{"sha": "c33806c9ee11db205ee8c02a42e31b1c3128e299", "data": {"nexml": {"@generator": "org.nexml.model.impl.DocumentImpl", "@id": "S19520", "@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": ["Palmer A.R.", "Kerr K.A.", "Portell R.W.", "Rosenberg M.", "Hendy A.J.", "Christy J.", "Luque J."], "^dc:creator": "Luque J., Christy J., Hendy A.J., Rosenberg M., Portell R.W., Kerr K.A., & Palmer A.R.", "^dc:date": "2017-09-28", "^dc:publisher": "Journal of Systematic Palaeontology", "^dc:title": "Quaternary intertidal and supratidal crabs (Decapoda, Brachyura) from tropical America and the systematic affinities of fossil fiddler crabs", "^dcterms:bibliographicCitation": "Luque J., Christy J., Hendy A.J., Rosenberg M., Portell R.W., Kerr K.A., & Palmer A.R. 2017. Quaternary intertidal and supratidal crabs (Decapoda, Brachyura) from tropical America and the systematic affinities of fossil fiddler crabs. Journal of Systematic Palaeontology, 00(00): 00\u009600.", "^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": "2.7.9"}, {"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": "2018-06-01T21:58:03.042Z", "@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": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2018-06-01T21:58:03.042Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "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:title", "^dcterms:bibliographicCitation", "^ot:comment", "^prism:creationDate", "^prism:modificationDate", "^prism:number", "^prism:publicationDate", "^prism:publicationName", "^prism:section", "^prism:volume", "^skos:changeNote", "^skos:historyNote", "^tb:identifier.study", "^tb:title.study"], "refersTo": {"@top": "nexml", "@idref": "S19520"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["@label"], "refersTo": {"@top": "trees", "@idref": "Tb43920", "@treesID": "Tb43920"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^skos:historyNote"], "refersTo": {"@top": "trees", "@idref": "Tb43920", "@treesID": "Tb43920"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": "Tl2909966", "@otusID": "Tls59460", "@otuID": "Tl2909966"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["@label"], "refersTo": {"@top": "otus", "@idref": "Tls59460", "@otusID": "Tls59460"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^skos:historyNote"], "refersTo": {"@top": "otus", "@idref": "Tls59460", "@otusID": "Tls59460"}, "@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": "Tr107194", "@treesID": "Tb43920", "@treeID": "Tr107194"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": [], "^ot:comment": "", "^ot:curatorName": ["sbyrum"], "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S19520"}, "^ot:focalClade": 935379, "^ot:focalCladeOTTTaxonName": "Brachyura (infraorder in Protostomia)", "^ot:otusElementOrder": ["Tls59460"], "^ot:studyId": "ot_1328", "^ot:studyPublication": {"@href": "https://doi.org/10.1080/14772019.2017.1362599"}, "^ot:studyPublicationReference": "Luque J., Christy J., Hendy A.J., Rosenberg M., Portell R.W., Kerr K.A., & Palmer A.R. 2017. Quaternary intertidal and supratidal crabs (Decapoda, Brachyura) from tropical America and the systematic affinities of fossil fiddler crabs. Journal of Systematic Palaeontology, 00(00): 00\u009600.", "^ot:studyYear": 2017, "^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": ["Tb43920"], "^prism:creationDate": "2016-07-05", "^prism:modificationDate": "2017-09-28", "^prism:number": "00", "^prism:publicationDate": "2017", "^prism:publicationName": "Journal of Systematic Palaeontology", "^prism:section": "Study", "^prism:volume": "00", "^skos:changeNote": "Generated on Fri Jun 01 21:57:49 UTC 2018", "^skos:historyNote": "Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter@663d8c41 $Rev$", "^tb:identifier.study": "19520", "^tb:title.study": "Intertidal and supratidal fossil crabs (Decapoda, Brachyura) from tropical America and their systematic affinities", "otusById": {"Tls59460": {"@label": "Taxa", "^skos:historyNote": "Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlOTUWriter@3d6d18a8 $Rev$", "otuById": {"Tl2909963": {"^ot:originalLabel": "Uca princeps", "^ot:ottId": 147531, "^ot:ottTaxonName": "Uca princeps", "^ot:taxonLink": {"@tb:identifier.taxon": 330776, "@tb:identifier.taxonVariant": 371208, "@ubio": "5464622", "@uniprot": "378832"}}, "Tl2909964": {"^ot:originalLabel": "Uca antiqua", "^ot:ottId": 6187548, "^ot:ottTaxonName": "Uca antiqua"}, "Tl2909965": {"^ot:originalLabel": "Uca beebei", "^ot:ottId": 813099, "^ot:ottTaxonName": "Uca beebei"}, "Tl2909966": {"^ot:originalLabel": "Uca monilifera", "^ot:taxonLink": {"@tb:identifier.taxon": 633295, "@tb:identifier.taxonVariant": 848307, "@ubio": "6198848"}}, "Tl2909967": {"^ot:originalLabel": "Uca ornata Bique", "^ot:ottId": 289211, "^ot:ottTaxonName": "Uca"}, "Tl2909968": {"^ot:originalLabel": "Uca insignis", "^ot:ottId": 375517, "^ot:ottTaxonName": "Uca insignis"}, "Tl2909969": {"^ot:originalLabel": "Uca heteropleura", "^ot:ottId": 1086640, "^ot:ottTaxonName": "Uca heteropleura", "^ot:taxonLink": {"@tb:identifier.taxon": 73322, "@tb:identifier.taxonVariant": 149980, "@ubio": "5954845", "@uniprot": "53314"}}, "Tl2909970": {"^ot:originalLabel": "Uca ornata", "^ot:ottId": 2981605, "^ot:ottTaxonName": "Uca ornata"}, "Tl2909971": {"^ot:originalLabel": "Uca intermedia", "^ot:ottId": 1086638, "^ot:ottTaxonName": "Uca intermedia", "^ot:taxonLink": {"@tb:identifier.taxon": 73323, "@tb:identifier.taxonVariant": 149981, "@ubio": "5954846", "@uniprot": "53315"}}, "Tl2909972": {"^ot:originalLabel": "Uca tangeri", "^ot:ottId": 289207, "^ot:ottTaxonName": "Uca tangeri", "^ot:taxonLink": {"@tb:identifier.taxon": 633293, "@tb:identifier.taxonVariant": 848305, "@ubio": "5539184"}}, "Tl2909973": {"^ot:originalLabel": "Uca marinae", "^ot:ottId": 6187552, "^ot:ottTaxonName": "Uca marinae"}, "Tl2909974": {"^ot:originalLabel": "Uca stenodactylus", "^ot:ottId": 2981588, "^ot:ottTaxonName": "Uca stenodactylus"}, "Tl2909975": {"^ot:originalLabel": "Uca stylifera", "^ot:ottId": 1086655, "^ot:ottTaxonName": "Uca stylifera", "^ot:taxonLink": {"@tb:identifier.taxon": 73324, "@tb:identifier.taxonVariant": 149982, "@ubio": "5954847", "@uniprot": "53316"}}, "Tl2909976": {"^ot:originalLabel": "Uca major", "^ot:ottId": 2981592, "^ot:ottTaxonName": "Uca major", "^ot:taxonLink": {"@tb:identifier.taxon": 633294, "@tb:identifier.taxonVariant": 848306, "@ubio": "6834165"}}, "Tl2909977": {"^ot:originalLabel": "Uca maracoani", "^ot:ottId": 875250, "^ot:ottTaxonName": "Uca maracoani", "^ot:taxonLink": {"@tb:identifier.taxon": 633292, "@tb:identifier.taxonVariant": 848304, "@ubio": "6549871"}}}}}, "treesById": {"Tb43920": {"@label": "Uca", "@otus": "Tls59460", "^ot:treeElementOrder": ["Tr107194"], "^skos:historyNote": "Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlTreeBlockWriter@40d8a882 $Rev$", "treeById": {"Tr107194": {"@label": "Fig. 8", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum parsimony ", "^ot:inGroupClade": "Tn16809975", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "Tn16809972", "^ot:specifiedRoot": "Tn16809972", "^ot:tag": [], "^ot:unrootedTree": false, "^tb:kind.tree": "Species Tree", "^tb:ntax.tree": 14, "^tb:quality.tree": "Unrated", "^tb:type.tree": "Single", "edgeBySourceId": {"Tn16809967": {"edge1808043": {"@source": "Tn16809967", "@target": "Tn16809970"}, "edge1808045": {"@source": "Tn16809967", "@target": "Tn16809983"}, "edge1808051": {"@source": "Tn16809967", "@target": "Tn16809984"}}, "Tn16809969": {"edge1808025": {"@source": "Tn16809969", "@target": "Tn16809971"}, "edge1808027": {"@source": "Tn16809969", "@target": "Tn16809987"}}, "Tn16809972": {"edge1808015": {"@source": "Tn16809972", "@target": "Tn16809986"}, "edge1808017": {"@source": "Tn16809972", "@target": "Tn16809974"}, "edge1808019": {"@source": "Tn16809972", "@target": "Tn16809975"}}, "Tn16809975": {"edge1808021": {"@source": "Tn16809975", "@target": "Tn16809968"}, "edge1808023": {"@source": "Tn16809975", "@target": "Tn16809969"}}, "Tn16809976": {"edge1808033": {"@source": "Tn16809976", "@target": "Tn16809985"}, "edge1808035": {"@source": "Tn16809976", "@target": "Tn16809977"}, "edge1808037": {"@source": "Tn16809976", "@target": "Tn16809980"}}, "Tn16809980": {"edge1808039": {"@source": "Tn16809980", "@target": "Tn16809988"}, "edge1808041": {"@source": "Tn16809980", "@target": "Tn16809967"}}, "Tn16809983": {"edge1808047": {"@source": "Tn16809983", "@target": "Tn16809973"}, "edge1808049": {"@source": "Tn16809983", "@target": "Tn16809978"}}, "Tn16809984": {"edge1808053": {"@source": "Tn16809984", "@target": "Tn16809982"}, "edge1808055": {"@source": "Tn16809984", "@target": "Tn16809981"}, "edge1808057": {"@source": "Tn16809984", "@target": "Tn16809979"}}, "Tn16809987": {"edge1808029": {"@source": "Tn16809987", "@target": "Tn16809989"}, "edge1808031": {"@source": "Tn16809987", "@target": "Tn16809976"}}}, "nodeById": {"Tn16809967": {}, "Tn16809968": {"@otu": "Tl2909972"}, "Tn16809969": {}, "Tn16809970": {"@otu": "Tl2909964"}, "Tn16809971": {"@otu": "Tl2909963"}, "Tn16809972": {"@root": true}, "Tn16809973": {"@otu": "Tl2909968"}, "Tn16809974": {"@otu": "Tl2909974"}, "Tn16809975": {}, "Tn16809976": {}, "Tn16809977": {"@otu": "Tl2909976"}, "Tn16809978": {"@otu": "Tl2909977"}, "Tn16809979": {"@otu": "Tl2909967"}, "Tn16809980": {}, "Tn16809981": {"@otu": "Tl2909973"}, "Tn16809982": {"@otu": "Tl2909970"}, "Tn16809983": {}, "Tn16809984": {}, "Tn16809985": {"@otu": "Tl2909971"}, "Tn16809986": {"@otu": "Tl2909965"}, "Tn16809987": {}, "Tn16809988": {"@otu": "Tl2909975"}, "Tn16809989": {"@otu": "Tl2909969"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "f351ee9028ffb4768888c543679326c247e0c7b2", "author_name": "sbyrum", "author_email": "s.byrum@ku.edu", "date": "Wed, 27 Jun 2018 21:07:32 +0000", "date_ISO_8601": "2018-06-27 21:07:32 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_1328' via OpenTree API"}, {"id": "e273ede47d7e17e8751c7d54314a96977499f7b1", "author_name": "sbyrum", "author_email": "s.byrum@ku.edu", "date": "Fri, 1 Jun 2018 22:13:59 +0000", "date_ISO_8601": "2018-06-01 22:13:59 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_1328' via OpenTree API"}, {"id": "819ab064e388c268d588ad13b3b7c1f72f18254b", "author_name": "sbyrum", "author_email": "s.byrum@ku.edu", "date": "Fri, 1 Jun 2018 21:57:55 +0000", "date_ISO_8601": "2018-06-01 21:57:55 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_1328' via OpenTree API"}]}