{"sha": "24afc85a444963f10ca51c6e20138fe592a4b525", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@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#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}]}, "^ot:annotationEvents": {"annotation": [{"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:dataDeposit"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6244"], "^ot:curatorName": "Joseph Brown", "^ot:focalClade": 872571, "^ot:focalCladeOTTTaxonName": "Procyonidae", "^ot:messages": {"message": []}, "^ot:otusElementOrder": ["otus2691"], "^ot:studyId": "pg_2691", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2006.10.003"}, "^ot:studyPublicationReference": "Koepfli, Klaus-Peter, Matthew E. Gompper, Eduardo Eizirik, Cheuk-Chung Ho, Leif Linden, Jesus E. Maldonado, Robert K. Wayne. 2007. Phylogeny of the Procyonidae (Mammalia: Carnivora): Molecules, morphology and the Great American Interchange. Molecular Phylogenetics and Evolution 43 (3): 1076-1095.", "^ot:studyYear": 2007, "^ot:tag": ["ingroup added;"], "^ot:treesElementOrder": ["trees2691"], "otusById": {"otus2691": {"otuById": {"otu404428": {"^ot:originalLabel": "Bassaricyon alleni", "^ot:ottId": 794090, "^ot:ottTaxonName": "Bassaricyon alleni"}, "otu404429": {"^ot:originalLabel": "Bassaricyon gabbii", "^ot:ottId": 178244, "^ot:ottTaxonName": "Bassaricyon gabbii"}, "otu404430": {"^ot:originalLabel": "Nasua narica", "^ot:ottId": 736280, "^ot:ottTaxonName": "Nasua narica"}, "otu404431": {"^ot:originalLabel": "Nasua nasua", "^ot:ottId": 348031, "^ot:ottTaxonName": "Nasua nasua"}, "otu404432": {"^ot:originalLabel": "Bassariscus astutus", "^ot:ottId": 685103, "^ot:ottTaxonName": "Bassariscus astutus"}, "otu404433": {"^ot:originalLabel": "Bassariscus sumichrasti", "^ot:ottId": 794088, "^ot:ottTaxonName": "Bassariscus sumichrasti"}, "otu404434": {"^ot:originalLabel": "Procyon cancrivorus", "^ot:ottId": 914060, "^ot:ottTaxonName": "Procyon cancrivorus"}, "otu404435": {"^ot:originalLabel": "Procyon lotor", "^ot:ottId": 348040, "^ot:ottTaxonName": "Procyon lotor"}, "otu404436": {"^ot:originalLabel": "Potos flavus", "^ot:ottId": 532115, "^ot:ottTaxonName": "Potos flavus"}, "otu404437": {"^ot:originalLabel": "Enhydra lutris", "^ot:ottId": 949676, "^ot:ottTaxonName": "Enhydra lutris"}, "otu404438": {"^ot:originalLabel": "Mustela vison", "^ot:ottId": 310482, "^ot:ottTaxonName": "Neovison vison"}, "otu404439": {"^ot:originalLabel": "Eira barbara", "^ot:ottId": 381140, "^ot:ottTaxonName": "Eira barbara"}, "otu404440": {"^ot:originalLabel": "Martes americana", "^ot:ottId": 923116, "^ot:ottTaxonName": "Martes americana"}, "otu404441": {"^ot:originalLabel": "Taxidea taxus", "^ot:ottId": 754612, "^ot:ottTaxonName": "Taxidea taxus"}}}}, "treesById": {"trees2691": {"@otus": "otus2691", "^ot:treeElementOrder": ["tree6244"], "treeById": {"tree6244": {"@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:substitutionCount", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "ML Figure 3", "^ot:inGroupClade": "node1082774", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1082773", "^ot:specifiedRoot": "node1082773", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1082773": {"edge1082774": {"@length": 0.0168896, "@source": "node1082773", "@target": "node1082774"}, "edge1082791": {"@length": 0.03147409, "@source": "node1082773", "@target": "node1082791"}}, "node1082774": {"edge1082775": {"@length": 0.01115513, "@source": "node1082774", "@target": "node1082775"}, "edge1082790": {"@length": 0.0521521, "@source": "node1082774", "@target": "node1082790"}}, "node1082775": {"edge1082776": {"@length": 0.02251364, "@source": "node1082775", "@target": "node1082776"}, "edge1082783": {"@length": 0.02225259, "@source": "node1082775", "@target": "node1082783"}}, "node1082776": {"edge1082777": {"@length": 0.03114829, "@source": "node1082776", "@target": "node1082777"}, "edge1082780": {"@length": 0.01675044, "@source": "node1082776", "@target": "node1082780"}}, "node1082777": {"edge1082778": {"@length": 0.00500745, "@source": "node1082777", "@target": "node1082778"}, "edge1082779": {"@length": 0.01014452, "@source": "node1082777", "@target": "node1082779"}}, "node1082780": {"edge1082781": {"@length": 0.02316188, "@source": "node1082780", "@target": "node1082781"}, "edge1082782": {"@length": 0.02463492, "@source": "node1082780", "@target": "node1082782"}}, "node1082783": {"edge1082784": {"@length": 0.00630388, "@source": "node1082783", "@target": "node1082784"}, "edge1082787": {"@length": 0.02072755, "@source": "node1082783", "@target": "node1082787"}}, "node1082784": {"edge1082785": {"@length": 0.02792289, "@source": "node1082784", "@target": "node1082785"}, "edge1082786": {"@length": 0.02410137, "@source": "node1082784", "@target": "node1082786"}}, "node1082787": {"edge1082788": {"@length": 0.0146898, "@source": "node1082787", "@target": "node1082788"}, "edge1082789": {"@length": 0.01565509, "@source": "node1082787", "@target": "node1082789"}}, "node1082791": {"edge1082792": {"@length": 0.00994685, "@source": "node1082791", "@target": "node1082792"}, "edge1082799": {"@length": 0.03571379, "@source": "node1082791", "@target": "node1082799"}}, "node1082792": {"edge1082793": {"@length": 0.01026126, "@source": "node1082792", "@target": "node1082793"}, "edge1082796": {"@length": 0.00907937, "@source": "node1082792", "@target": "node1082796"}}, "node1082793": {"edge1082794": {"@length": 0.03045966, "@source": "node1082793", "@target": "node1082794"}, "edge1082795": {"@length": 0.04026155, "@source": "node1082793", "@target": "node1082795"}}, "node1082796": {"edge1082797": {"@length": 0.0309547, "@source": "node1082796", "@target": "node1082797"}, "edge1082798": {"@length": 0.02856543, "@source": "node1082796", "@target": "node1082798"}}}, "nodeById": {"node1082773": {"@root": true}, "node1082774": {}, "node1082775": {}, "node1082776": {}, "node1082777": {}, "node1082778": {"@otu": "otu404428"}, "node1082779": {"@otu": "otu404429"}, "node1082780": {}, "node1082781": {"@otu": "otu404430"}, "node1082782": {"@otu": "otu404431"}, "node1082783": {}, "node1082784": {}, "node1082785": {"@otu": "otu404432"}, "node1082786": {"@otu": "otu404433"}, "node1082787": {}, "node1082788": {"@otu": "otu404434"}, "node1082789": {"@otu": "otu404435"}, "node1082790": {"@otu": "otu404436"}, "node1082791": {}, "node1082792": {}, "node1082793": {}, "node1082794": {"@otu": "otu404437"}, "node1082795": {"@otu": "otu404438"}, "node1082796": {}, "node1082797": {"@otu": "otu404439"}, "node1082798": {"@otu": "otu404440"}, "node1082799": {"@otu": "otu404441"}}}}}}}}, "branch2sha": {"master": "24afc85a444963f10ca51c6e20138fe592a4b525"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "d33fb39501605772a074dffc82affa5344ea9a94", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Wed, 11 Jun 2014 22:18:34 -0500", "date_ISO_8601": "2014-06-11 22:18:34 -0500", "relative_date": "12 years ago", "message_subject": "corrected study ids"}, {"id": "f8a738aeda20a73750847484e110a85c7a3e0a12", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 10 Jun 2014 23:36:42 -0500", "date_ISO_8601": "2014-06-10 23:36:42 -0500", "relative_date": "12 years ago", "message_subject": "Migrating info from gcmdr to nexsons", "message_body": "using peyotl d69c8b180fce7703c7203a0b51712eab57e2988c\ndev/decorate_pg_studies_with_gcmdr_info.py\nto set:\n  ^ot:candidateTreeForSynthesis\n  ^ot:specifiedRoot, and\n  ^ot:unrootedTree\nproperties based on the use of the trees for synthesis study\nlists in gcmdr commit 35bf307e72bed4f59724762dde4a12965abcea92"}, {"id": "593d6fbab385716dc0a12f3fc95133e8b7479b37", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Tue, 29 Apr 2014 20:05:19 -0500", "date_ISO_8601": "2014-04-29 20:05:19 -0500", "relative_date": "12 years ago", "message_subject": "initial commit with phylografter files from 29 Apr, 2014"}]}