{"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": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@id": "peyotl-validator", "@name": "validate_ot_nexson.py", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": ["--embed", "--agent-only"], "otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2014-08-18T20:28:56.777Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"autoAcceptExactMatches": false, "searchContext": {"$": "Arthropods"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2014-08-18T20:28:56.777Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": []}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2024-12-13T20:42:20.698Z", "@description": "Describes external namesets merged into this study", "@id": "merged-namesets-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "MERGED_NAMESET_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"namesets": {"nameset": [{"description": {"$": "Nameset merged by `Valeria Ensenat Rivera`. 2 mappings tried, 2 successfully applied. Nameset was pasted directly in curation app."}}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node1147568", "@treesID": "trees2838", "@treeID": "tree6594", "@nodeID": "node1147568"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node1147569", "@treesID": "trees2838", "@treeID": "tree6594", "@nodeID": "node1147569"}, "@severity": "WARNING"}, {"@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@top": "otus", "@idref": "otu421881", "@otusID": "otus2838", "@otuID": "otu421881"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu421887", "otu421888"], "refersTo": {"@top": "otus", "@idref": "otus2838", "@otusID": "otus2838"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["highestMintedElementIDs"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree6594", "@treesID": "trees2838", "@treeID": "tree6594"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree6594"], "^ot:comment": "Focal clade says \"Pleocyemata\", but looks like \"Decapoda\" (JWB).", "^ot:curatorName": ["Chris Owen", "Joseph W. Brown", "Valeria Ensenat Rivera"], "^ot:dataDeposit": {"@href": ""}, "^ot:focalClade": 736321, "^ot:focalCladeOTTTaxonName": "Pleocyemata", "^ot:otusElementOrder": ["otus2838"], "^ot:studyId": "pg_2838", "^ot:studyPublication": {"@href": "http://dx.doi.org/10.1093/sysbio/syu008"}, "^ot:studyPublicationReference": "Bracken-Grissom, Heather D., Shane T. Ahyong, Richard D. Wilkinson, Rodney M. Feldmann, Carrie E. Schweitzer, Jesse W. Breinholt, Matthew Bendall, Ferran Palero, Tin-Yam Chan, Darryl L. Felder, Rafael Robles, Ka-Hou Chu, Ling-Ming Tsang, Dohyup Kim, Joel W. Martin, and Keith A. Crandall. 2014.  \r\nThe emergence of the lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida). 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"duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "4dcbf630c7120e99259e24e58661e2bbfb95b57c", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 22 Jul 2025 17:16:26 +0000", "date_ISO_8601": "2025-07-22 17:16:26 +0000", "relative_date": "10 months ago", "message_subject": "Update document 'pg_2838' via OpenTree API"}, {"id": "4d2254941a3d601123d3d5a80ee298f16093925a", "author_name": "Valeria Ensenat Rivera", "author_email": "valeria.ensenatrivera@gwmail.gwu.edu", "date": "Tue, 22 Jul 2025 17:13:50 +0000", "date_ISO_8601": "2025-07-22 17:13:50 +0000", "relative_date": "10 months ago", "message_subject": "New entries", "message_body": "Fixed spelling of _Geocharax tasmanicus_.\nNew species entry for _Hoplometopus macrodontus_.\nNew species entry for _Faxonius ronaldi_.\nNew species entry for _Faxonius virilis_.\nNew species entry for _Phyllamphion elegans_.\n\n(Update document 'pg_2838' via OpenTree API)"}, {"id": "2355876d543c4d37c581dda705ef7368819ab6d0", "author_name": "Valeria Ensenat Rivera", "author_email": "ANONYMOUS", "date": "Fri, 13 Dec 2024 21:41:30 +0000", "date_ISO_8601": "2024-12-13 21:41:30 +0000", "relative_date": "1 year, 5 months ago", "message_subject": "Taxonomic names update", "message_body": "Geocharax gracilis is now Geocharax tasmanicus.\nFallicambarus fodiens is now Creaserinus fodiens.\nFallicambarus byersi is now Creaserinus byersi.\nCambarus miltus is now Lacunicambarus miltus,\nOrconectes ronaldi is now Faxonius ronaldi.\nOrconectes virilis is now Faxonius virilis.\nOrconectes macrus is now Faxonius macrus.\nThaumastocheles dochmiodon is now Thaumastocheles japonicus.\nEnoplometopus macrodontus is now Hoplometopus macrodontus.\nJasus tristani is now Jasus paulensis.\nPalinurellus wieneckii is now Phyllamphion elegans.\nPolycheles enthrix is now Neopolycheles enthrix.\n\n(Update document 'pg_2838' via OpenTree API)"}, {"id": "084b60a5c714e63f04fb2739c76bda60498fb5b8", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Wed, 19 Aug 2015 14:27:53 +0000", "date_ISO_8601": "2015-08-19 14:27:53 +0000", "relative_date": "11 years ago", "message_subject": "map", "message_body": "(Update Study #pg_2838 via OpenTree API)"}, {"id": "04dba99c1d0c4dcbbbf63ad2631bed18578ae027", "author_name": "Joseph W. Brown", "author_email": "ANONYMOUS", "date": "Mon, 18 Aug 2014 20:31:39 +0000", "date_ISO_8601": "2014-08-18 20:31:39 +0000", "relative_date": "12 years ago", "message_subject": "comment", "message_body": "(Update Study #pg_2838 via OpenTree API)"}, {"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"}]}