{"sha": "24afc85a444963f10ca51c6e20138fe592a4b525", "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": "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": "2.7.3"}, {"name": "pythonImplementation", "value": "CPython"}]}}]}, "^ot:annotationEvents": {"annotation": [{"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:branchLengthDescription", "^ot:branchLengthMode", "^ot:branchLengthTimeUnit", "^ot:outGroupEdge"], "refersTo": {"@top": "trees", "@idref": "tree5539", "@treesID": "trees349", "@treeID": "tree5539"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": ["otu75271", "otu75272", "otu75277"], "@otusID": "otus349", "@otuID": ["otu75271", "otu75272", "otu75277"]}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75265", "otu75270", "otu75275", "otu75278", "otu75281", "otu75285", "otu75293", "otu75295", "otu75303", "otu75304", "otu75305"], "refersTo": {"@top": "otus", "@idref": "otus349", "@otusID": "otus349"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75271", "otu75272", "otu75277"], "refersTo": {"@top": "otus", "@idref": "otus349", "@otusID": "otus349"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75273", "otu75298"], "refersTo": {"@top": "otus", "@idref": "otus349", "@otusID": "otus349"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75274", "otu75279", "otu75284", "otu75286", "otu75292", "otu75296", "otu75299"], "refersTo": {"@top": "otus", "@idref": "otus349", "@otusID": "otus349"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu75283", "otu75302"], "refersTo": {"@top": "otus", "@idref": "otus349", "@otusID": "otus349"}, "@severity": "WARNING"}]}]}, "^ot:curatorName": "Romina Gazis", "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S847"}, "^ot:focalClade": 536378, "^ot:focalCladeOTTTaxonName": "Retiboletus", "^ot:otusElementOrder": ["otus349"], "^ot:studyId": "pg_349", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1002/1522-239X(200205)113:1/2<30::AID-FEDR30>3.0.CO;2-D"}, "^ot:studyPublicationReference": "Binder M., & Bresinsky A. 2002. Retiboletus, a new genus for a species-complex in the Boletaceae producing retipolides. Feddes Repertorium, 113(1-2): 30-40.", "^ot:studyYear": 2002, "^ot:treesElementOrder": ["trees349"], "otusById": {"otus349": {"otuById": {"otu75264": {"^ot:originalLabel": "Boletus calopus", "^ot:ottId": 800233, "^ot:ottTaxonName": "Boletus calopus", "^ot:treebaseOTUId": "Tl129851"}, "otu75265": {"^ot:originalLabel": "Retiboletus retipes U11914", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl129854"}, "otu75266": {"^ot:originalLabel": "Suillus cavipes", "^ot:ottId": 428802, "^ot:ottTaxonName": "Suillus cavipes", "^ot:treebaseOTUId": "Tl129862"}, "otu75267": {"^ot:originalLabel": "Suillus luteus", "^ot:ottId": 428806, "^ot:ottTaxonName": "Suillus luteus", "^ot:treebaseOTUId": "Tl6753"}, "otu75268": {"^ot:originalLabel": "Retiboletus griseus", "^ot:ottId": 219874, "^ot:ottTaxonName": "Retiboletus griseus", "^ot:treebaseOTUId": "Tl7274"}, "otu75269": {"^ot:originalLabel": "Tylopilus indecisus", "^ot:ottId": 697634, "^ot:ottTaxonName": "Tylopilus indecisus", "^ot:treebaseOTUId": "Tl7275"}, "otu75270": {"^ot:originalLabel": "Retiboletus retipes Japan1", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7276"}, "otu75271": {"^ot:originalLabel": "Phyllorus pelletieri", "^ot:treebaseOTUId": "Tl7277"}, "otu75272": {"^ot:originalLabel": "Xerocomus subtomentosus", "^ot:treebaseOTUId": "Tl7278"}, "otu75273": {"^ot:originalLabel": "Chalciporus piperatus", "^ot:ottId": 946376, "^ot:ottTaxonName": "Chalciporus piperatus", "^ot:treebaseOTUId": "Tl7279"}, "otu75274": {"^ot:originalLabel": "Retiboletus ornatipes 5", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7280"}, "otu75275": {"^ot:originalLabel": "Retiboletus retipes 161", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7281"}, "otu75276": {"^ot:originalLabel": "Boletus coniferarum", "^ot:ottId": 123434, "^ot:ottTaxonName": "Boletus coniferarum", "^ot:treebaseOTUId": "Tl7282"}, "otu75277": {"^ot:originalLabel": "Tylopilus sp204", "^ot:treebaseOTUId": "Tl7283"}, "otu75278": {"^ot:originalLabel": "Retiboletus retipes 116", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7284"}, "otu75279": {"^ot:originalLabel": "Retiboletus ornatipes 219", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7285"}, "otu75280": {"^ot:originalLabel": "Xerocomus illudens", "^ot:ottId": 793446, "^ot:ottTaxonName": "Xerocomus illudens", "^ot:treebaseOTUId": "Tl7286"}, "otu75281": {"^ot:originalLabel": "Retiboletus retipes Japan3", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7287"}, "otu75282": {"^ot:originalLabel": "Boletus reticulatus", "^ot:ottId": 697639, "^ot:ottTaxonName": "Boletus reticulatus", "^ot:treebaseOTUId": "Tl7288"}, "otu75283": {"^ot:originalLabel": "Retiboletus flavoniger RH7247", "^ot:ottId": 5304085, "^ot:ottTaxonName": "Retiboletus flavoniger", "^ot:treebaseOTUId": "Tl7289"}, "otu75284": {"^ot:originalLabel": "Retiboletus ornatipes 11", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7290"}, "otu75285": {"^ot:originalLabel": "Retiboletus retipes 57", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7291"}, "otu75286": {"^ot:originalLabel": "Retiboletus ornatipes 215", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7292"}, "otu75287": {"^ot:originalLabel": "Boletus radicans", "^ot:ottId": 517663, "^ot:ottTaxonName": "Boletus radicans", "^ot:treebaseOTUId": "Tl7293"}, "otu75288": {"^ot:originalLabel": "Tylopilus felleus", "^ot:ottId": 646170, "^ot:ottTaxonName": "Tylopilus felleus", "^ot:treebaseOTUId": "Tl7294"}, "otu75289": {"^ot:originalLabel": "Boletus appendiculatus", "^ot:ottId": 123439, "^ot:ottTaxonName": "Boletus appendiculatus", "^ot:treebaseOTUId": "Tl7295"}, "otu75290": {"^ot:originalLabel": "Boletus aereus", "^ot:ottId": 123440, "^ot:ottTaxonName": "Boletus aereus", "^ot:treebaseOTUId": "Tl7297"}, "otu75291": {"^ot:originalLabel": "Coniophora puteana", "^ot:ottId": 429072, "^ot:ottTaxonName": "Coniophora puteana", "^ot:treebaseOTUId": "Tl7298"}, "otu75292": {"^ot:originalLabel": "Retiboletus ornatipes 201", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7299"}, "otu75293": {"^ot:originalLabel": "Retiboletus retipes 93", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7301"}, "otu75294": {"^ot:originalLabel": "Fistulinella viscida", "^ot:ottId": 697632, "^ot:ottTaxonName": "Fistulinella viscida", "^ot:treebaseOTUId": "Tl7302"}, "otu75295": {"^ot:originalLabel": "Retiboletus retipes 22", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7303"}, "otu75296": {"^ot:originalLabel": "Retiboletus ornatipes 94", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7304"}, "otu75297": {"^ot:originalLabel": "Boletus edulis Be2", "^ot:ottId": 1017219, "^ot:ottTaxonName": "Boletus edulis", "^ot:treebaseOTUId": "Tl7305"}, "otu75298": {"^ot:originalLabel": "Chalciporus amarellus", "^ot:ottId": 946376, "^ot:ottTaxonName": "Chalciporus piperatus", "^ot:treebaseOTUId": "Tl7306"}, "otu75299": {"^ot:originalLabel": "Retiboletus ornatipes 186", "^ot:ottId": 610332, "^ot:ottTaxonName": "Retiboletus ornatipes", "^ot:treebaseOTUId": "Tl7307"}, "otu75300": {"^ot:originalLabel": "Retiboletus nigerrimus", "^ot:ottId": 536373, "^ot:ottTaxonName": "Retiboletus nigerrimus", "^ot:treebaseOTUId": "Tl7308"}, "otu75301": {"^ot:originalLabel": "Boletus fechtneri", "^ot:ottId": 650685, "^ot:ottTaxonName": "Boletus fechtneri", "^ot:treebaseOTUId": "Tl7309"}, "otu75302": {"^ot:originalLabel": "Retiboletus flavoniger RH7189", "^ot:ottId": 5304085, "^ot:ottTaxonName": "Retiboletus flavoniger", "^ot:treebaseOTUId": "Tl7310"}, "otu75303": {"^ot:originalLabel": "Retiboletus retipes RH7567", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7311"}, "otu75304": {"^ot:originalLabel": "Retiboletus retipes Japan2", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7312"}, "otu75305": {"^ot:originalLabel": "Retiboletus retipes 96", "^ot:ottId": 5304086, "^ot:ottTaxonName": "Retiboletus retipes", "^ot:treebaseOTUId": "Tl7313"}}}}, "treesById": {"trees349": {"@otus": "otus349", "^ot:treeElementOrder": ["tree5539"], "treeById": {"tree5539": {"@xsi:type": "nex:FloatTree", "^ot:curatedType": "ML, LSU (rooted)", "^ot:inGroupClade": "node953405", "^ot:rootNodeId": "node953400", "edgeBySourceId": {"node953400": {"edge953401": {"@source": "node953400", "@target": "node953401"}, "edge953474": {"@source": "node953400", "@target": "node953474"}}, "node953401": {"edge953402": {"@source": "node953401", "@target": "node953402"}, "edge953471": {"@source": "node953401", "@target": "node953471"}}, "node953402": {"edge953403": {"@source": "node953402", "@target": "node953403"}, "edge953468": {"@source": "node953402", "@target": "node953468"}}, "node953403": {"edge953404": {"@source": "node953403", "@target": "node953404"}, "edge953457": {"@source": "node953403", "@target": "node953457"}}, "node953404": {"edge953405": {"@source": "node953404", "@target": "node953405"}, "edge953447": {"@source": "node953404", "@target": "node953447"}}, "node953405": {"edge953406": {"@source": "node953405", "@target": "node953406"}, "edge953444": {"@source": "node953405", "@target": "node953444"}}, "node953406": {"edge953407": {"@source": "node953406", "@target": "node953407"}, "edge953427": {"@source": "node953406", "@target": "node953427"}}, "node953407": {"edge953408": {"@source": "node953407", "@target": "node953408"}, "edge953424": {"@source": "node953407", "@target": "node953424"}}, "node953408": {"edge953409": {"@source": "node953408", "@target": "node953409"}, "edge953423": {"@source": "node953408", "@target": "node953423"}}, "node953409": {"edge953410": {"@source": "node953409", "@target": "node953410"}, "edge953418": {"@source": "node953409", "@target": "node953418"}, "edge953419": {"@source": "node953409", "@target": "node953419"}}, "node953410": {"edge953411": {"@source": "node953410", "@target": "node953411"}, "edge953412": {"@source": "node953410", "@target": "node953412"}}, "node953412": {"edge953413": {"@source": "node953412", "@target": "node953413"}, "edge953414": {"@source": "node953412", "@target": "node953414"}, "edge953417": {"@source": "node953412", "@target": "node953417"}}, "node953414": {"edge953415": {"@source": "node953414", "@target": "node953415"}, "edge953416": {"@source": "node953414", "@target": "node953416"}}, "node953419": {"edge953420": {"@source": "node953419", "@target": "node953420"}, "edge953421": {"@source": "node953419", "@target": "node953421"}, "edge953422": {"@source": "node953419", "@target": "node953422"}}, "node953424": {"edge953425": {"@source": "node953424", "@target": "node953425"}, "edge953426": {"@source": "node953424", "@target": "node953426"}}, "node953427": {"edge953428": {"@source": "node953427", "@target": "node953428"}, "edge953441": {"@source": "node953427", "@target": "node953441"}}, "node953428": {"edge953429": {"@source": "node953428", "@target": "node953429"}, "edge953440": {"@source": "node953428", "@target": "node953440"}}, "node953429": {"edge953430": {"@source": "node953429", "@target": "node953430"}, "edge953435": {"@source": "node953429", "@target": "node953435"}}, "node953430": {"edge953431": {"@source": "node953430", "@target": "node953431"}, "edge953434": {"@source": "node953430", "@target": "node953434"}}, "node953431": {"edge953432": {"@source": "node953431", "@target": "node953432"}, "edge953433": {"@source": "node953431", "@target": "node953433"}}, "node953435": {"edge953436": {"@source": "node953435", "@target": "node953436"}, "edge953437": {"@source": "node953435", "@target": "node953437"}}, "node953437": {"edge953438": {"@source": "node953437", "@target": "node953438"}, "edge953439": {"@source": "node953437", "@target": "node953439"}}, "node953441": {"edge953442": {"@source": "node953441", "@target": "node953442"}, "edge953443": {"@source": "node953441", "@target": "node953443"}}, "node953444": {"edge953445": {"@source": "node953444", "@target": "node953445"}, "edge953446": {"@source": "node953444", "@target": "node953446"}}, "node953447": {"edge953448": {"@source": "node953447", "@target": "node953448"}, "edge953451": {"@source": "node953447", "@target": "node953451"}, "edge953456": {"@source": "node953447", "@target": "node953456"}}, "node953448": {"edge953449": {"@source": "node953448", "@target": "node953449"}, "edge953450": {"@source": "node953448", "@target": "node953450"}}, "node953451": {"edge953452": {"@source": "node953451", "@target": "node953452"}, "edge953453": {"@source": "node953451", "@target": "node953453"}}, "node953453": {"edge953454": {"@source": "node953453", "@target": "node953454"}, "edge953455": {"@source": "node953453", "@target": "node953455"}}, "node953457": {"edge953458": {"@source": "node953457", "@target": "node953458"}, "edge953463": {"@source": "node953457", "@target": "node953463"}}, "node953458": {"edge953459": {"@source": "node953458", "@target": "node953459"}, "edge953460": {"@source": "node953458", "@target": "node953460"}}, "node953460": {"edge953461": {"@source": "node953460", "@target": "node953461"}, "edge953462": {"@source": "node953460", "@target": "node953462"}}, "node953463": {"edge953464": {"@source": "node953463", "@target": "node953464"}, "edge953465": {"@source": "node953463", "@target": "node953465"}}, "node953465": {"edge953466": {"@source": "node953465", "@target": "node953466"}, "edge953467": {"@source": "node953465", "@target": "node953467"}}, "node953468": {"edge953469": {"@source": "node953468", "@target": "node953469"}, "edge953470": {"@source": "node953468", "@target": "node953470"}}, "node953471": {"edge953472": {"@source": "node953471", "@target": "node953472"}, "edge953473": {"@length": 2.0, "@source": "node953471", "@target": "node953473"}}, "node953474": {"edge953475": {"@source": "node953474", "@target": "node953475"}, "edge953478": {"@source": "node953474", "@target": "node953478"}}, "node953475": {"edge953476": {"@source": "node953475", "@target": "node953476"}, "edge953477": {"@source": "node953475", "@target": "node953477"}}}, "nodeById": {"node953400": {"@root": true}, "node953401": {}, "node953402": {}, "node953403": {}, "node953404": {}, "node953405": {}, "node953406": {}, "node953407": {}, "node953408": {}, "node953409": {}, "node953410": {}, "node953411": {"@otu": "otu75286"}, "node953412": {}, "node953413": {"@otu": "otu75284"}, "node953414": {}, "node953415": {"@otu": "otu75274"}, "node953416": {"@otu": "otu75296"}, "node953417": {"@otu": "otu75293"}, "node953418": {"@otu": "otu75279"}, "node953419": {}, "node953420": {"@otu": "otu75292"}, "node953421": {"@otu": "otu75275"}, "node953422": {"@otu": "otu75299"}, "node953423": {"@otu": "otu75300"}, "node953424": {}, "node953425": {"@otu": "otu75277"}, "node953426": {"@otu": "otu75268"}, "node953427": {}, "node953428": {}, "node953429": {}, "node953430": {}, "node953431": {}, "node953432": {"@otu": "otu75304"}, "node953433": {"@otu": "otu75281"}, "node953434": {"@otu": "otu75270"}, "node953435": {}, "node953436": {"@otu": "otu75303"}, "node953437": {}, "node953438": {"@otu": "otu75305"}, "node953439": {"@otu": "otu75295"}, "node953440": {"@otu": "otu75285"}, "node953441": {}, "node953442": {"@otu": "otu75278"}, "node953443": {"@otu": "otu75265"}, "node953444": {}, "node953445": {"@otu": "otu75283"}, "node953446": {"@otu": "otu75302"}, "node953447": {}, "node953448": {}, "node953449": {"@otu": "otu75288"}, "node953450": {"@otu": "otu75269"}, "node953451": {}, "node953452": {"@otu": "otu75271"}, "node953453": {}, "node953454": {"@otu": "otu75280"}, "node953455": {"@otu": "otu75272"}, "node953456": {"@otu": "otu75294"}, "node953457": {}, "node953458": {}, "node953459": {"@otu": "otu75297"}, "node953460": {}, "node953461": {"@otu": "otu75282"}, "node953462": {"@otu": "otu75290"}, "node953463": {}, "node953464": {"@otu": "otu75287"}, "node953465": {}, "node953466": {"@otu": "otu75276"}, "node953467": {"@otu": "otu75264"}, "node953468": {}, "node953469": {"@otu": "otu75301"}, "node953470": {"@otu": "otu75289"}, "node953471": {}, "node953472": {"@otu": "otu75298"}, "node953473": {"@otu": "otu75273"}, "node953474": {}, "node953475": {}, "node953476": {"@otu": "otu75267"}, "node953477": {"@otu": "otu75266"}, "node953478": {"@otu": "otu75291"}}}}}}}}, "branch2sha": {"master": "24afc85a444963f10ca51c6e20138fe592a4b525"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"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": "fb9410bc19523ea9ec208a35959e8a4cab0030d5", "author_name": "Mark T. Holder", "author_email": "mtholder@gmail.com", "date": "Thu, 29 May 2014 11:33:49 -0500", "date_ISO_8601": "2014-05-29 11:33:49 -0500", "relative_date": "12 years ago", "message_subject": "otu labels to the new system.", "message_body": "Ran peyotl/dev/phylografter_workaround.py to\nfix this.\nNoted (in phylografter issue 119), that study\n2918 is not valid."}, {"id": "ee1f1d7005bd2a2741cef4563a3646057713193b", "author_name": "Mark T. Holder", "author_email": "None", "date": "Thu, 29 May 2014 15:23:06 +0000", "date_ISO_8601": "2014-05-29 15:23:06 +0000", "relative_date": "12 years ago", "message_subject": "Sync from phylografter", "message_body": "(Update Study #pg_349 via OpenTree API)"}, {"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"}]}