{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "otus": {"@id": "otus2357", "otu": [{"@id": "otu333034", "@about": "#otu333034", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Rothevania valdivianus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 4563510}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Rothevania valdivianus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915989"}]}, {"@id": "otu333035", "@about": "#otu333035", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Evaniscus tibialis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 3321799}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Evaniscus tibialis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915990"}]}, {"@id": "otu333036", "@about": "#otu333036", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Decevania reticulata"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 4405753}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Deroparia reticulata"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915991"}]}, {"@id": "otu333037", "@about": "#otu333037", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Evaniscus sulcigenis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 3321800}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Evaniscus sulcigenis"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915992"}]}, {"@id": "otu333038", "@about": "#otu333038", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Evaniscus rafaeli"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915993"}]}, {"@id": "otu333039", "@about": "#otu333039", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Evaniscus lansdownei"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915994"}]}, {"@id": "otu333040", "@about": "#otu333040", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Hyptia thoracica"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 355544}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Hyptia thoracica"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915995"}]}, {"@id": "otu333041", "@about": "#otu333041", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Evaniscus rufithorax"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 355480}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Evaniscus rufithorax"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915996"}]}, {"@id": "otu333042", "@about": "#otu333042", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Alobevania gattiae"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915997"}]}, {"@id": "otu333043", "@about": "#otu333043", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:originalLabel", "@datatype": "xsd:string", "$": "Evaniscus marginatus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottId", "@datatype": "xsd:int", "$": 355481}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:ottTaxonName", "@datatype": "xsd:string", "$": "Evaniscus marginatus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:treebaseOTUId", "@datatype": "xsd:string", "$": "Tl915998"}]}], "@about": "#otus2357"}, "trees": {"@otus": "otus2357", "@id": "trees2357", "tree": [{"@label": "Maximum parsimony (exhaustive search)", "@xsi:type": "nex:FloatTree", "node": [{"@root": true, "@id": "node1133563", "@about": "#node1133563"}, {"@id": "node1133564", "@about": "#node1133564"}, {"@id": "node1133565", "@about": "#node1133565"}, {"@id": "node1133566", "@about": "#node1133566"}, {"@id": "node1133567", "@about": "#node1133567"}, {"@id": "node1133568", "@about": "#node1133568"}, {"@otu": "otu333041", "@id": "node1133569", "@about": "#node1133569", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333037", "@id": "node1133570", "@about": "#node1133570", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333043", "@id": "node1133571", "@about": "#node1133571", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333039", "@id": "node1133572", "@about": "#node1133572", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@id": "node1133573", "@about": "#node1133573"}, {"@otu": "otu333035", "@id": "node1133574", "@about": "#node1133574", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333038", "@id": "node1133575", "@about": "#node1133575", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333034", "@id": "node1133576", "@about": "#node1133576", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333040", "@id": "node1133577", "@about": "#node1133577", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333042", "@id": "node1133578", "@about": "#node1133578", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}, {"@otu": "otu333036", "@id": "node1133579", "@about": "#node1133579", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:isLeaf", "@datatype": "xsd:boolean", "$": true}]}], "edge": [{"@source": "node1133563", "@target": "node1133564", "@id": "edge1133564", "@about": "#edge1133564"}, {"@source": "node1133564", "@target": "node1133565", "@id": "edge1133565", "@about": "#edge1133565"}, {"@source": "node1133565", "@target": "node1133566", "@id": "edge1133566", "@about": "#edge1133566"}, {"@source": "node1133566", "@target": "node1133567", "@id": "edge1133567", "@about": "#edge1133567"}, {"@source": "node1133567", "@target": "node1133568", "@id": "edge1133568", "@about": "#edge1133568"}, {"@source": "node1133568", "@target": "node1133569", "@id": "edge1133569", "@about": "#edge1133569"}, {"@source": "node1133568", "@target": "node1133570", "@id": "edge1133570", "@about": "#edge1133570"}, {"@source": "node1133567", "@target": "node1133571", "@id": "edge1133571", "@about": "#edge1133571"}, {"@source": "node1133566", "@target": "node1133572", "@id": "edge1133572", "@about": "#edge1133572"}, {"@source": "node1133565", "@target": "node1133573", "@id": "edge1133573", "@about": "#edge1133573"}, {"@source": "node1133573", "@target": "node1133574", "@id": "edge1133574", "@about": "#edge1133574"}, {"@source": "node1133573", "@target": "node1133575", "@id": "edge1133575", "@about": "#edge1133575"}, {"@source": "node1133564", "@target": "node1133576", "@id": "edge1133576", "@about": "#edge1133576"}, {"@source": "node1133564", "@target": "node1133577", "@id": "edge1133577", "@about": "#edge1133577"}, {"@source": "node1133563", "@target": "node1133578", "@id": "edge1133578", "@about": "#edge1133578"}, {"@source": "node1133563", "@target": "node1133579", "@id": "edge1133579", "@about": "#edge1133579"}], "@id": "tree6538", "@about": "#tree6538", "meta": [{"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthDescription", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthMode", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:branchLengthTimeUnit", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatedType", "@datatype": "xsd:string", "$": "Maximum parsimony "}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:inGroupClade", "@datatype": "xsd:string", "$": "node1133565"}, {"@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", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:specifiedRoot", "@datatype": "xsd:string", "$": "node1133563"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:tag", "@datatype": "xsd:string", "$": "ingroup added;"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:unrootedTree", "@datatype": "xsd:boolean", "$": false}]}], "@about": "#trees2357"}, "@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": "2014-08-18T15:58:12.623Z", "@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": {"$": "Insects"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}], "@about": "#otu-mapping-hints"}, {"@dateCreated": "2014-08-18T15:58:12.623Z", "@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": {"$": "meta"}}}], "@about": "#supporting-files-metadata"}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu333038", "otu333039", "otu333042"], "refersTo": {"@top": "otus", "@idref": "otus2357", "@otusID": "otus2357"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree6538", "@treesID": "trees2357", "@treeID": "tree6538"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu333038", "otu333039", "otu333042"], "@otusID": "otus2357", "@otuID": ["otu333038", "otu333039", "otu333042"]}, "@severity": "WARNING"}], "@about": "#peyotl-validator-event"}], "@xsi:type": "nex:LiteralMeta", "@property": "ot:annotationEvents"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:candidateTreeForSynthesis", "@datatype": "xsd:string", "$": "tree6538"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:comment", "@datatype": "xsd:string", "$": ""}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "Chris Owen"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "Joseph W. Brown"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:curatorName", "@datatype": "xsd:string", "$": "Gaurav Vaidya"}, {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S13316", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:dataDeposit"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalClade", "@datatype": "xsd:int", "$": 73749}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:focalCladeOTTTaxonName", "@datatype": "xsd:string", "$": "Evaniscus"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:notIntendedForSynthesis", "@datatype": "xsd:boolean", "$": false}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyId", "@datatype": "xsd:string", "$": "pg_2357"}, {"@href": "http://dx.doi.org/10.3897/zookeys.223.3572", "@xsi:type": "nex:ResourceMeta", "@rel": "ot:studyPublication"}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyPublicationReference", "@datatype": "xsd:string", "$": "Mullins P.L., Kawada R., Balhoff J.P., & Deans A. 2012. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38."}, {"@xsi:type": "nex:LiteralMeta", "@property": "ot:studyYear", "@datatype": "xsd:int", "$": 2012}]}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "4cd3e28b30de796eb55eba95f210b5708fa75178", "author_name": "Gaurav Vaidya", "author_email": "ANONYMOUS", "date": "Sun, 17 Jul 2016 00:06:56 +0000", "date_ISO_8601": "2016-07-17 00:06:56 +0000", "relative_date": "10 years ago", "message_subject": "Fixed DOI", "message_body": "(Update document 'pg_2357' via OpenTree API)"}, {"id": "792dc0ad678e9f2f0da09eb8804eddd6502b3836", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Mon, 18 Aug 2014 20:38:53 +0000", "date_ISO_8601": "2014-08-18 20:38:53 +0000", "relative_date": "12 years ago", "message_subject": "tree name / method", "message_body": "(Update Study #pg_2357 via OpenTree API)"}, {"id": "968bef53d764ba9e515958f74fab089af770e304", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Mon, 18 Aug 2014 15:58:55 +0000", "date_ISO_8601": "2014-08-18 15:58:55 +0000", "relative_date": "12 years ago", "message_subject": "mapping", "message_body": "(Update Study #pg_2357 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": "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"}]}