{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "0.0.0", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "otus": {"@id": "otus2051", "otu": [{"@id": "otu309015", "@about": "#otu309015", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria pearsonii"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 3927732}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Crotalaria pearsonii"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921467"}]}, {"@id": "otu309016", "@about": "#otu309016", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria kolbergii"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921468"}]}, {"@id": "otu309017", "@about": "#otu309017", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria meyeriana"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 425413}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Crotalaria meyerana"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921469"}]}, {"@id": "otu309018", "@about": "#otu309018", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria colorata"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 697894}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Crotalaria colorata"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921470"}]}, {"@id": "otu309019", "@about": "#otu309019", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria monophylla"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 5264753}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Crotalaria monophylla"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921471"}]}, {"@id": "otu309020", "@about": "#otu309020", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria giessii"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921472"}]}, {"@id": "otu309021", "@about": "#otu309021", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria excisa"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 1093704}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Crotalaria excisa"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921473"}]}, {"@id": "otu309022", "@about": "#otu309022", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Crotalaria humilis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 605124}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Crotalaria humilis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl921474"}]}], "@about": "#otus2051"}, "trees": {"@otus": "otus2051", "@id": "trees2051", "tree": [{"@label": "tree", "@xsi:type": "nex:FloatTree", "node": [{"@root": true, "@id": "node785267", "@about": "#node785267"}, {"@otu": "otu309019", "@id": "node785268", "@about": "#node785268", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node785269", "@about": "#node785269"}, {"@id": "node785270", "@about": "#node785270"}, {"@id": "node785271", "@about": "#node785271"}, {"@id": "node785272", "@about": "#node785272"}, {"@otu": "otu309018", "@id": "node785273", "@about": "#node785273", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu309017", "@id": "node785274", "@about": "#node785274", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu309020", "@id": "node785275", "@about": "#node785275", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node785276", "@about": "#node785276"}, {"@otu": "otu309021", "@id": "node785277", "@about": "#node785277", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu309022", "@id": "node785278", "@about": "#node785278", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node785279", "@about": "#node785279"}, {"@otu": "otu309016", "@id": "node785280", "@about": "#node785280", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu309015", "@id": "node785281", "@about": "#node785281", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}], "edge": [{"@source": "node785267", "@target": "node785268", "@id": "edge785268", "@about": "#edge785268"}, {"@source": "node785267", "@target": "node785269", "@id": "edge785269", "@about": "#edge785269"}, {"@source": "node785269", "@target": "node785270", "@id": "edge785270", "@about": "#edge785270"}, {"@source": "node785270", "@target": "node785271", "@id": "edge785271", "@about": "#edge785271"}, {"@source": "node785271", "@target": "node785272", "@id": "edge785272", "@about": "#edge785272"}, {"@source": "node785272", "@target": "node785273", "@id": "edge785273", "@about": "#edge785273"}, {"@source": "node785272", "@target": "node785274", "@id": "edge785274", "@about": "#edge785274"}, {"@source": "node785271", "@target": "node785275", "@id": "edge785275", "@about": "#edge785275"}, {"@source": "node785270", "@target": "node785276", "@id": "edge785276", "@about": "#edge785276"}, {"@source": "node785276", "@target": "node785277", "@id": "edge785277", "@about": "#edge785277"}, {"@source": "node785276", "@target": "node785278", "@id": "edge785278", "@about": "#edge785278"}, {"@source": "node785269", "@target": "node785279", "@id": "edge785279", "@about": "#edge785279"}, {"@source": "node785279", "@target": "node785280", "@id": "edge785280", "@about": "#edge785280"}, {"@source": "node785279", "@target": "node785281", "@id": "edge785281", "@about": "#edge785281"}], "@id": "tree4226", "@about": "#tree4226", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthDescription", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthMode", "@datatype": "xsd:string", "$": "ot:undefined"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatedType", "@datatype": "xsd:string", "$": "Strict"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:inGroupClade", "@datatype": "xsd:string", "$": "node785269"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:nodeLabelMode", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:nodeLabelTimeUnit", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:outGroupEdge", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:specifiedRoot", "@datatype": "xsd:string", "$": "node785267"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:unrootedTree", "@datatype": "xsd:boolean", "$": false}]}], "@about": "#trees2051"}, "@about": "#study", "meta": [{"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"}]}, "@about": "#peyotl-validator"}, {"@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", "@about": "#opentree-curation-webapp"}], "@xsi:type": "nex:LiteralMeta", "@property": "ot:agents"}, {"annotation": [{"@dateCreated": "2018-10-31T14:06:44.715Z", "@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": {"$": "Rosids"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}], "@about": "#otu-mapping-hints"}, {"@dateCreated": "2018-10-31T14:06:44.715Z", "@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": {"$": "meta"}}}], "@about": "#supporting-files-metadata"}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu309016", "otu309020"], "refersTo": {"@top": "otus", "@idref": "otus2051", "@otusID": "otus2051"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree4226", "@treesID": "trees2051", "@treeID": "tree4226"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree4226", "@treesID": "trees2051", "@treeID": "tree4226"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu309016", "otu309020"], "@otusID": "otus2051", "@otuID": ["otu309016", "otu309020"]}, "@severity": "WARNING"}], "@about": "#peyotl-validator-event"}], "@xsi:type": "nex:LiteralMeta", "@property": "ot:annotationEvents"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:comment", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "bryan drew"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "Joe Miller"}, {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S12676", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:dataDeposit"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalCladeOTTTaxonName", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyId", "@datatype": "xsd:string", "$": "pg_2051"}, {"@href": "", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:studyPublication"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyPublicationReference", "@datatype": "xsd:string", "$": "le Roux, M. M., & van Wyk, B. E. (2013). A Taxonomic Revision of Amphitrichae, a New Section of Crotalaria (Fabaceae). Systematic Botany, 38(3), 638-652."}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyYear", "@datatype": "xsd:int", "$": 2013}]}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "979fc300dd47e7d411a64681647fd4a4342a23cf", "author_name": "Joe Miller", "author_email": "joe@acaciamulga.net", "date": "Wed, 31 Oct 2018 14:09:07 +0000", "date_ISO_8601": "2018-10-31 14:09:07 +0000", "relative_date": "7 years ago", "message_subject": "rooted", "message_body": "(Update document 'pg_2051' 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"}]}