{"sha": "19ec8a2da4b35c55075f155f9fb4d01281774fe5", "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"}]}}]}, "^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:dataDeposit"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1832"], "^ot:curatorName": "bryan drew", "^ot:focalClade": 511898, "^ot:focalCladeOTTTaxonName": "Echinops", "^ot:messages": {"message": []}, "^ot:otusElementOrder": ["otus934"], "^ot:studyId": "pg_934", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1007/BF02804288"}, "^ot:studyPublicationReference": "Garnatje, T. [et al. 2005], Susanna, A., Garcia-Jacas, N., Vilatersana, R., & Vall\u00e8s, J. 2005. A first approach to the molecular phylogeny of the genus Echinops (Asteraceae): Sectional delimitation and relationships with the genus Acantholepis Less. Folia Geobot. 40: 407-419/", "^ot:studyYear": 2005, "^ot:tag": [], "^ot:treesElementOrder": ["trees934"], "otusById": {"otus934": {"otuById": {"otu207457": {"^ot:originalLabel": "Echinops emiliae", "^ot:ottId": 234582, "^ot:ottTaxonName": "Echinops emiliae"}, "otu207458": {"^ot:originalLabel": "Echinops strigosus", "^ot:ottId": 808894, "^ot:ottTaxonName": "Echinops strigosus"}, "otu207459": {"^ot:originalLabel": "Echinops nanus", "^ot:ottId": 234578, "^ot:ottTaxonName": "Echinops nanus"}, "otu207460": {"^ot:originalLabel": "Acantholepis orientalis", "^ot:ottId": 182566, "^ot:ottTaxonName": "Acantholepis orientalis"}, "otu207461": {"^ot:originalLabel": "Echinops onopordum", "^ot:ottId": 234592, "^ot:ottTaxonName": "Echinops onopordum"}, "otu207462": {"^ot:originalLabel": "Echinops talassicus", "^ot:ottId": 808888, "^ot:ottTaxonName": "Echinops talassicus"}, "otu207463": {"^ot:originalLabel": "Echinops tschimganicus", "^ot:ottId": 808909, "^ot:ottTaxonName": "Echinops tschimganicus"}, "otu207464": {"^ot:originalLabel": "Echinops ritro", "^ot:ottId": 643726, "^ot:ottTaxonName": "Echinops ritro"}, "otu207465": {"^ot:originalLabel": "Echinops albicaulis", "^ot:ottId": 147671, "^ot:ottTaxonName": "Echinops albicaulis"}, "otu207466": {"^ot:originalLabel": "Echinops microcephalus", "^ot:ottId": 234580, "^ot:ottTaxonName": "Echinops microcephalus"}, "otu207467": {"^ot:originalLabel": "Echinops niveus", "^ot:ottId": 234594, "^ot:ottTaxonName": "Echinops niveus"}, "otu207468": {"^ot:originalLabel": "Echinops banaticus", "^ot:ottId": 802161, "^ot:ottTaxonName": "Echinops bannaticus"}, "otu207469": {"^ot:originalLabel": "Echinops tournefortii", "^ot:ottId": 808907, "^ot:ottTaxonName": "Echinops tournefortii"}, "otu207470": {"^ot:originalLabel": "Echinops szovitsii", "^ot:ottId": 808885, "^ot:ottTaxonName": "Echinops szovitsii"}, "otu207471": {"^ot:originalLabel": "Echinops ruthenicus", "^ot:ottId": 808896, "^ot:ottTaxonName": "Echinops ritro subsp. ruthenicus"}, "otu207472": {"^ot:originalLabel": "Echinops orientalis", "^ot:ottId": 808902, "^ot:ottTaxonName": "Echinops orientalis"}, "otu207473": {"^ot:originalLabel": "Echinops persicus", "^ot:ottId": 808904, "^ot:ottTaxonName": "Echinops persicus"}, "otu207474": {"^ot:originalLabel": "Echinops exaltatus", "^ot:ottId": 222360, "^ot:ottTaxonName": "Echinops exaltatus"}, "otu207475": {"^ot:originalLabel": "Echinops sphaerocephalusV", "^ot:ottId": 25036, "^ot:ottTaxonName": "Echinops sphaerocephalus"}, "otu207476": {"^ot:originalLabel": "Echinops siculus", "^ot:ottId": 808890, "^ot:ottTaxonName": "Echinops ritro subsp. siculus"}, "otu207477": {"^ot:originalLabel": "Echinops saissanicus", "^ot:ottId": 808900, "^ot:ottTaxonName": "Echinops saissanicus"}, "otu207478": {"^ot:originalLabel": "Echinops galaticus", "^ot:ottId": 234586, "^ot:ottTaxonName": "Echinops galaticus"}, "otu207479": {"^ot:originalLabel": "Echinops humilis", "^ot:ottId": 368803, "^ot:ottTaxonName": "Echinops humilis"}, "otu207480": {"^ot:originalLabel": "Echinops heteromorphus", "^ot:ottId": 234574, "^ot:ottTaxonName": "Echinops heteromorphus"}, "otu207481": {"^ot:originalLabel": "Echinops ecbatanus", "^ot:ottId": 425526, "^ot:ottTaxonName": "Echinops ecbatanus"}, "otu207482": {"^ot:originalLabel": "Echinops cornigerus", "^ot:ottId": 234584, "^ot:ottTaxonName": "Echinops cornigerus"}, "otu207483": {"^ot:originalLabel": "Echinops hedgei", "^ot:ottId": 234576, "^ot:ottTaxonName": "Echinops hedgei"}, "otu207484": {"^ot:originalLabel": "Echinops fontqueri", "^ot:ottId": 234588, "^ot:ottTaxonName": "Echinops fontqueri"}, "otu207485": {"^ot:originalLabel": "Echinops bithynicus", "^ot:ottId": 147673, "^ot:ottTaxonName": "Echinops spinosissimus subsp. bithynicus"}, "otu207486": {"^ot:originalLabel": "Echinops spinosissimus", "^ot:ottId": 13142, "^ot:ottTaxonName": "Echinops spinosissimus"}, "otu207487": {"^ot:originalLabel": "Echinops viscosus", "^ot:ottId": 13146, "^ot:ottTaxonName": "Echinops viscosus"}, "otu207488": {"^ot:originalLabel": "Cousiniopsis atractyloides", "^ot:ottId": 13135, "^ot:ottTaxonName": "Cousiniopsis atractyloides"}, "otu207489": {"^ot:originalLabel": "Cardopatium corymbosum", "^ot:ottId": 756698, "^ot:ottTaxonName": "Cardopatium corymbosum"}}}}, "treesById": {"trees934": {"@otus": "otus934", "^ot:treeElementOrder": ["tree1832"], "treeById": {"tree1832": {"@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:substitutionCount", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "BI", "^ot:inGroupClade": "node491214", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node491207", "^ot:specifiedRoot": "node491207", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node491207": {"edge491208": {"@length": 0.11006134415, "@source": "node491207", "@target": "node491208"}, "edge491258": {"@length": 0.11006134414981393, "@source": "node491207", "@target": "node491258"}}, "node491208": {"edge491209": {"@length": 0.03112486156314004, "@source": "node491208", "@target": "node491209"}, "edge491210": {"@length": 0.06467486447131116, "@source": "node491208", "@target": "node491210"}, "edge491211": {"@length": 0.06827092276671615, "@source": "node491208", "@target": "node491211"}, "edge491214": {"@length": 0.04208605222256556, "@source": "node491208", "@target": "node491214"}}, "node491211": {"edge491212": {"@length": 0.031487450831983455, "@source": "node491211", "@target": "node491212"}, "edge491213": {"@length": 0.053315979180414086, "@source": "node491211", "@target": "node491213"}}, "node491214": {"edge491215": {"@length": 0.011188221812306554, "@source": "node491214", "@target": "node491215"}, "edge491216": {"@length": 0.016520786653838937, "@source": "node491214", "@target": "node491216"}}, "node491216": {"edge491217": {"@length": 0.023608349909439996, "@source": "node491216", "@target": "node491217"}, "edge491220": {"@length": 0.004117173237542349, "@source": "node491216", "@target": "node491220"}, "edge491225": {"@length": 0.009031440244568756, "@source": "node491216", "@target": "node491225"}, "edge491237": {"@length": 0.0061025247433536545, "@source": "node491216", "@target": "node491237"}, "edge491240": {"@length": 0.02125612362722773, "@source": "node491216", "@target": "node491240"}, "edge491241": {"@length": 0.010836691336442328, "@source": "node491216", "@target": "node491241"}, "edge491242": {"@length": 0.005013997186250785, "@source": "node491216", "@target": "node491242"}}, "node491217": {"edge491218": {"@length": 0.005106802575568281, "@source": "node491217", "@target": "node491218"}, "edge491219": {"@length": 0.005674248391770609, "@source": "node491217", "@target": "node491219"}}, "node491220": {"edge491221": {"@length": 0.0036848682963296353, "@source": "node491220", "@target": "node491221"}, "edge491224": {"@length": 0.006980102473736816, "@source": "node491220", "@target": "node491224"}}, "node491221": {"edge491222": {"@length": 0.01484410191999741, "@source": "node491221", "@target": "node491222"}, "edge491223": {"@length": 0.01420136428971297, "@source": "node491221", "@target": "node491223"}}, "node491225": {"edge491226": {"@length": 0.003887478440176173, "@source": "node491225", "@target": "node491226"}, "edge491236": {"@length": 0.004317648970665888, "@source": "node491225", "@target": "node491236"}}, "node491226": {"edge491227": {"@length": 0.003859261748759224, "@source": "node491226", "@target": "node491227"}, "edge491228": {"@length": 0.008786651008104218, "@source": "node491226", "@target": "node491228"}, "edge491235": {"@length": 0.0016157965931944407, "@source": "node491226", "@target": "node491235"}}, "node491228": {"edge491229": {"@length": 0.004306761038714746, "@source": "node491228", "@target": "node491229"}, "edge491234": {"@length": 0.0017010362199952334, "@source": "node491228", "@target": "node491234"}}, "node491229": {"edge491230": {"@length": 0.00416028049837508, "@source": "node491229", "@target": "node491230"}, "edge491231": {"@length": 0.00170585868068035, "@source": "node491229", "@target": "node491231"}, "edge491232": {"@length": 0.001727732741560739, "@source": "node491229", "@target": "node491232"}, "edge491233": {"@length": 0.0016641320112925073, "@source": "node491229", "@target": "node491233"}}, "node491237": {"edge491238": {"@length": 0.01966737093683707, "@source": "node491237", "@target": "node491238"}, "edge491239": {"@length": 0.009521162480183254, "@source": "node491237", "@target": "node491239"}}, "node491242": {"edge491243": {"@length": 0.02104864044802135, "@source": "node491242", "@target": "node491243"}, "edge491244": {"@length": 0.010716259043558551, "@source": "node491242", "@target": "node491244"}}, "node491244": {"edge491245": {"@length": 0.005641891221296824, "@source": "node491244", "@target": "node491245"}, "edge491250": {"@length": 0.003902836369716056, "@source": "node491244", "@target": "node491250"}}, "node491245": {"edge491246": {"@length": 0.013084268531484644, "@source": "node491245", "@target": "node491246"}, "edge491249": {"@length": 0.006381087713920763, "@source": "node491245", "@target": "node491249"}}, "node491246": {"edge491247": {"@length": 0.004753622932516577, "@source": "node491246", "@target": "node491247"}, "edge491248": {"@length": 0.004113084302300007, "@source": "node491246", "@target": "node491248"}}, "node491250": {"edge491251": {"@length": 0.005655394838766814, "@source": "node491250", "@target": "node491251"}, "edge491252": {"@length": 0.00911516803731166, "@source": "node491250", "@target": "node491252"}}, "node491252": {"edge491253": {"@length": 0.01070833856459047, "@source": "node491252", "@target": "node491253"}, "edge491254": {"@length": 0.007148429280822266, "@source": "node491252", "@target": "node491254"}}, "node491254": {"edge491255": {"@length": 0.001613891030948389, "@source": "node491254", "@target": "node491255"}, "edge491256": {"@length": 0.0016674592428719825, "@source": "node491254", "@target": "node491256"}, "edge491257": {"@length": 0.0016550627836971477, "@source": "node491254", "@target": "node491257"}}, "node491258": {"edge491259": {"@length": 0.07716558335437695, "@source": "node491258", "@target": "node491259"}, "edge491260": {"@length": 0.16256497484308519, "@source": "node491258", "@target": "node491260"}}}, "nodeById": {"node491207": {"@root": true}, "node491208": {}, "node491209": {"@otu": "otu207457"}, "node491210": {"@otu": "otu207458"}, "node491211": {}, "node491212": {"@otu": "otu207459"}, "node491213": {"@otu": "otu207460"}, "node491214": {}, "node491215": {"@otu": "otu207461"}, "node491216": {}, "node491217": {}, "node491218": {"@otu": "otu207462"}, "node491219": {"@otu": "otu207463"}, "node491220": {}, "node491221": {}, "node491222": {"@otu": "otu207464"}, "node491223": {"@otu": "otu207465"}, "node491224": {"@otu": "otu207466"}, "node491225": {}, "node491226": {}, "node491227": {"@otu": "otu207467"}, "node491228": {}, "node491229": {}, "node491230": {"@otu": "otu207468"}, "node491231": {"@otu": "otu207469"}, "node491232": {"@otu": "otu207470"}, "node491233": {"@otu": "otu207471"}, "node491234": {"@otu": "otu207472"}, "node491235": {"@otu": "otu207473"}, "node491236": {"@otu": "otu207474"}, "node491237": {}, "node491238": {"@otu": "otu207475"}, "node491239": {"@otu": "otu207476"}, "node491240": {"@otu": "otu207477"}, "node491241": {"@otu": "otu207478"}, "node491242": {}, "node491243": {"@otu": "otu207479"}, "node491244": {}, "node491245": {}, "node491246": {}, "node491247": {"@otu": "otu207480"}, "node491248": {"@otu": "otu207481"}, "node491249": {"@otu": "otu207482"}, "node491250": {}, "node491251": {"@otu": "otu207483"}, "node491252": {}, "node491253": {"@otu": "otu207484"}, "node491254": {}, "node491255": {"@otu": "otu207485"}, "node491256": {"@otu": "otu207486"}, "node491257": {"@otu": "otu207487"}, "node491258": {}, "node491259": {"@otu": "otu207488"}, "node491260": {"@otu": "otu207489"}}}}}}}}, "branch2sha": {"master": "19ec8a2da4b35c55075f155f9fb4d01281774fe5"}, "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": "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"}]}