{"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"}]}}]}, "^ot:annotationEvents": {"annotation": [{"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": []}]}, "^ot:candidateTreeForSynthesis": ["tree2660"], "^ot:curatorName": "Chris Owen", "^ot:dataDeposit": {"@href": "http://purl.org/phylo/treebase/phylows/study/TB2:S1784"}, "^ot:focalClade": 935379, "^ot:focalCladeOTTTaxonName": "Brachyura", "^ot:messages": {"message": []}, "^ot:otusElementOrder": ["otus1336"], "^ot:studyId": "pg_1336", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1016/j.ympev.2007.03.022 "}, "^ot:studyPublicationReference": "Ahyong, S., Lai J., Sharkey D., Colgan D., & Ng P. 2007. Phylogenetics of the brachyuran crabs (Crustacea: Decapoda): the status of Podotremata based on small subunit nuclear ribosomal RNA. Molecular Phylogenetics and Evolution 45 (2): 576-586.", "^ot:studyYear": 2007, "^ot:tag": [], "^ot:treesElementOrder": ["trees1336"], "otusById": {"otus1336": {"otuById": {"otu243485": {"^ot:originalLabel": "Carcinus maenas", "^ot:ottId": 1089892, "^ot:ottTaxonName": "Carcinus maenas", "^ot:treebaseOTUId": "Tl187904"}, "otu243486": {"^ot:originalLabel": "Trapezia symodoce", "^ot:ottId": 211903, "^ot:ottTaxonName": "Trapezia cymodoce", "^ot:treebaseOTUId": "Tl47784"}, "otu243487": {"^ot:originalLabel": "Ranina ranina", "^ot:ottId": 668220, "^ot:ottTaxonName": "Ranina ranina", "^ot:treebaseOTUId": "Tl47785"}, "otu243488": {"^ot:originalLabel": "Hypoconcha spinosissima", "^ot:ottId": 611205, "^ot:ottTaxonName": "Hypoconcha spinosissima", "^ot:treebaseOTUId": "Tl47786"}, "otu243489": {"^ot:originalLabel": "Tymolus brucei", "^ot:ottId": 38071, "^ot:ottTaxonName": "Tymolus brucei", "^ot:treebaseOTUId": "Tl47787"}, "otu243490": {"^ot:originalLabel": "Paromola japonica", "^ot:ottId": 32435, "^ot:ottTaxonName": "Paromola japonica", "^ot:treebaseOTUId": "Tl47788"}, "otu243491": {"^ot:originalLabel": "Symethis corallica", "^ot:ottId": 38074, "^ot:ottTaxonName": "Symethis corallica", "^ot:treebaseOTUId": "Tl47789"}, "otu243492": {"^ot:originalLabel": "Menaethius monoceros", "^ot:ottId": 308482, "^ot:ottTaxonName": "Menaethius monoceros", "^ot:treebaseOTUId": "Tl47790"}, "otu243493": {"^ot:originalLabel": "Munida quadrispina", "^ot:ottId": 965744, "^ot:ottTaxonName": "Munida quadrispina", "^ot:treebaseOTUId": "Tl47791"}, "otu243494": {"^ot:originalLabel": "Chlorodiella nigra", "^ot:ottId": 990046, "^ot:ottTaxonName": "Chlorodiella nigra", "^ot:treebaseOTUId": "Tl47792"}, "otu243495": {"^ot:originalLabel": "Calappa bilineata", "^ot:ottId": 89918, "^ot:ottTaxonName": "Calappa bilineata", "^ot:treebaseOTUId": "Tl47793"}, "otu243496": {"^ot:originalLabel": "Corycodus sp", "^ot:ottId": 38069, "^ot:ottTaxonName": "Corycodus sp. ZRC 2006.123", "^ot:treebaseOTUId": "Tl47794"}, "otu243497": {"^ot:originalLabel": "Tanaoa pustulosus", "^ot:ottId": 2977808, "^ot:ottTaxonName": "Tanaoa pustulosus", "^ot:treebaseOTUId": "Tl47795"}, "otu243498": {"^ot:originalLabel": "Latreillia valida", "^ot:ottId": 2977049, "^ot:ottTaxonName": "Latreillia valida", "^ot:treebaseOTUId": "Tl47796"}, "otu243499": {"^ot:originalLabel": "Homolodromia kai", "^ot:ottId": 611207, "^ot:ottTaxonName": "Homolodromia kai", "^ot:treebaseOTUId": "Tl47797"}, "otu243500": {"^ot:originalLabel": "Pylocheles macrops", "^ot:ottId": 1069195, "^ot:ottTaxonName": "Xylocheles macrops", "^ot:treebaseOTUId": "Tl47798"}, "otu243501": {"^ot:originalLabel": "Daira perlata", "^ot:ottId": 990069, "^ot:ottTaxonName": "Daira perlata", "^ot:treebaseOTUId": "Tl47799"}, "otu243502": {"^ot:originalLabel": "Raninoides sp", "^ot:ottId": 808059, "^ot:ottTaxonName": "Raninoides louisianensis", "^ot:treebaseOTUId": "Tl47800"}, "otu243503": {"^ot:originalLabel": "Lauridromia dehaani", "^ot:ottId": 728460, "^ot:ottTaxonName": "Lauridromia dehaani", "^ot:treebaseOTUId": "Tl47801"}, "otu243504": {"^ot:originalLabel": "Dorippoides facchino", "^ot:ottId": 687188, "^ot:ottTaxonName": "Dorippoides facchino", "^ot:treebaseOTUId": "Tl47802"}, "otu243505": {"^ot:originalLabel": "Macrophthalmus setosus", "^ot:ottId": 32457, "^ot:ottTaxonName": "Macrophthalmus setosus", "^ot:treebaseOTUId": "Tl47803"}, "otu243506": {"^ot:originalLabel": "Amarinus paralacustris", "^ot:ottId": 664129, "^ot:ottTaxonName": "Amarinus paralacustris", "^ot:treebaseOTUId": "Tl47804"}, "otu243507": {"^ot:originalLabel": "Homolochunia sibogae", "^ot:ottId": 38077, "^ot:ottTaxonName": "Homolomannia sibogae", "^ot:treebaseOTUId": "Tl47805"}, "otu243508": {"^ot:originalLabel": "Moloha majora", "^ot:ottId": 611209, "^ot:ottTaxonName": "Moloha majora", "^ot:treebaseOTUId": "Tl47806"}, "otu243509": {"^ot:originalLabel": "Carpilius convexus", "^ot:ottId": 677780, "^ot:ottTaxonName": "Carpilius convexus", "^ot:treebaseOTUId": "Tl47807"}, "otu243510": {"^ot:originalLabel": "Leptograpsus variegatus", "^ot:ottId": 43264, "^ot:ottTaxonName": "Leptograpsus variegatus", "^ot:treebaseOTUId": "Tl47808"}, "otu243511": {"^ot:originalLabel": "Cymonomoides delli", "^ot:ottId": 664121, "^ot:ottTaxonName": "Cymonomoides delli", "^ot:treebaseOTUId": "Tl47809"}, "otu243512": {"^ot:originalLabel": "Eriphia sebana", "^ot:ottId": 974226, "^ot:ottTaxonName": "Eriphia sebana", "^ot:treebaseOTUId": "Tl47810"}, "otu243513": {"^ot:originalLabel": "Schizophrys aspera", "^ot:ottId": 308484, "^ot:ottTaxonName": "Schizophrys aspera", "^ot:treebaseOTUId": "Tl47811"}, "otu243514": {"^ot:originalLabel": "Rhinolambrus longispinus", "^ot:ottId": 687185, "^ot:ottTaxonName": "Rhinolambrus longispinus", "^ot:treebaseOTUId": "Tl47812"}, "otu243515": {"^ot:originalLabel": "Aethra scruposa", "^ot:ottId": 89927, "^ot:ottTaxonName": "Aethra scruposa", "^ot:treebaseOTUId": "Tl47813"}, "otu243516": {"^ot:originalLabel": "Metadynomene tanensis", "^ot:ottId": 611204, "^ot:ottTaxonName": "Metadynomene tanensis", "^ot:treebaseOTUId": "Tl47814"}, "otu243517": {"^ot:originalLabel": "Hepatus ephileticus", "^ot:ottId": 808066, "^ot:ottTaxonName": "Hepatus epheliticus", "^ot:treebaseOTUId": "Tl47815"}}}}, "treesById": {"trees1336": {"@otus": "otus1336", "^ot:treeElementOrder": ["tree2660"], "treeById": {"tree2660": {"@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:changesCount", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "MPT", "^ot:inGroupClade": "node590807", "^ot:outGroupEdge": "", "^ot:rootNodeId": "node590803", "^ot:specifiedRoot": "node590803", "^ot:tag": ["choose me", "ingroup added;"], "^ot:unrootedTree": false, "edgeBySourceId": {"node590803": {"edge590804": {"@source": "node590803", "@target": "node590804"}, "edge590805": {"@source": "node590803", "@target": "node590805"}}, "node590805": {"edge590806": {"@source": "node590805", "@target": "node590806"}, "edge590807": {"@source": "node590805", "@target": "node590807"}}, "node590807": {"edge590808": {"@source": "node590807", "@target": "node590808"}, "edge590822": {"@source": "node590807", "@target": "node590822"}}, "node590808": {"edge590809": {"@source": "node590808", "@target": "node590809"}, "edge590814": {"@source": "node590808", "@target": "node590814"}}, "node590809": {"edge590810": {"@source": "node590809", "@target": "node590810"}, "edge590813": {"@source": "node590809", "@target": "node590813"}}, "node590810": {"edge590811": {"@source": "node590810", "@target": "node590811"}, "edge590812": {"@source": "node590810", "@target": "node590812"}}, "node590814": {"edge590815": {"@source": "node590814", "@target": "node590815"}, "edge590816": {"@source": "node590814", "@target": "node590816"}}, "node590816": {"edge590817": {"@source": "node590816", "@target": "node590817"}, "edge590818": {"@source": "node590816", "@target": "node590818"}, "edge590821": {"@source": "node590816", "@target": "node590821"}}, "node590818": {"edge590819": {"@source": "node590818", "@target": "node590819"}, "edge590820": {"@source": "node590818", "@target": "node590820"}}, "node590822": {"edge590823": {"@source": "node590822", "@target": "node590823"}, "edge590828": {"@source": "node590822", "@target": "node590828"}}, "node590823": {"edge590824": {"@source": "node590823", "@target": "node590824"}, "edge590827": {"@source": "node590823", "@target": "node590827"}}, "node590824": {"edge590825": {"@source": "node590824", "@target": "node590825"}, "edge590826": {"@source": "node590824", "@target": "node590826"}}, "node590828": {"edge590829": {"@source": "node590828", "@target": "node590829"}, "edge590834": {"@source": "node590828", "@target": "node590834"}}, "node590829": {"edge590830": {"@source": "node590829", "@target": "node590830"}, "edge590833": {"@source": "node590829", "@target": "node590833"}}, "node590830": {"edge590831": {"@source": "node590830", "@target": "node590831"}, "edge590832": {"@source": "node590830", "@target": "node590832"}}, "node590834": {"edge590835": {"@source": "node590834", "@target": "node590835"}, "edge590862": {"@source": "node590834", "@target": "node590862"}}, "node590835": {"edge590836": {"@source": "node590835", "@target": "node590836"}, "edge590839": {"@source": "node590835", "@target": "node590839"}}, "node590836": {"edge590837": {"@source": "node590836", "@target": "node590837"}, "edge590838": {"@source": "node590836", "@target": "node590838"}}, "node590839": {"edge590840": {"@source": "node590839", "@target": "node590840"}, "edge590861": {"@source": "node590839", "@target": "node590861"}}, "node590840": {"edge590841": {"@source": "node590840", "@target": "node590841"}, "edge590844": {"@source": "node590840", "@target": "node590844"}}, "node590841": {"edge590842": {"@source": "node590841", "@target": "node590842"}, "edge590843": {"@source": "node590841", "@target": "node590843"}}, "node590844": {"edge590845": {"@source": "node590844", "@target": "node590845"}, "edge590860": {"@source": "node590844", "@target": "node590860"}}, "node590845": {"edge590846": {"@source": "node590845", "@target": "node590846"}, "edge590847": {"@source": "node590845", "@target": "node590847"}, "edge590859": {"@source": "node590845", "@target": "node590859"}}, "node590847": {"edge590848": {"@source": "node590847", "@target": "node590848"}, "edge590854": {"@source": "node590847", "@target": "node590854"}}, "node590848": {"edge590849": {"@source": "node590848", "@target": "node590849"}, "edge590850": {"@source": "node590848", "@target": "node590850"}, "edge590853": {"@source": "node590848", "@target": "node590853"}}, "node590850": {"edge590851": {"@source": "node590850", "@target": "node590851"}, "edge590852": {"@source": "node590850", "@target": "node590852"}}, "node590854": {"edge590855": {"@source": "node590854", "@target": "node590855"}, "edge590856": {"@source": "node590854", "@target": "node590856"}}, "node590856": {"edge590857": {"@source": "node590856", "@target": "node590857"}, "edge590858": {"@source": "node590856", "@target": "node590858"}}, "node590862": {"edge590863": {"@source": "node590862", "@target": "node590863"}, "edge590864": {"@source": "node590862", "@target": "node590864"}}}, "nodeById": {"node590803": {"@root": true}, "node590804": {"@otu": "otu243493"}, "node590805": {}, "node590806": {"@otu": "otu243500"}, "node590807": {}, "node590808": {}, "node590809": {}, "node590810": {}, "node590811": {"@otu": "otu243503"}, "node590812": {"@otu": "otu243516"}, "node590813": {"@otu": "otu243488"}, "node590814": {}, "node590815": {"@otu": "otu243499"}, "node590816": {}, "node590817": {"@otu": "otu243490"}, "node590818": {}, "node590819": {"@otu": "otu243508"}, "node590820": {"@otu": "otu243498"}, "node590821": {"@otu": "otu243507"}, "node590822": {}, "node590823": {}, "node590824": {}, "node590825": {"@otu": "otu243487"}, "node590826": {"@otu": "otu243502"}, "node590827": {"@otu": "otu243491"}, "node590828": {}, "node590829": {}, "node590830": {}, "node590831": {"@otu": "otu243489"}, "node590832": {"@otu": "otu243511"}, "node590833": {"@otu": "otu243496"}, "node590834": {}, "node590835": {}, "node590836": {}, "node590837": {"@otu": "otu243504"}, "node590838": {"@otu": "otu243506"}, "node590839": {}, "node590840": {}, "node590841": {}, "node590842": {"@otu": "otu243514"}, "node590843": {"@otu": "otu243485"}, "node590844": {}, "node590845": {}, "node590846": {"@otu": "otu243494"}, "node590847": {}, "node590848": {}, "node590849": {"@otu": "otu243509"}, "node590850": {}, "node590851": {"@otu": "otu243501"}, "node590852": {"@otu": "otu243517"}, "node590853": {"@otu": "otu243515"}, "node590854": {}, "node590855": {"@otu": "otu243497"}, "node590856": {}, "node590857": {"@otu": "otu243510"}, "node590858": {"@otu": "otu243505"}, "node590859": {"@otu": "otu243512"}, "node590860": {"@otu": "otu243486"}, "node590861": {"@otu": "otu243495"}, "node590862": {}, "node590863": {"@otu": "otu243492"}, "node590864": {"@otu": "otu243513"}}}}}}}}, "branch2sha": {"master": "c33806c9ee11db205ee8c02a42e31b1c3128e299"}, "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"}]}