", "^ot:ottId": 259517, "^ot:ottTaxonName": "Balanus crenatus"}, "otu2": {"^ot:originalLabel": "Pyrgopsella youngii", "^ot:ottId": 826819, "^ot:ottTaxonName": "Pyrgopsella youngi"}, "otu20": {"^ot:originalLabel": "Balanus glandula", "^ot:ottId": 404546, "^ot:ottTaxonName": "Balanus glandula"}, "otu21": {"^ot:originalLabel": "Semibalanus balanoides", "^ot:ottId": 374192, "^ot:ottTaxonName": "Semibalanus balanoides"}, "otu22": {"^ot:originalLabel": "Semibalanus cariosus", "^ot:ottId": 949511, "^ot:ottTaxonName": "Semibalanus cariosus"}, "otu23": {"^ot:originalLabel": "Austromegabalanus psittacus", "^ot:ottId": 324426, "^ot:ottTaxonName": "Austromegabalanus psittacus"}, "otu24": {"^ot:originalLabel": "Megabalanus spinosus", "^ot:ottId": 324425, "^ot:ottTaxonName": "Megabalanus spinosus"}, "otu25": {"^ot:originalLabel": "Megabalanus stultus", "^ot:ottId": 436304, "^ot:ottTaxonName": "Megabalanus stultus"}, "otu26": {"^ot:originalLabel": "Megabalanus tintinnabulum", "^ot:ottId": 203266, "^ot:ottTaxonName": "Megabalanus tintinnabulum"}, "otu27": {"^ot:originalLabel": "Megabalanus californicus", "^ot:ottId": 404551, "^ot:ottTaxonName": "Megabalanus californicus"}, "otu28": {"^ot:originalLabel": "Elminius modestus", "^ot:ottId": 664816, "^ot:ottTaxonName": "Elminius modestus"}, "otu29": {"^ot:originalLabel": "Elminius kingi", "^ot:ottId": 898719, "^ot:ottTaxonName": "Elminius kingii"}, "otu3": {"^ot:originalLabel": "Trevathana dentata", "^ot:ottId": 588449, "^ot:ottTaxonName": "Trevathana dentata"}, "otu30": {"^ot:originalLabel": "Tetraclita squamosa", "^ot:ottId": 680010, "^ot:ottTaxonName": "Tetraclita squamosa"}, "otu31": {"^ot:originalLabel": "Tetraclita japonica", "^ot:ottId": 221273, "^ot:ottTaxonName": "Tetraclita japonica"}, "otu4": {"^ot:originalLabel": "Hoekia", "^ot:ottId": 826812, "^ot:ottTaxonName": "Hoekia"}, "otu5": {"^ot:originalLabel": "Savignium crenatum", "^ot:ottId": 680018, "^ot:ottTaxonName": "Savignium crenatum"}, "otu6": {"^ot:originalLabel": "Darwiniella conjugatum", "^ot:ottId": 148174, "^ot:ottTaxonName": "Darwiniella conjugatum"}, "otu7": {"^ot:originalLabel": "Hiroa stubbingsi", "^ot:ottId": 588438, "^ot:ottTaxonName": "Hiroa stubbingsi"}, "otu8": {"^ot:originalLabel": "Creusia indica", "^ot:ottId": 2958456, "^ot:ottTaxonName": "Creusia indicum"}, "otu9": {"^ot:originalLabel": "Pyrgoma cancellata", "^ot:ottId": 580651, "^ot:ottTaxonName": "Pyrgoma cancellatum"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1"], "treeById": {"tree1": {"@label": "Fig. 2", "@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"}, "edge58": {"@source": "node1", "@target": "node59"}}, "node10": {"edge10": {"@source": "node10", "@target": "node11"}, "edge13": {"@source": "node10", "@target": "node14"}}, "node11": {"edge11": {"@source": "node11", "@target": "node12"}, "edge12": {"@source": "node11", "@target": "node13"}}, "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"}, "edge55": {"@source": "node2", "@target": "node56"}}, "node24": {"edge24": {"@source": "node24", "@target": "node25"}, "edge27": {"@source": "node24", "@target": "node28"}}, "node25": {"edge25": {"@source": "node25", "@target": "node26"}, "edge26": {"@source": "node25", "@target": "node27"}}, "node28": {"edge28": {"@source": "node28", "@target": "node29"}, "edge29": {"@source": "node28", "@target": "node30"}}, "node3": {"edge3": {"@source": "node3", "@target": "node4"}, "edge30": {"@source": "node3", "@target": "node31"}}, "node31": {"edge31": {"@source": "node31", "@target": "node32"}, "edge34": {"@source": "node31", "@target": "node35"}}, "node32": {"edge32": {"@source": "node32", "@target": "node33"}, "edge33": {"@source": "node32", "@target": "node34"}}, "node35": {"edge35": {"@source": "node35", "@target": "node36"}, "edge38": {"@source": "node35", "@target": "node39"}}, "node36": {"edge36": {"@source": "node36", "@target": "node37"}, "edge37": {"@source": "node36", "@target": "node38"}}, "node39": {"edge39": {"@source": "node39", "@target": "node40"}, "edge46": {"@source": "node39", "@target": "node47"}}, "node4": {"edge23": {"@source": "node4", "@target": "node24"}, "edge4": {"@source": "node4", "@target": "node5"}}, "node40": {"edge40": {"@source": "node40", "@target": "node41"}, "edge43": {"@source": "node40", "@target": "node44"}}, "node41": {"edge41": {"@source": "node41", "@target": "node42"}, "edge42": {"@source": "node41", "@target": "node43"}}, "node44": {"edge44": {"@source": "node44", "@target": "node45"}, "edge45": {"@source": "node44", "@target": "node46"}}, "node47": {"edge47": {"@source": "node47", "@target": "node48"}, "edge48": {"@source": "node47", "@target": "node49"}}, "node49": {"edge49": {"@source": "node49", "@target": "node50"}, "edge50": {"@source": "node49", "@target": "node51"}}, "node5": {"edge22": {"@source": "node5", "@target": "node23"}, "edge5": {"@source": "node5", "@target": "node6"}}, "node51": {"edge51": {"@source": "node51", "@target": "node52"}, "edge52": {"@source": "node51", "@target": "node53"}}, "node53": {"edge53": {"@source": "node53", "@target": "node54"}, "edge54": {"@source": "node53", "@target": "node55"}}, "node56": {"edge56": {"@source": "node56", "@target": "node57"}, "edge57": {"@source": "node56", "@target": "node58"}}, "node59": {"edge59": {"@source": "node59", "@target": "node60"}, "edge60": {"@source": "node59", "@target": "node61"}}, "node6": {"edge21": {"@source": "node6", "@target": "node22"}, "edge6": {"@source": "node6", "@target": "node7"}}, "node7": {"edge16": {"@source": "node7", "@target": "node17"}, "edge7": {"@source": "node7", "@target": "node8"}}, "node8": {"edge15": {"@source": "node8", "@target": "node16"}, "edge8": {"@source": "node8", "@target": "node9"}}, "node9": {"edge14": {"@source": "node9", "@target": "node15"}, "edge9": {"@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {}, "node12": {"@otu": "otu1"}, "node13": {"@otu": "otu2"}, "node14": {"@otu": "otu3"}, "node15": {"@otu": "otu4"}, "node16": {"@otu": "otu5"}, "node17": {}, "node18": {}, "node19": {"@otu": "otu6"}, "node2": {}, "node20": {"@otu": "otu7"}, "node21": {"@otu": "otu8"}, "node22": {"@otu": "otu9"}, "node23": {"@otu": "otu10"}, "node24": {}, "node25": {}, "node26": {"@otu": "otu11"}, "node27": {"@otu": "otu12"}, "node28": {}, "node29": {"@otu": "otu13"}, "node3": {}, "node30": {"@otu": "otu14"}, "node31": {}, "node32": {}, "node33": {"@otu": "otu15"}, "node34": {"@otu": "otu16"}, "node35": {}, "node36": {}, "node37": {"@otu": "otu17"}, "node38": {"@otu": "otu18"}, "node39": {}, "node4": {}, "node40": {}, "node41": {}, "node42": {"@otu": "otu19"}, "node43": {"@otu": "otu20"}, "node44": {}, "node45": {"@otu": "otu21"}, "node46": {"@otu": "otu22"}, "node47": {}, "node48": {"@otu": "otu23"}, "node49": {}, "node5": {}, "node50": {"@otu": "otu24"}, "node51": {}, "node52": {"@otu": "otu25"}, "node53": {}, "node54": {"@otu": "otu26"}, "node55": {"@otu": "otu27"}, "node56": {}, "node57": {"@otu": "otu28"}, "node58": {"@otu": "otu29"}, "node59": {}, "node6": {}, "node60": {"@otu": "otu30"}, "node61": {"@otu": "otu31"}, "node7": {}, "node8": {}, "node9": {}}}}}}}}, "branch2sha": {"master": "6bed60428352c04d00341ad513a8efb9442e4d8a"}, "commentHTML": "<p>Tree reconstructed manually from PDF in publication</p>", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "148e32e91e84b3f314bba9352b6de110326a7a91", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Tue, 23 Feb 2016 14:25:20 +0000", "date_ISO_8601": "2016-02-23 14:25:20 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_640' via OpenTree API"}, {"id": "484ae0b73095fe55af98769f01c5e4e3db0697dd", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Mon, 22 Feb 2016 17:37:05 +0000", "date_ISO_8601": "2016-02-22 17:37:05 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_640' via OpenTree API"}, {"id": "09f6338866f7b3d7a9ed5c677e4e2446174ef850", "author_name": "Christine Ewers-Saucedo", "author_email": "ANONYMOUS", "date": "Mon, 22 Feb 2016 17:28:30 +0000", "date_ISO_8601": "2016-02-22 17:28:30 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_640' via OpenTree API"}]}