{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2017-08-24T17:57:55.927Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Nematodes"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2017-08-24T17:57:55.927Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "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": ["otu311797", "otu311800", "otu311806"], "refersTo": {"@top": "otus", "@idref": "otus2089", "@otusID": "otus2089"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree4326", "@treesID": "trees2089", "@treeID": "tree4326"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree4326", "@treesID": "trees2089", "@treeID": "tree4326"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree4327", "@treesID": "trees2089", "@treeID": "tree4327"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree4327", "@treesID": "trees2089", "@treeID": "tree4327"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu311797", "otu311800", "otu311806"], "@otusID": "otus2089", "@otuID": ["otu311797", "otu311800", "otu311806"]}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["Chris Owen", "Benjamin Redelings"], "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S1185"}, "^ot:focalClade": 395055, "^ot:focalCladeOTTTaxonName": "Caenorhabditis", "^ot:otusElementOrder": ["otus2089"], "^ot:studyId": "pg_2089", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1073/pnas.0403094101"}, "^ot:studyPublicationReference": "Kiontke K., Gavin N., Raynes Y., Roehrig C., Piano F., & Fitch D. 2004. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proceedings of the National Academy of Sciences of the United States of America 101 (24): 9003-9008.", "^ot:studyYear": 2004, "^ot:tag": [], "^ot:treesElementOrder": ["trees2089"], "otusById": {"otus2089": {"otuById": {"otu311794": {"^ot:originalLabel": "Caenorhabditis briggsae", "^ot:ottId": 395053, "^ot:ottTaxonName": "Caenorhabditis briggsae", "^ot:treebaseOTUId": "Tl148423"}, "otu311795": {"^ot:originalLabel": "Caenorhabditis elegans", "^ot:ottId": 395048, "^ot:ottTaxonName": "Caenorhabditis elegans", "^ot:treebaseOTUId": "Tl148428"}, "otu311796": {"^ot:originalLabel": "Caenorhabditis drosophilae", "^ot:ottId": 362927, "^ot:ottTaxonName": "Caenorhabditis drosophilae", "^ot:treebaseOTUId": "Tl57212"}, "otu311797": {"^ot:originalLabel": "Protorhabditis sp DF5055", "^ot:treebaseOTUId": "Tl60758"}, "otu311798": {"^ot:originalLabel": "Rhabditella axei", "^ot:ottId": 318128, "^ot:ottTaxonName": "Rhabditella axei", "^ot:treebaseOTUId": "Tl60759"}, "otu311799": {"^ot:originalLabel": "Caenorhabditis sp DF5070", "^ot:ottId": 215931, "^ot:ottTaxonName": "Caenorhabditis sp. DF5070", "^ot:treebaseOTUId": "Tl60760"}, "otu311800": {"^ot:originalLabel": "Oscheius myriophila", "^ot:treebaseOTUId": "Tl60761"}, "otu311801": {"^ot:originalLabel": "Caenorhabditis sp PS1010", "^ot:ottId": 94476, "^ot:ottTaxonName": "Caenorhabditis angaria", "^ot:treebaseOTUId": "Tl60762"}, "otu311802": {"^ot:originalLabel": "Caenorhabditis sp SB341", "^ot:ottId": 215928, "^ot:ottTaxonName": "Caenorhabditis sp. SB341", "^ot:treebaseOTUId": "Tl60763"}, "otu311803": {"^ot:originalLabel": "Caenorhabditis japonica", "^ot:ottId": 215930, "^ot:ottTaxonName": "Caenorhabditis japonica", "^ot:treebaseOTUId": "Tl60764"}, "otu311804": {"^ot:originalLabel": "Caenorhabditis plicata", "^ot:ottId": 215924, "^ot:ottTaxonName": "Caenorhabditis plicata", "^ot:treebaseOTUId": "Tl60765"}, "otu311805": {"^ot:originalLabel": "Caenorhabditis sp CB5161", "^ot:ottId": 90647, "^ot:ottTaxonName": "Caenorhabditis brenneri", "^ot:treebaseOTUId": "Tl60766"}, "otu311806": {"^ot:originalLabel": "Caenorhabditis remanei", "^ot:treebaseOTUId": "Tl60767"}, "otu311807": {"^ot:originalLabel": "Prodontorhabditis wirthi", "^ot:ottId": 215929, "^ot:ottTaxonName": "Prodontorhabditis wirthi", "^ot:treebaseOTUId": "Tl60768"}}}}, "treesById": {"trees2089": {"@otus": "otus2089", "^ot:treeElementOrder": ["tree4326", "tree4327"], "treeById": {"tree4326": {"@label": "Untitled (tree4326)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:changesCount", "^ot:curatedType": "Fig. 1 MP", "^ot:inGroupClade": "node793517", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node793515", "^ot:specifiedRoot": "node793515", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node793515": {"edge793516": {"@source": "node793515", "@target": "node793516"}, "edge793539": {"@source": "node793515", "@target": "node793539"}}, "node793516": {"edge793517": {"@source": "node793516", "@target": "node793517"}, "edge793536": {"@source": "node793516", "@target": "node793536"}}, "node793517": {"edge793518": {"@source": "node793517", "@target": "node793518"}, "edge793535": {"@source": "node793517", "@target": "node793535"}}, "node793518": {"edge793519": {"@source": "node793518", "@target": "node793519"}, "edge793534": {"@source": "node793518", "@target": "node793534"}}, "node793519": {"edge793520": {"@source": "node793519", "@target": "node793520"}, "edge793531": {"@source": "node793519", "@target": "node793531"}}, "node793520": {"edge793521": {"@source": "node793520", "@target": "node793521"}, "edge793530": {"@source": "node793520", "@target": "node793530"}}, "node793521": {"edge793522": {"@source": "node793521", "@target": "node793522"}, "edge793529": {"@source": "node793521", "@target": "node793529"}}, "node793522": {"edge793523": {"@source": "node793522", "@target": "node793523"}, "edge793528": {"@source": "node793522", "@target": "node793528"}}, "node793523": {"edge793524": {"@source": "node793523", "@target": "node793524"}, "edge793527": {"@source": "node793523", "@target": "node793527"}}, "node793524": {"edge793525": {"@source": "node793524", "@target": "node793525"}, "edge793526": {"@source": "node793524", "@target": "node793526"}}, "node793531": {"edge793532": {"@source": "node793531", "@target": "node793532"}, "edge793533": {"@source": "node793531", "@target": "node793533"}}, "node793536": {"edge793537": {"@source": "node793536", "@target": "node793537"}, "edge793538": {"@source": "node793536", "@target": "node793538"}}, "node793539": {"edge793540": {"@source": "node793539", "@target": "node793540"}, "edge793541": {"@source": "node793539", "@target": "node793541"}}}, "nodeById": {"node793515": {"@root": true}, "node793516": {}, "node793517": {}, "node793518": {}, "node793519": {}, "node793520": {}, "node793521": {}, "node793522": {}, "node793523": {}, "node793524": {}, "node793525": {"@otu": "otu311794"}, "node793526": {"@otu": "otu311806"}, "node793527": {"@otu": "otu311805"}, "node793528": {"@otu": "otu311795"}, "node793529": {"@otu": "otu311803"}, "node793530": {"@otu": "otu311801"}, "node793531": {}, "node793532": {"@otu": "otu311796"}, "node793533": {"@otu": "otu311799"}, "node793534": {"@otu": "otu311804"}, "node793535": {"@otu": "otu311802"}, "node793536": {}, "node793537": {"@otu": "otu311807"}, "node793538": {"@otu": "otu311797"}, "node793539": {}, "node793540": {"@otu": "otu311800"}, "node793541": {"@otu": "otu311798"}}}, "tree4327": {"@label": "Untitled (tree4327)", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:changesCount", "^ot:curatedType": "Alternative Tree", "^ot:inGroupClade": "node793544", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [{"$": "The other tree in the study might be is probably better."}], "^ot:rootNodeId": "node793542", "^ot:specifiedRoot": "node793542", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node793542": {"edge793543": {"@source": "node793542", "@target": "node793543"}, "edge793566": {"@source": "node793542", "@target": "node793566"}}, "node793543": {"edge793544": {"@source": "node793543", "@target": "node793544"}, "edge793563": {"@source": "node793543", "@target": "node793563"}}, "node793544": {"edge793545": {"@source": "node793544", "@target": "node793545"}, "edge793562": {"@source": "node793544", "@target": "node793562"}}, "node793545": {"edge793546": {"@source": "node793545", "@target": "node793546"}, "edge793561": {"@source": "node793545", "@target": "node793561"}}, "node793546": {"edge793547": {"@source": "node793546", "@target": "node793547"}, "edge793556": {"@source": "node793546", "@target": "node793556"}}, "node793547": {"edge793548": {"@source": "node793547", "@target": "node793548"}, "edge793555": {"@source": "node793547", "@target": "node793555"}}, "node793548": {"edge793549": {"@source": "node793548", "@target": "node793549"}, "edge793554": {"@source": "node793548", "@target": "node793554"}}, "node793549": {"edge793550": {"@source": "node793549", "@target": "node793550"}, "edge793553": {"@source": "node793549", "@target": "node793553"}}, "node793550": {"edge793551": {"@source": "node793550", "@target": "node793551"}, "edge793552": {"@source": "node793550", "@target": "node793552"}}, "node793556": {"edge793557": {"@source": "node793556", "@target": "node793557"}, "edge793558": {"@source": "node793556", "@target": "node793558"}}, "node793558": {"edge793559": {"@source": "node793558", "@target": "node793559"}, "edge793560": {"@source": "node793558", "@target": "node793560"}}, "node793563": {"edge793564": {"@source": "node793563", "@target": "node793564"}, "edge793565": {"@source": "node793563", "@target": "node793565"}}, "node793566": {"edge793567": {"@source": "node793566", "@target": "node793567"}, "edge793568": {"@source": "node793566", "@target": "node793568"}}}, "nodeById": {"node793542": {"@root": true}, "node793543": {}, "node793544": {}, "node793545": {}, "node793546": {}, "node793547": {}, "node793548": {}, "node793549": {}, "node793550": {}, "node793551": {"@otu": "otu311794"}, "node793552": {"@otu": "otu311806"}, "node793553": {"@otu": "otu311805"}, "node793554": {"@otu": "otu311795"}, "node793555": {"@otu": "otu311803"}, "node793556": {}, "node793557": {"@otu": "otu311801"}, "node793558": {}, "node793559": {"@otu": "otu311796"}, "node793560": {"@otu": "otu311799"}, "node793561": {"@otu": "otu311804"}, "node793562": {"@otu": "otu311802"}, "node793563": {}, "node793564": {"@otu": "otu311807"}, "node793565": {"@otu": "otu311797"}, "node793566": {}, "node793567": {"@otu": "otu311800"}, "node793568": {"@otu": "otu311798"}}}}}}}}, "branch2sha": {"master": "24afc85a444963f10ca51c6e20138fe592a4b525"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "c83a4f43b34d7470ec7fcef0a4af76afae53ca57", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Thu, 24 Aug 2017 18:01:02 +0000", "date_ISO_8601": "2017-08-24 18:01:02 +0000", "relative_date": "9 years ago", "message_subject": "Update document 'pg_2089' via OpenTree API"}, {"id": "35e6312bb68f243bba890dfad0294f9c37f58c8a", "author_name": "Benjamin Redelings", "author_email": "benjamin.redelings@gmail.com", "date": "Thu, 24 Aug 2017 17:58:54 +0000", "date_ISO_8601": "2017-08-24 17:58:54 +0000", "relative_date": "9 years ago", "message_subject": "Update document 'pg_2089' via OpenTree API"}, {"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": "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"}]}