{"sha": "1bbbe21bdd9a32ef81abeb3f038a977fdc0e8e7b", "data": {"nexml": {"@generator": "org.nexml.model.impl.DocumentImpl", "@id": "S20935", "@nexml2json": "1.2.1", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "dc": "http://purl.org/dc/elements/1.1/", "dcterms": "http://purl.org/dc/terms/", "nex": "http://www.nexml.org/2009", "prism": "http://prismstandard.org/namespaces/1.2/basic/", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "skos": "http://www.w3.org/2004/02/skos/core#", "tb": "http://purl.org/phylo/treebase/2.0/terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^dc:contributor": ["Takamatsu S.", "Shinoda T.", "Sakamoto H.", "Siahaan S."], "^dc:creator": "Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S.", "^dc:date": "2018-05-07", "^dc:publisher": "Mycoscience", "^dc:subject": ["Quercus subgen. Cyclobalanopsidis", "PCR-RFLP", "Life cycle", "DNA sequence", "Cystotheca wrightii"], "^dc:title": "Geographic and temporal distributions of four genotypes found in Erysiphe gracilis, a powdery mildew of evergreen oak (Erysiphales)", "^dcterms:bibliographicCitation": "Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S. 2018. Geographic and temporal distributions of four genotypes found in Erysiphe gracilis, a powdery mildew of evergreen oak (Erysiphales). Mycoscience, 59(2): 110-118.", "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.15+"}, {"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": "2018-09-27T19:57:20.960Z", "@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": {"$": ""}, "old": {"$": ""}}, {"@active": true, "@valid": true, "new": {"$": "$1"}, "old": {"$": "^(\\S*\\s+\\S*).*"}}]}, "useFuzzyMatching": true}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2018-09-27T19:57:20.960Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^dc:contributor", "^dc:creator", "^dc:date", "^dc:publisher", "^dc:subject", "^dc:title", "^dcterms:bibliographicCitation", "^ot:comment", "^prism:creationDate", "^prism:doi", "^prism:endingPage", "^prism:modificationDate", "^prism:number", "^prism:pageRange", "^prism:publicationDate", "^prism:publicationName", "^prism:section", "^prism:startingPage", "^prism:volume", "^skos:changeNote", "^skos:historyNote", "^tb:identifier.study", "^tb:title.study"], "refersTo": {"@top": "nexml", "@idref": "S20935"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["@label"], "refersTo": {"@top": "trees", "@idref": "Tb42108", "@treesID": "Tb42108"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^skos:historyNote"], "refersTo": {"@top": "trees", "@idref": "Tb42108", "@treesID": "Tb42108"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["@label"], "refersTo": {"@top": "otus", "@idref": "Tls57166", "@otusID": "Tls57166"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["Tl2776357", "Tl2776358", "Tl2776359", "Tl2776360", "Tl2776361", "Tl2776362", "Tl2776363", "Tl2776364", "Tl2776365", "Tl2776367", "Tl2776368"], "refersTo": {"@top": "otus", "@idref": "Tls57166", "@otusID": "Tls57166"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["Tl2776366", "Tl2776369"], "refersTo": {"@top": "otus", "@idref": "Tls57166", "@otusID": "Tls57166"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^skos:historyNote"], "refersTo": {"@top": "otus", "@idref": "Tls57166", "@otusID": "Tls57166"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthTimeUnit"], "refersTo": {"@top": "trees", "@idref": "Tr103879", "@treesID": "Tb42108", "@treeID": "Tr103879"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis", "^tb:kind.tree", "^tb:ntax.tree", "^tb:quality.tree", "^tb:type.tree"], "refersTo": {"@top": "trees", "@idref": "Tr103879", "@treesID": "Tb42108", "@treeID": "Tr103879"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["Jesseholmes"], "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S20935"}, "^ot:focalCladeOTTTaxonName": "", "^ot:otusElementOrder": ["Tls57166"], "^ot:studyId": "ot_1786", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.myc.2017.08.002"}, "^ot:studyPublicationReference": "Siahaan S., Sakamoto H., Shinoda T., & Takamatsu S. 2018. Geographic and temporal distributions of four genotypes found in Erysiphe gracilis, a powdery mildew of evergreen oak (Erysiphales). Mycoscience, 59(2): 110-118.", "^ot:studyYear": 2018, "^ot:tag": [], "^ot:taxonLinkPrefixes": {"@ubio": "http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:", "@uniprot": "http://purl.uniprot.org/taxonomy/"}, "^ot:treesElementOrder": ["Tb42108"], "^prism:creationDate": "2017-04-21", "^prism:doi": "10.1016/j.myc.2017.08.002", "^prism:endingPage": "118", "^prism:modificationDate": "2018-05-07", "^prism:number": "2", "^prism:pageRange": "110-118", "^prism:publicationDate": "2018", "^prism:publicationName": "Mycoscience", "^prism:section": "Study", "^prism:startingPage": "110", "^prism:volume": "59", "^skos:changeNote": "Generated on Thu Sep 27 19:57:17 UTC 2018", "^skos:historyNote": "Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter@564a1c20 $Rev$", "^tb:identifier.study": "20935", "^tb:title.study": "Geographic and temporal distributions of four genotypes found in Erysiphe gracilis, a powdery mildew of evergreen oak (Erysiphales)", "otusById": {"Tls57166": {"@label": "Taxa", "^skos:historyNote": "Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlOTUWriter@5bd60b45 $Rev$", "otuById": {"Tl2776357": {"^ot:originalLabel": "Erysiphe gracilis genotype I ex Q. glauca MUMH3608", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776358": {"^ot:originalLabel": "Erysiphe gracilis genotype II ex Q. glauca MUMH5725", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776359": {"^ot:originalLabel": "Erysiphe gracilis genotype I ex Q. glauca MUMH4107", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis", "^ot:taxonLink": {"@tb:identifier.taxon": 10479, "@tb:identifier.taxonVariant": 25072, "@ubio": "3028938", "@uniprot": "87898"}}, "Tl2776360": {"^ot:originalLabel": "Erysiphe gracilis genotype III ex Q. glauca TUAMH3181", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776361": {"^ot:originalLabel": "Erysiphe gracilis genotype IV ex Q. glauca MUMH5842", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776362": {"^ot:originalLabel": "Erysiphe gracilis genotype I ex Q. glauca MUMH5536", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776363": {"^ot:originalLabel": "Erysiphe gracilis genotype IV ex Q. glauca MUMH5839", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776364": {"^ot:originalLabel": "Erysiphe gracilis genotype IV ex Q. salicina MUMH5804", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776365": {"^ot:originalLabel": "Erysiphe gracilis genotype II ex Q. myrsinaefolia MUMH6161", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776366": {"^ot:originalLabel": "Erysiphe japonica ex Q. crispula MUMH4163", "^ot:ottId": 208301, "^ot:ottTaxonName": "Typhulochaeta japonica", "^ot:taxonLink": {"@tb:identifier.taxon": 38388, "@tb:identifier.taxonVariant": 88772, "@ubio": "3169648"}}, "Tl2776367": {"^ot:originalLabel": "Erysiphe gracilis genotype II ex Q. glauca MUMH5381", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776368": {"^ot:originalLabel": "Erysiphe gracilis genotype III ex Q. glauca MUMH5868", "^ot:ottId": 1006538, "^ot:ottTaxonName": "Erysiphe gracilis"}, "Tl2776369": {"^ot:originalLabel": "Erysiphe japonica ex Q. serrata MUMH4582", "^ot:ottId": 208301, "^ot:ottTaxonName": "Typhulochaeta japonica"}}}}, "treesById": {"Tb42108": {"@label": "Erysiphe gracilis", "@otus": "Tls57166", "^ot:treeElementOrder": ["Tr103879"], "^skos:historyNote": "Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlTreeBlockWriter@1b50cfee $Rev$", "treeById": {"Tr103879": {"@label": "Fig. 2", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "Tn16309346", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "Tn16309330", "^ot:specifiedRoot": "Tn16309330", "^ot:tag": [], "^ot:unrootedTree": false, "^tb:kind.tree": "Species Tree", "^tb:ntax.tree": 13, "^tb:quality.tree": "Unrated", "^tb:type.tree": "Single", "edgeBySourceId": {"Tn16309330": {"edge3439": {"@source": "Tn16309330", "@target": "Tn16309346"}, "edge3477": {"@source": "Tn16309330", "@target": "Tn16309336"}}, "Tn16309331": {"edge3471": {"@source": "Tn16309331", "@target": "Tn16309337"}, "edge3473": {"@source": "Tn16309331", "@target": "Tn16309351"}, "edge3475": {"@source": "Tn16309331", "@target": "Tn16309342"}}, "Tn16309333": {"edge3455": {"@source": "Tn16309333", "@target": "Tn16309338"}, "edge3461": {"@source": "Tn16309333", "@target": "Tn16309343"}}, "Tn16309336": {"edge3479": {"@source": "Tn16309336", "@target": "Tn16309347"}, "edge3481": {"@source": "Tn16309336", "@target": "Tn16309344"}}, "Tn16309338": {"edge3457": {"@source": "Tn16309338", "@target": "Tn16309329"}, "edge3459": {"@source": "Tn16309338", "@target": "Tn16309335"}}, "Tn16309339": {"edge3453": {"@source": "Tn16309339", "@target": "Tn16309333"}, "edge3463": {"@source": "Tn16309339", "@target": "Tn16309341"}}, "Tn16309341": {"edge3465": {"@source": "Tn16309341", "@target": "Tn16309350"}, "edge3467": {"@source": "Tn16309341", "@target": "Tn16309332"}}, "Tn16309345": {"edge3443": {"@source": "Tn16309345", "@target": "Tn16309348"}, "edge3451": {"@source": "Tn16309345", "@target": "Tn16309339"}}, "Tn16309346": {"edge3441": {"@source": "Tn16309346", "@target": "Tn16309345"}, "edge3469": {"@source": "Tn16309346", "@target": "Tn16309331"}}, "Tn16309348": {"edge3445": {"@source": "Tn16309348", "@target": "Tn16309349"}, "edge3447": {"@source": "Tn16309348", "@target": "Tn16309334"}, "edge3449": {"@source": "Tn16309348", "@target": "Tn16309340"}}}, "nodeById": {"Tn16309329": {"@otu": "Tl2776367"}, "Tn16309330": {"@root": true}, "Tn16309331": {}, "Tn16309332": {"@otu": "Tl2776368"}, "Tn16309333": {}, "Tn16309334": {"@otu": "Tl2776359"}, "Tn16309335": {"@otu": "Tl2776358"}, "Tn16309336": {}, "Tn16309337": {"@otu": "Tl2776364"}, "Tn16309338": {}, "Tn16309339": {}, "Tn16309340": {"@otu": "Tl2776357"}, "Tn16309341": {}, "Tn16309342": {"@otu": "Tl2776363"}, "Tn16309343": {"@otu": "Tl2776365"}, "Tn16309344": {"@otu": "Tl2776366"}, "Tn16309345": {}, "Tn16309346": {}, "Tn16309347": {"@otu": "Tl2776369"}, "Tn16309348": {}, "Tn16309349": {"@otu": "Tl2776362"}, "Tn16309350": {"@otu": "Tl2776360"}, "Tn16309351": {"@otu": "Tl2776361"}}}}}}}}, "branch2sha": {"master": "1bbbe21bdd9a32ef81abeb3f038a977fdc0e8e7b"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "d26a71fd635e2d18d5f48aba1b15914452cdc331", "author_name": "Jesseholmes", "author_email": "ANONYMOUS", "date": "Thu, 27 Sep 2018 20:08:28 +0000", "date_ISO_8601": "2018-09-27 20:08:28 +0000", "relative_date": "8 years ago", "message_subject": "Upload tree", "message_body": "Uploaded tree and mapped OTUs\n\n(Update document 'ot_1786' via OpenTree API)"}, {"id": "804b64661add5bea56703865d8e672941d97b7b4", "author_name": "Jesseholmes", "author_email": "ANONYMOUS", "date": "Thu, 27 Sep 2018 19:57:18 +0000", "date_ISO_8601": "2018-09-27 19:57:18 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_1786' via OpenTree API"}]}