{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2015-09-29T14:37:44.754Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "All life"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2015-09-29T14:37:44.754Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "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": "node674391", "@treesID": "trees1719", "@treeID": "tree3462", "@nodeID": "node674391"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node674396", "@treesID": "trees1719", "@treeID": "tree3462", "@nodeID": "node674396"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu271881", "otu271884"], "refersTo": {"@top": "otus", "@idref": "otus1719", "@otusID": "otus1719"}, "@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": "tree3462", "@treesID": "trees1719", "@treeID": "tree3462"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit"], "refersTo": {"@top": "trees", "@idref": "tree3463", "@treesID": "trees1719", "@treeID": "tree3463"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree3462"], "^ot:comment": "", "^ot:curatorName": ["Romina Gazis"], "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S688"}, "^ot:focalClade": 728371, "^ot:focalCladeOTTTaxonName": "Hypocreales", "^ot:notIntendedForSynthesis": false, "^ot:otusElementOrder": ["otus1719"], "^ot:studyId": "pg_1719", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.2307/3761605"}, "^ot:studyPublicationReference": "Haugland R., Vesper S., & Harmon S. 2001. Phylogenetic relationships of Memnoniella and Stachybotrys species and evaluation of morphological features for Memnoniella species identification. Mycologia, 93(1): 54-65.", "^ot:studyYear": 2001, "^ot:tag": [], "^ot:treesElementOrder": ["trees1719"], "^xhtml:license": {"@href": "http://creativecommons.org/publicdomain/zero/1.0/", "@name": "CC0"}, "otusById": {"otus1719": {"otuById": {"otu271868": {"^ot:originalLabel": "Fusarium sambucinum NRRL13708", "^ot:ottId": 728368, "^ot:ottTaxonName": "Gibberella pulicaris", "^ot:treebaseOTUId": "Tl105160"}, "otu271869": {"^ot:originalLabel": "Memnoniella subsimplex ATCC32334", "^ot:ottId": 688528, "^ot:ottTaxonName": "Memnoniella subsimplex", "^ot:treebaseOTUId": "Tl105161"}, "otu271870": {"^ot:originalLabel": "Memnoniella echinata ATCC34173", "^ot:ottId": 688532, "^ot:ottTaxonName": "Memnoniella echinata", "^ot:treebaseOTUId": "Tl105162"}, "otu271871": {"^ot:originalLabel": "Memnoniella echinata NRRL1694", "^ot:ottId": 688532, "^ot:ottTaxonName": "Memnoniella echinata", "^ot:treebaseOTUId": "Tl105163"}, "otu271872": {"^ot:originalLabel": "Memnoniella subsimplex ATCC18838", "^ot:ottId": 688528, "^ot:ottTaxonName": "Memnoniella subsimplex", "^ot:treebaseOTUId": "Tl105164"}, "otu271873": {"^ot:originalLabel": "Memnoniella echinata ATCC20513", "^ot:ottId": 688532, "^ot:ottTaxonName": "Memnoniella echinata", "^ot:treebaseOTUId": "Tl105165"}, "otu271874": {"^ot:originalLabel": "Memnoniella subsimplex ATCC22700", "^ot:ottId": 688528, "^ot:ottTaxonName": "Memnoniella subsimplex", "^ot:treebaseOTUId": "Tl105166"}, "otu271875": {"^ot:originalLabel": "Memnoniella echinata NRRL1982", "^ot:ottId": 688532, "^ot:ottTaxonName": "Memnoniella echinata", "^ot:treebaseOTUId": "Tl105167"}, "otu271876": {"^ot:originalLabel": "Memnoniella echinata ATCC22697", "^ot:ottId": 688532, "^ot:ottTaxonName": "Memnoniella echinata", "^ot:treebaseOTUId": "Tl105168"}, "otu271877": {"^ot:originalLabel": "Stachybotrys bisbyi", "^ot:ottId": 688524, "^ot:ottTaxonName": "Stachybotrys elegans", "^ot:treebaseOTUId": "Tl120479"}, "otu271878": {"^ot:originalLabel": "Stachybotrys kampalensis", "^ot:ottId": 688525, "^ot:ottTaxonName": "Stachybotrys kampalensis", "^ot:treebaseOTUId": "Tl120484"}, "otu271879": {"^ot:originalLabel": "Stachybotrys chartarum", "^ot:ottId": 735919, "^ot:ottTaxonName": "Stachybotrys chartarum", "^ot:treebaseOTUId": "Tl120498"}, "otu271880": {"^ot:originalLabel": "Fusarium sambucinum", "^ot:ottId": 728368, "^ot:ottTaxonName": "Gibberella pulicaris", "^ot:treebaseOTUId": "Tl54377"}, "otu271881": {"^ot:originalLabel": "Memnoniella subsimplex ATCC32888", "^ot:ottId": 688528, "^ot:ottTaxonName": "Memnoniella subsimplex", "^ot:treebaseOTUId": "Tl64645"}, "otu271882": {"^ot:originalLabel": "Stachybotrys parvispora", "^ot:ottId": 165547, "^ot:ottTaxonName": "Stachybotrys parvispora", "^ot:treebaseOTUId": "Tl64646"}, "otu271883": {"^ot:originalLabel": "Stachybotrys nephrospora", "^ot:ottId": 165551, "^ot:ottTaxonName": "Stachybotrys nephrospora", "^ot:treebaseOTUId": "Tl64647"}, "otu271884": {"^ot:originalLabel": "Memnoniella sp. ATCC22699", "^ot:ottId": 688528, "^ot:ottTaxonName": "Memnoniella subsimplex", "^ot:treebaseOTUId": "Tl64648"}, "otu271885": {"^ot:originalLabel": "Memnoniella echinata UAMH6594", "^ot:ottId": 688532, "^ot:ottTaxonName": "Memnoniella echinata", "^ot:treebaseOTUId": "Tl64649"}, "otu271886": {"^ot:originalLabel": "Stachybotrys albipes", "^ot:ottId": 688535, "^ot:ottTaxonName": "Melanopsamma pomiformis", "^ot:treebaseOTUId": "Tl64650"}, "otu271887": {"^ot:originalLabel": "Stachybotrys microspora", "^ot:ottId": 165548, "^ot:ottTaxonName": "Stachybotrys microspora", "^ot:treebaseOTUId": "Tl64651"}, "otu271888": {"^ot:originalLabel": "Stachybotrys dichroa", "^ot:ottId": 688527, "^ot:ottTaxonName": "Stachybotrys dichroa", "^ot:treebaseOTUId": "Tl64652"}, "otu271889": {"^ot:originalLabel": "Stachybotrys cylindrospora", "^ot:ottId": 688526, "^ot:ottTaxonName": "Stachybotrys cylindrospora", "^ot:treebaseOTUId": "Tl64653"}}}}, "treesById": {"trees1719": {"@otus": "otus1719", "^ot:treeElementOrder": ["tree3462", "tree3463"], "treeById": {"tree3462": {"@label": "MP, ITS", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:changesCount", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "node674383", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node674382", "^ot:specifiedRoot": "node674382", "^ot:tag": ["MP", "ITS"], "^ot:unrootedTree": false, "edgeBySourceId": {"node674382": {"edge674383": {"@source": "node674382", "@target": "node674383"}, "edge674404": {"@source": "node674382", "@target": "node674404"}, "edge674405": {"@source": "node674382", "@target": "node674405"}}, "node674383": {"edge674384": {"@source": "node674383", "@target": "node674384"}, "edge674401": {"@source": "node674383", "@target": "node674401"}}, "node674384": {"edge674385": {"@source": "node674384", "@target": "node674385"}, "edge674400": {"@source": "node674384", "@target": "node674400"}}, "node674385": {"edge674386": {"@source": "node674385", "@target": "node674386"}, "edge674399": {"@source": "node674385", "@target": "node674399"}}, "node674386": {"edge674387": {"@source": "node674386", "@target": "node674387"}, "edge674398": {"@source": "node674386", "@target": "node674398"}}, "node674387": {"edge674388": {"@source": "node674387", "@target": "node674388"}, "edge674397": {"@source": "node674387", "@target": "node674397"}}, "node674388": {"edge674389": {"@source": "node674388", "@target": "node674389"}, "edge674392": {"@source": "node674388", "@target": "node674392"}}, "node674389": {"edge674390": {"@source": "node674389", "@target": "node674390"}, "edge674391": {"@source": "node674389", "@target": "node674391"}}, "node674392": {"edge674393": {"@source": "node674392", "@target": "node674393"}, "edge674394": {"@source": "node674392", "@target": "node674394"}}, "node674394": {"edge674395": {"@source": "node674394", "@target": "node674395"}, "edge674396": {"@source": "node674394", "@target": "node674396"}}, "node674401": {"edge674402": {"@source": "node674401", "@target": "node674402"}, "edge674403": {"@source": "node674401", "@target": "node674403"}}}, "nodeById": {"node674382": {"@root": true}, "node674383": {}, "node674384": {}, "node674385": {}, "node674386": {}, "node674387": {}, "node674388": {}, "node674389": {}, "node674390": {"@otu": "otu271885"}, "node674391": {"@otu": "otu271884", "^ot:isTaxonExemplar": true}, "node674392": {}, "node674393": {"@otu": "otu271888"}, "node674394": {}, "node674395": {"@otu": "otu271878"}, "node674396": {"@otu": "otu271881", "^ot:isTaxonExemplar": false}, "node674397": {"@otu": "otu271879"}, "node674398": {"@otu": "otu271889"}, "node674399": {"@otu": "otu271887"}, "node674400": {"@otu": "otu271883"}, "node674401": {}, "node674402": {"@otu": "otu271886"}, "node674403": {"@otu": "otu271877"}, "node674404": {"@otu": "otu271882"}, "node674405": {"@otu": "otu271880"}}}, "tree3463": {"@label": "NJ, ITS", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "NJ, ITS", "^ot:inGroupClade": "node674406", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:rootNodeId": "tree3463_ROOT", "^ot:specifiedRoot": "tree3463_ROOT", "^ot:tag": [], "^ot:unrootedTree": true, "edgeBySourceId": {"node674406": {"edge674407": {"@source": "node674406", "@target": "node674407"}, "edge674424": {"@source": "node674406", "@target": "node674424"}}, "node674407": {"edge674408": {"@source": "node674407", "@target": "node674408"}, "edge674423": {"@source": "node674407", "@target": "node674423"}}, "node674408": {"edge674409": {"@source": "node674408", "@target": "node674409"}, "edge674422": {"@source": "node674408", "@target": "node674422"}}, "node674409": {"edge674410": {"@source": "node674409", "@target": "node674410"}, "edge674419": {"@source": "node674409", "@target": "node674419"}}, "node674410": {"edge674411": {"@source": "node674410", "@target": "node674411"}, "edge674418": {"@source": "node674410", "@target": "node674418"}}, "node674411": {"edge674412": {"@source": "node674411", "@target": "node674412"}, "edge674417": {"@source": "node674411", "@target": "node674417"}}, "node674412": {"edge674413": {"@source": "node674412", "@target": "node674413"}, "edge674416": {"@source": "node674412", "@target": "node674416"}}, "node674413": {"edge674414": {"@source": "node674413", "@target": "node674414"}, "edge674415": {"@source": "node674413", "@target": "node674415"}}, "node674419": {"edge674420": {"@source": "node674419", "@target": "node674420"}, "edge674421": {"@source": "node674419", "@target": "node674421"}}, "node674424": {"edge674425": {"@source": "node674424", "@target": "node674425"}, "edge674428": {"@source": "node674424", "@target": "node674428"}}, "node674425": {"edge674426": {"@source": "node674425", "@target": "node674426"}, "edge674427": {"@source": "node674425", "@target": "node674427"}}, "tree3463_ROOT": {"edge674429": {"@source": "tree3463_ROOT", "@target": "node674429"}, "tree3463_ROOT_EDGE": {"@source": "tree3463_ROOT", "@target": "node674406"}}}, "nodeById": {"node674406": {}, "node674407": {}, "node674408": {}, "node674409": {}, "node674410": {}, "node674411": {}, "node674412": {}, "node674413": {}, "node674414": {"@otu": "otu271885"}, "node674415": {"@otu": "otu271884"}, "node674416": {"@otu": "otu271888"}, "node674417": {"@otu": "otu271879"}, "node674418": {"@otu": "otu271889"}, "node674419": {}, "node674420": {"@otu": "otu271887"}, "node674421": {"@otu": "otu271883"}, "node674422": {"@otu": "otu271878"}, "node674423": {"@otu": "otu271881"}, "node674424": {}, "node674425": {}, "node674426": {"@otu": "otu271886"}, "node674427": {"@otu": "otu271877"}, "node674428": {"@otu": "otu271882"}, "node674429": {"@otu": "otu271880"}, "tree3463_ROOT": {"@root": true}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "e44bf3694b6d8c13dd6930bb183ac61cd7875bc3", "author_name": "Romina Gazis", "author_email": "gazisromina@gmail.com", "date": "Tue, 29 Sep 2015 14:42:17 +0000", "date_ISO_8601": "2015-09-29 14:42:17 +0000", "relative_date": "11 years ago", "message_subject": "contains paraphyletic terminal", "message_body": "(Update Study #pg_1719 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"}]}