{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2015-09-28T19:20:39.501Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2015-09-28T19:20:39.501Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node439453", "@treesID": "trees733", "@treeID": "tree1324", "@nodeID": "node439453"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node439454", "@treesID": "trees733", "@treeID": "tree1324", "@nodeID": "node439454"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu190244", "otu190254"], "refersTo": {"@top": "otus", "@idref": "otus733", "@otusID": "otus733"}, "@severity": "WARNING"}, {"@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": "tree1324", "@treesID": "trees733", "@treeID": "tree1324"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1324"], "^ot:comment": "", "^ot:curatorName": ["Romina Gazis"], "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S659"}, "^ot:focalClade": 607950, "^ot:focalCladeOTTTaxonName": "Claviceps", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus733"], "^ot:studyId": "pg_733", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1017/S0953756201003562"}, "^ot:studyPublicationReference": "Pazoutova S. 2001. The phylogeny and evolution of the genus Claviceps. Mycological Research, 105(3): 275-283.", "^ot:studyYear": 2001, "^ot:tag": [], "^ot:treesElementOrder": ["trees733"], "^xhtml:license": {"@href": "http://creativecommons.org/publicdomain/zero/1.0/", "@name": "CC0"}, "otusById": {"otus733": {"otuById": {"otu190238": {"^ot:originalLabel": "Claviceps africana", "^ot:ottId": 36795, "^ot:ottTaxonName": "Claviceps africana", "^ot:treebaseOTUId": "Tl119302"}, "otu190239": {"^ot:originalLabel": "Epichloe amarillans", "^ot:ottId": 369201, "^ot:ottTaxonName": "Epichloe amarillans", "^ot:treebaseOTUId": "Tl119305"}, "otu190240": {"^ot:originalLabel": "Claviceps fusiformis", "^ot:ottId": 664935, "^ot:ottTaxonName": "Claviceps fusiformis", "^ot:treebaseOTUId": "Tl119308"}, "otu190241": {"^ot:originalLabel": "Claviceps paspali", "^ot:ottId": 664936, "^ot:ottTaxonName": "Claviceps paspali", "^ot:treebaseOTUId": "Tl119309"}, "otu190242": {"^ot:originalLabel": "Claviceps purpurea", "^ot:ottId": 103008, "^ot:ottTaxonName": "Claviceps purpurea", "^ot:treebaseOTUId": "Tl119312"}, "otu190243": {"^ot:originalLabel": "Claviceps sorghicola", "^ot:ottId": 36781, "^ot:ottTaxonName": "Claviceps sorghicola", "^ot:treebaseOTUId": "Tl119317"}, "otu190244": {"^ot:originalLabel": "Claviceps sp. SG", "^ot:ottId": 607950, "^ot:ottTaxonName": "Claviceps", "^ot:treebaseOTUId": "Tl67815"}, "otu190245": {"^ot:originalLabel": "Claviceps pusilla", "^ot:ottId": 1036009, "^ot:ottTaxonName": "Claviceps pusilla", "^ot:treebaseOTUId": "Tl67816"}, "otu190246": {"^ot:originalLabel": "Claviceps sulcata", "^ot:ottId": 348520, "^ot:ottTaxonName": "Claviceps sulcata", "^ot:treebaseOTUId": "Tl67817"}, "otu190247": {"^ot:originalLabel": "Claviceps viridis", "^ot:ottId": 348521, "^ot:ottTaxonName": "Claviceps viridis", "^ot:treebaseOTUId": "Tl67818"}, "otu190248": {"^ot:originalLabel": "Claviceps phalaridis", "^ot:ottId": 5316970, "^ot:ottTaxonName": "Cepsiclava phalaridis", "^ot:treebaseOTUId": "Tl67819"}, "otu190249": {"^ot:originalLabel": "Claviceps sorghi", "^ot:ottId": 715213, "^ot:ottTaxonName": "Claviceps sorghi", "^ot:treebaseOTUId": "Tl67820"}, "otu190250": {"^ot:originalLabel": "Claviceps gigantea", "^ot:ottId": 348512, "^ot:ottTaxonName": "Claviceps gigantea", "^ot:treebaseOTUId": "Tl67821"}, "otu190251": {"^ot:originalLabel": "Claviceps grohii", "^ot:ottId": 348508, "^ot:ottTaxonName": "Claviceps grohii", "^ot:treebaseOTUId": "Tl67822"}, "otu190252": {"^ot:originalLabel": "Claviceps citrina", "^ot:ottId": 121675, "^ot:ottTaxonName": "Claviceps citrina", "^ot:treebaseOTUId": "Tl67823"}, "otu190253": {"^ot:originalLabel": "Claviceps zizaniae", "^ot:ottId": 563618, "^ot:ottTaxonName": "Claviceps zizaniae", "^ot:treebaseOTUId": "Tl67824"}, "otu190254": {"^ot:originalLabel": "Claviceps sp. PM", "^ot:ottId": 607950, "^ot:ottTaxonName": "Claviceps", "^ot:treebaseOTUId": "Tl67825"}}}}, "treesById": {"trees733": {"@otus": "otus733", "^ot:treeElementOrder": ["tree1324"], "treeById": {"tree1324": {"@label": "Fig. 4. Quartet puzzling tree with maximum likelihood branch lengths. E. amarillans was defined as the outgroup.", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "node439436", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node439434", "^ot:specifiedRoot": "node439434", "^ot:tag": ["ITS"], "^ot:unrootedTree": false, "edgeBySourceId": {"node439434": {"edge439435": {"@source": "node439434", "@target": "node439435"}, "edge439436": {"@source": "node439434", "@target": "node439436"}}, "node439436": {"edge439437": {"@source": "node439436", "@target": "node439437"}, "edge439448": {"@source": "node439436", "@target": "node439448"}}, "node439437": {"edge439438": {"@source": "node439437", "@target": "node439438"}, "edge439439": {"@source": "node439437", "@target": "node439439"}}, "node439439": {"edge439440": {"@source": "node439439", "@target": "node439440"}, "edge439441": {"@source": "node439439", "@target": "node439441"}}, "node439441": {"edge439442": {"@source": "node439441", "@target": "node439442"}, "edge439443": {"@source": "node439441", "@target": "node439443"}}, "node439443": {"edge439444": {"@source": "node439443", "@target": "node439444"}, "edge439445": {"@source": "node439443", "@target": "node439445"}}, "node439445": {"edge439446": {"@source": "node439445", "@target": "node439446"}, "edge439447": {"@source": "node439445", "@target": "node439447"}}, "node439448": {"edge439449": {"@source": "node439448", "@target": "node439449"}, "edge439450": {"@source": "node439448", "@target": "node439450"}}, "node439450": {"edge439451": {"@source": "node439450", "@target": "node439451"}, "edge439452": {"@source": "node439450", "@target": "node439452"}, "edge439455": {"@source": "node439450", "@target": "node439455"}}, "node439452": {"edge439453": {"@source": "node439452", "@target": "node439453"}, "edge439454": {"@source": "node439452", "@target": "node439454"}}, "node439455": {"edge439456": {"@source": "node439455", "@target": "node439456"}, "edge439457": {"@source": "node439455", "@target": "node439457"}}, "node439457": {"edge439458": {"@source": "node439457", "@target": "node439458"}, "edge439459": {"@source": "node439457", "@target": "node439459"}}, "node439459": {"edge439460": {"@source": "node439459", "@target": "node439460"}, "edge439461": {"@source": "node439459", "@target": "node439461"}}, "node439461": {"edge439462": {"@source": "node439461", "@target": "node439462"}, "edge439463": {"@source": "node439461", "@target": "node439463"}}, "node439463": {"edge439464": {"@source": "node439463", "@target": "node439464"}, "edge439465": {"@source": "node439463", "@target": "node439465"}}}, "nodeById": {"node439434": {"@root": true}, "node439435": {"@otu": "otu190239"}, "node439436": {}, "node439437": {}, "node439438": {"@otu": "otu190241"}, "node439439": {}, "node439440": {"@otu": "otu190253"}, "node439441": {}, "node439442": {"@otu": "otu190251"}, "node439443": {}, "node439444": {"@otu": "otu190246"}, "node439445": {}, "node439446": {"@otu": "otu190242"}, "node439447": {"@otu": "otu190240"}, "node439448": {}, "node439449": {"@otu": "otu190252"}, "node439450": {}, "node439451": {"@otu": "otu190248"}, "node439452": {}, "node439453": {"@otu": "otu190244", "^ot:isTaxonExemplar": true}, "node439454": {"@otu": "otu190254", "^ot:isTaxonExemplar": false}, "node439455": {}, "node439456": {"@otu": "otu190243"}, "node439457": {}, "node439458": {"@otu": "otu190247"}, "node439459": {}, "node439460": {"@otu": "otu190245"}, "node439461": {}, "node439462": {"@otu": "otu190238"}, "node439463": {}, "node439464": {"@otu": "otu190250"}, "node439465": {"@otu": "otu190249"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "7370293f75d7410a057b86cc64996bc549fa48f6", "author_name": "Romina Gazis", "author_email": "gazisromina@gmail.com", "date": "Tue, 29 Sep 2015 00:24:32 +0000", "date_ISO_8601": "2015-09-29 00:24:32 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #pg_733 via OpenTree API"}, {"id": "5fb8ddf7233f3ce47c522b17e08160f44020cc0c", "author_name": "Romina Gazis", "author_email": "gazisromina@gmail.com", "date": "Mon, 28 Sep 2015 19:35:37 +0000", "date_ISO_8601": "2015-09-28 19:35:37 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #pg_733 via OpenTree API"}, {"id": "1c73466dad3f7fcbac333eb6ff7c61861c0613c1", "author_name": "Romina Gazis", "author_email": "gazisromina@gmail.com", "date": "Mon, 28 Sep 2015 19:21:46 +0000", "date_ISO_8601": "2015-09-28 19:21:46 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #pg_733 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"}]}