{"sha": "1bbbe21bdd9a32ef81abeb3f038a977fdc0e8e7b", "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": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu221819", "otu221842"], "refersTo": {"@top": "otus", "@idref": "otus1094", "@otusID": "otus1094"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu221822", "otu221840"], "refersTo": {"@top": "otus", "@idref": "otus1094", "@otusID": "otus1094"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu221831", "otu221833"], "refersTo": {"@top": "otus", "@idref": "otus1094", "@otusID": "otus1094"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:inGroupClade"], "refersTo": {"@top": "trees", "@idref": "tree2138", "@treesID": "trees1094", "@treeID": "tree2138"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree2138"], "^ot:curatorName": "bryan drew", "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S749"}, "^ot:focalClade": 266257, "^ot:focalCladeOTTTaxonName": "Sarcostemma", "^ot:messages": {"message": []}, "^ot:otusElementOrder": ["otus1094"], "^ot:studyId": "pg_1094", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1007/BF00985463"}, "^ot:studyPublicationReference": "Liede S., & Tuber A. 2000. Sarcostemma R. Br. (Apocynaceae - Asclepiadoideae) - a Controversial Generic Circumscription Reconsidered: Evidence from trnL-F Spacers. Plant Systematics and Evolution, 225: 133-140.", "^ot:studyYear": 2000, "^ot:tag": [], "^ot:treesElementOrder": ["trees1094"], "otusById": {"otus1094": {"otuById": {"otu221817": {"^ot:originalLabel": "Folotsia grandiflora", "^ot:ottId": 795391, "^ot:ottTaxonName": "Cynanchum grandidieri", "^ot:treebaseOTUId": "Tl123525"}, "otu221818": {"^ot:originalLabel": "Gomphocarpus physocarpus", "^ot:ottId": 316628, "^ot:ottTaxonName": "Gomphocarpus physocarpus", "^ot:treebaseOTUId": "Tl123526"}, "otu221819": {"^ot:originalLabel": "Philibertia gilliesii 3098", "^ot:ottId": 640598, "^ot:ottTaxonName": "Philibertia gilliesii", "^ot:treebaseOTUId": "Tl123527"}, "otu221820": {"^ot:originalLabel": "Platykeleba insignis", "^ot:ottId": 266258, "^ot:ottTaxonName": "Cynanchum insigne", "^ot:treebaseOTUId": "Tl123528"}, "otu221821": {"^ot:originalLabel": "Cynanchum montevidense", "^ot:ottId": 795386, "^ot:ottTaxonName": "Cynanchum montevidense", "^ot:treebaseOTUId": "Tl123529"}, "otu221822": {"^ot:originalLabel": "Funastrum clausum 2958", "^ot:ottId": 947315, "^ot:ottTaxonName": "Funastrum clausum", "^ot:treebaseOTUId": "Tl123530"}, "otu221823": {"^ot:originalLabel": "Philibertia vaileae", "^ot:ottId": 640580, "^ot:ottTaxonName": "Philibertia picta", "^ot:treebaseOTUId": "Tl123532"}, "otu221824": {"^ot:originalLabel": "Karimbolea verrucosa", "^ot:ottId": 840963, "^ot:ottTaxonName": "Cynanchum verrucosum", "^ot:treebaseOTUId": "Tl123533"}, "otu221825": {"^ot:originalLabel": "Blepharodon grandiflorum", "^ot:ottId": 891044, "^ot:ottTaxonName": "Blepharodon grandiflorum", "^ot:treebaseOTUId": "Tl123534"}, "otu221826": {"^ot:originalLabel": "Funastrum elegans 2605", "^ot:ottId": 795395, "^ot:ottTaxonName": "Funastrum elegans", "^ot:treebaseOTUId": "Tl123535"}, "otu221827": {"^ot:originalLabel": "Cynanchum nummulariaefolium", "^ot:ottId": 795379, "^ot:ottTaxonName": "Diplolepis nummulariifolia", "^ot:treebaseOTUId": "Tl123536"}, "otu221828": {"^ot:originalLabel": "Blepharodon mucronatum", "^ot:ottId": 891057, "^ot:ottTaxonName": "Blepharodon mucronatum", "^ot:treebaseOTUId": "Tl123537"}, "otu221829": {"^ot:originalLabel": "Pergularia daemia", "^ot:ottId": 334782, "^ot:ottTaxonName": "Pergularia daemia", "^ot:treebaseOTUId": "Tl123538"}, "otu221830": {"^ot:originalLabel": "Philibertia lysimachioides", "^ot:ottId": 640571, "^ot:ottTaxonName": "Philibertia lysimachioides", "^ot:treebaseOTUId": "Tl123539"}, "otu221831": {"^ot:originalLabel": "Funastrum odoratum 2575", "^ot:ottId": 316627, "^ot:ottTaxonName": "Funastrum odoratum", "^ot:treebaseOTUId": "Tl123541"}, "otu221832": {"^ot:originalLabel": "Oxystelma bornouense", "^ot:ottId": 840968, "^ot:ottTaxonName": "Oxystelma bornouense", "^ot:treebaseOTUId": "Tl123542"}, "otu221833": {"^ot:originalLabel": "Funastrum odoratum 2560", "^ot:ottId": 316627, "^ot:ottTaxonName": "Funastrum odoratum", "^ot:treebaseOTUId": "Tl123543"}, "otu221834": {"^ot:originalLabel": "Pentacyphus lehmannii", "^ot:ottId": 640596, "^ot:ottTaxonName": "Pentacyphus lehmannii", "^ot:treebaseOTUId": "Tl123544"}, "otu221835": {"^ot:originalLabel": "Cynanchum ellipticum", "^ot:ottId": 891062, "^ot:ottTaxonName": "Cynanchum ellipticum", "^ot:treebaseOTUId": "Tl123545"}, "otu221836": {"^ot:originalLabel": "Sarcostemma pearsonii", "^ot:ottId": 266255, "^ot:ottTaxonName": "Sarcostemma pearsonii", "^ot:treebaseOTUId": "Tl123546"}, "otu221837": {"^ot:originalLabel": "Oxystelma esculentum", "^ot:ottId": 840969, "^ot:ottTaxonName": "Oxystelma esculentum", "^ot:treebaseOTUId": "Tl123547"}, "otu221838": {"^ot:originalLabel": "Sarcostemma viminale", "^ot:ottId": 266268, "^ot:ottTaxonName": "Cynanchum viminale", "^ot:treebaseOTUId": "Tl123548"}, "otu221839": {"^ot:originalLabel": "Funastrum arenarium", "^ot:ottId": 316625, "^ot:ottTaxonName": "Funastrum arenarium", "^ot:treebaseOTUId": "Tl123549"}, "otu221840": {"^ot:originalLabel": "Funastrum clausum 2599", "^ot:ottId": 947315, "^ot:ottTaxonName": "Funastrum clausum", "^ot:treebaseOTUId": "Tl123550"}, "otu221841": {"^ot:originalLabel": "Cynanchum compactum", "^ot:ottId": 891060, "^ot:ottTaxonName": "Cynanchum compactum", "^ot:treebaseOTUId": "Tl123551"}, "otu221842": {"^ot:originalLabel": "Philibertia gilliesii 3054", "^ot:ottId": 640598, "^ot:ottTaxonName": "Philibertia gilliesii", "^ot:treebaseOTUId": "Tl123552"}, "otu221843": {"^ot:originalLabel": "Tylophora flexuosa perr", "^ot:ottId": 223271, "^ot:ottTaxonName": "Tylophora flexuosa", "^ot:treebaseOTUId": "Tl56952"}, "otu221844": {"^ot:originalLabel": "Gymnema sylvestris", "^ot:ottId": 809613, "^ot:ottTaxonName": "Gymnema sylvestre", "^ot:treebaseOTUId": "Tl56954"}}}}, "treesById": {"trees1094": {"@otus": "otus1094", "^ot:treeElementOrder": ["tree2138"], "treeById": {"tree2138": {"@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Fig. 1", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node527799", "^ot:specifiedRoot": "node527799", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node527799": {"edge527800": {"@source": "node527799", "@target": "node527800"}, "edge527801": {"@source": "node527799", "@target": "node527801"}}, "node527801": {"edge527802": {"@source": "node527801", "@target": "node527802"}, "edge527805": {"@source": "node527801", "@target": "node527805"}, "edge527806": {"@source": "node527801", "@target": "node527806"}, "edge527831": {"@source": "node527801", "@target": "node527831"}, "edge527843": {"@source": "node527801", "@target": "node527843"}}, "node527802": {"edge527803": {"@source": "node527802", "@target": "node527803"}, "edge527804": {"@source": "node527802", "@target": "node527804"}}, "node527806": {"edge527807": {"@source": "node527806", "@target": "node527807"}, "edge527830": {"@source": "node527806", "@target": "node527830"}}, "node527807": {"edge527808": {"@source": "node527807", "@target": "node527808"}, "edge527809": {"@source": "node527807", "@target": "node527809"}}, "node527809": {"edge527810": {"@source": "node527809", "@target": "node527810"}, "edge527819": {"@source": "node527809", "@target": "node527819"}}, "node527810": {"edge527811": {"@source": "node527810", "@target": "node527811"}, "edge527814": {"@source": "node527810", "@target": "node527814"}}, "node527811": {"edge527812": {"@source": "node527811", "@target": "node527812"}, "edge527813": {"@source": "node527811", "@target": "node527813"}}, "node527814": {"edge527815": {"@source": "node527814", "@target": "node527815"}, "edge527816": {"@source": "node527814", "@target": "node527816"}, "edge527817": {"@source": "node527814", "@target": "node527817"}, "edge527818": {"@source": "node527814", "@target": "node527818"}}, "node527819": {"edge527820": {"@source": "node527819", "@target": "node527820"}, "edge527827": {"@source": "node527819", "@target": "node527827"}}, "node527820": {"edge527821": {"@source": "node527820", "@target": "node527821"}, "edge527822": {"@source": "node527820", "@target": "node527822"}}, "node527822": {"edge527823": {"@source": "node527822", "@target": "node527823"}, "edge527824": {"@source": "node527822", "@target": "node527824"}}, "node527824": {"edge527825": {"@source": "node527824", "@target": "node527825"}, "edge527826": {"@source": "node527824", "@target": "node527826"}}, "node527827": {"edge527828": {"@source": "node527827", "@target": "node527828"}, "edge527829": {"@source": "node527827", "@target": "node527829"}}, "node527831": {"edge527832": {"@source": "node527831", "@target": "node527832"}, "edge527833": {"@source": "node527831", "@target": "node527833"}, "edge527834": {"@source": "node527831", "@target": "node527834"}}, "node527834": {"edge527835": {"@source": "node527834", "@target": "node527835"}, "edge527838": {"@source": "node527834", "@target": "node527838"}, "edge527839": {"@source": "node527834", "@target": "node527839"}, "edge527840": {"@source": "node527834", "@target": "node527840"}}, "node527835": {"edge527836": {"@source": "node527835", "@target": "node527836"}, "edge527837": {"@source": "node527835", "@target": "node527837"}}, "node527840": {"edge527841": {"@source": "node527840", "@target": "node527841"}, "edge527842": {"@source": "node527840", "@target": "node527842"}}, "node527843": {"edge527844": {"@source": "node527843", "@target": "node527844"}, "edge527845": {"@source": "node527843", "@target": "node527845"}}}, "nodeById": {"node527799": {"@root": true}, "node527800": {"@otu": "otu221844"}, "node527801": {}, "node527802": {}, "node527803": {"@otu": "otu221818"}, "node527804": {"@otu": "otu221829"}, "node527805": {"@otu": "otu221843"}, "node527806": {}, "node527807": {}, "node527808": {"@otu": "otu221827"}, "node527809": {}, "node527810": {}, "node527811": {}, "node527812": {"@otu": "otu221825"}, "node527813": {"@otu": "otu221828"}, "node527814": {}, "node527815": {"@otu": "otu221842"}, "node527816": {"@otu": "otu221819"}, "node527817": {"@otu": "otu221830"}, "node527818": {"@otu": "otu221823"}, "node527819": {}, "node527820": {}, "node527821": {"@otu": "otu221839"}, "node527822": {}, "node527823": {"@otu": "otu221826"}, "node527824": {}, "node527825": {"@otu": "otu221833"}, "node527826": {"@otu": "otu221831"}, "node527827": {}, "node527828": {"@otu": "otu221840"}, "node527829": {"@otu": "otu221822"}, "node527830": {"@otu": "otu221834"}, "node527831": {}, "node527832": {"@otu": "otu221821"}, "node527833": {"@otu": "otu221835"}, "node527834": {}, "node527835": {}, "node527836": {"@otu": "otu221841"}, "node527837": {"@otu": "otu221820"}, "node527838": {"@otu": "otu221817"}, "node527839": {"@otu": "otu221824"}, "node527840": {}, "node527841": {"@otu": "otu221836"}, "node527842": {"@otu": "otu221838"}, "node527843": {}, "node527844": {"@otu": "otu221832"}, "node527845": {"@otu": "otu221837"}}}}}}}}, "branch2sha": {"master": "1bbbe21bdd9a32ef81abeb3f038a977fdc0e8e7b"}, "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"}]}