{"sha": "6bed60428352c04d00341ad513a8efb9442e4d8a", "data": {"nexml": {"@generator": "Phylografter nexml-json exporter", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-06-27T16:13:19.193Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Mammals"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-06-27T16:13:19.193Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu423450", "otu423453"], "@otusID": "otus2843", "@otuID": ["otu423450", "otu423453"]}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu423450", "otu423453"], "refersTo": {"@top": "otus", "@idref": "otus2843", "@otusID": "otus2843"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6604"], "^ot:comment": "", "^ot:curatorName": ["Joseph Brown", "Joseph W. Brown"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 222358, "^ot:focalCladeOTTTaxonName": "Talpidae", "^ot:messages": {"message": []}, "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus2843"], "^ot:studyId": "pg_2843", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2013.10.002"}, "^ot:studyPublicationReference": "He, Kai, Akio Shinohara, Xue-Long Jiang, Kevin L. Campbell. 2014. Multilocus phylogeny of talpine moles (Talpini, Talpidae, Eulipotyphla) and its implications for systematics. Molecular Phylogenetics and Evolution 70: 513-521.", "^ot:studyYear": 2014, "^ot:tag": [], "^ot:treesElementOrder": ["trees2843"], "otusById": {"otus2843": {"otuById": {"otu423441": {"^ot:originalLabel": "Condylura cristata", "^ot:ottId": 292504, "^ot:ottTaxonName": "Condylura cristata"}, "otu423442": {"^ot:originalLabel": "Talpa altaica", "^ot:ottId": 243622, "^ot:ottTaxonName": "Talpa altaica"}, "otu423443": {"^ot:originalLabel": "Talpa europaea", "^ot:ottId": 222362, "^ot:ottTaxonName": "Talpa europaea"}, "otu423444": {"^ot:originalLabel": "Euroscaptor mizura", "^ot:ottId": 201752, "^ot:ottTaxonName": "Euroscaptor mizura"}, "otu423445": {"^ot:originalLabel": "Mogera insularis", "^ot:ottId": 201749, "^ot:ottTaxonName": "Mogera insularis"}, "otu423446": {"^ot:originalLabel": "Mogera imaizumii", "^ot:ottId": 201757, "^ot:ottTaxonName": "Mogera imaizumii"}, "otu423447": {"^ot:originalLabel": "Mogera wogura", "^ot:ottId": 634080, "^ot:ottTaxonName": "Mogera wogura"}, "otu423448": {"^ot:originalLabel": "Scaptochirus moschatus", "^ot:ottId": 872314, "^ot:ottTaxonName": "Scaptochirus moschatus"}, "otu423449": {"^ot:originalLabel": "Parascaptor leucura", "^ot:ottId": 3614309, "^ot:ottTaxonName": "Parascaptor leucura"}, "otu423450": {"^ot:originalLabel": "Parascaptor sp."}, "otu423451": {"^ot:originalLabel": "Euroscaptor parvidens", "^ot:ottId": 3614252, "^ot:ottTaxonName": "Euroscaptor parvidens"}, "otu423452": {"^ot:originalLabel": "Euroscaptor malayana", "^ot:ottId": 911109, "^ot:ottTaxonName": "Euroscaptor malayana"}, "otu423453": {"^ot:originalLabel": "Euroscaptor sp."}, "otu423454": {"^ot:originalLabel": "Euroscaptor longirostris", "^ot:ottId": 293562, "^ot:ottTaxonName": "Euroscaptor longirostris"}}}}, "treesById": {"trees2843": {"@otus": "otus2843", "^ot:treeElementOrder": ["tree6604"], "treeById": {"tree6604": {"@label": "Fig. 2b *BEAST", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:time", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Bayesian inference ", "^ot:inGroupClade": "node1153011", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node1153009", "^ot:specifiedRoot": "node1153009", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1153009": {"edge1153010": {"@length": 33.75107105732171, "@source": "node1153009", "@target": "node1153010"}, "edge1153011": {"@length": 16.876007864556016, "@source": "node1153009", "@target": "node1153011"}}, "node1153011": {"edge1153012": {"@length": 10.157216619502435, "@source": "node1153011", "@target": "node1153012"}, "edge1153015": {"@length": 4.5532695917984185, "@source": "node1153011", "@target": "node1153015"}}, "node1153012": {"edge1153013": {"@length": 6.717846573263259, "@source": "node1153012", "@target": "node1153013"}, "edge1153014": {"@length": 6.717846573263259, "@source": "node1153012", "@target": "node1153014"}}, "node1153015": {"edge1153016": {"@length": 12.321793600967275, "@source": "node1153015", "@target": "node1153016"}, "edge1153017": {"@length": 0.9071482966952615, "@source": "node1153015", "@target": "node1153017"}}, "node1153017": {"edge1153018": {"@length": 4.45725650560761, "@source": "node1153017", "@target": "node1153018"}, "edge1153023": {"@length": 1.56335852383177, "@source": "node1153017", "@target": "node1153023"}}, "node1153018": {"edge1153019": {"@length": 6.957388798664404, "@source": "node1153018", "@target": "node1153019"}, "edge1153020": {"@length": 3.5273937253599037, "@source": "node1153018", "@target": "node1153020"}}, "node1153020": {"edge1153021": {"@length": 3.4299950733045, "@source": "node1153020", "@target": "node1153021"}, "edge1153022": {"@length": 3.4299950733045, "@source": "node1153020", "@target": "node1153022"}}, "node1153023": {"edge1153024": {"@length": 0.7928775003276023, "@source": "node1153023", "@target": "node1153024"}, "edge1153029": {"@length": 0.6340161772736899, "@source": "node1153023", "@target": "node1153029"}}, "node1153024": {"edge1153025": {"@length": 9.058409280112642, "@source": "node1153024", "@target": "node1153025"}, "edge1153026": {"@length": 2.5887069905525983, "@source": "node1153024", "@target": "node1153026"}}, "node1153026": {"edge1153027": {"@length": 6.469702289560043, "@source": "node1153026", "@target": "node1153027"}, "edge1153028": {"@length": 6.469702289560043, "@source": "node1153026", "@target": "node1153028"}}, "node1153029": {"edge1153030": {"@length": 9.217270603166554, "@source": "node1153029", "@target": "node1153030"}, "edge1153031": {"@length": 6.316162399050473, "@source": "node1153029", "@target": "node1153031"}}, "node1153031": {"edge1153032": {"@length": 2.901108204116081, "@source": "node1153031", "@target": "node1153032"}, "edge1153033": {"@length": 0.7590442034453098, "@source": "node1153031", "@target": "node1153033"}}, "node1153033": {"edge1153034": {"@length": 2.1420640006707714, "@source": "node1153033", "@target": "node1153034"}, "edge1153035": {"@length": 2.1420640006707714, "@source": "node1153033", "@target": "node1153035"}}}, "nodeById": {"node1153009": {"@root": true}, "node1153010": {"@otu": "otu423441"}, "node1153011": {}, "node1153012": {}, "node1153013": {"@otu": "otu423442"}, "node1153014": {"@otu": "otu423443"}, "node1153015": {}, "node1153016": {"@otu": "otu423444"}, "node1153017": {}, "node1153018": {}, "node1153019": {"@otu": "otu423445"}, "node1153020": {}, "node1153021": {"@otu": "otu423446"}, "node1153022": {"@otu": "otu423447"}, "node1153023": {}, "node1153024": {}, "node1153025": {"@otu": "otu423448"}, "node1153026": {}, "node1153027": {"@otu": "otu423449"}, "node1153028": {"@otu": "otu423450"}, "node1153029": {}, "node1153030": {"@otu": "otu423451"}, "node1153031": {}, "node1153032": {"@otu": "otu423452"}, "node1153033": {}, "node1153034": {"@otu": "otu423453"}, "node1153035": {"@otu": "otu423454"}}}}}}}}, "branch2sha": {"master": "6bed60428352c04d00341ad513a8efb9442e4d8a"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "fa215749a226e6018cc60ebd30bf7e59dcfc8989", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Fri, 27 Jun 2014 17:14:02 +0100", "date_ISO_8601": "2014-06-27 17:14:02 +0100", "relative_date": "12 years ago", "message_subject": "Update Study #pg_2843 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"}]}