{"action":"created","issue":{"url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/154","labels_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/154/labels{/name}","comments_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/154/comments","events_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/154/events","html_url":"https://github.com/OpenTreeOfLife/treemachine/issues/154","id":55602621,"number":154,"title":"incorrect association of a node in the synthetic tree: wrong taxonomic node","user":{"login":"mtholder","id":136067,"avatar_url":"https://avatars.githubusercontent.com/u/136067?v=3","gravatar_id":"","url":"https://api.github.com/users/mtholder","html_url":"https://github.com/mtholder","followers_url":"https://api.github.com/users/mtholder/followers","following_url":"https://api.github.com/users/mtholder/following{/other_user}","gists_url":"https://api.github.com/users/mtholder/gists{/gist_id}","starred_url":"https://api.github.com/users/mtholder/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mtholder/subscriptions","organizations_url":"https://api.github.com/users/mtholder/orgs","repos_url":"https://api.github.com/users/mtholder/repos","events_url":"https://api.github.com/users/mtholder/events{/privacy}","received_events_url":"https://api.github.com/users/mtholder/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-01-27T10:53:33Z","updated_at":"2015-05-20T13:29:45Z","closed_at":null,"body":"https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@860705/Halicnemia\r\nshows up labelled as Halicnemia_ott776728 but it actually has the taxonomic composition of the taxonomic parent: Heteroxyidae_ott668403\r\nsee curl calls below.\r\n\r\nrequesting the genus:\r\n\r\n    $ curl -X POST -H \"Content-Type\":\"application/json\" -H \"Accept\":\"application/json\" http://api.opentreeoflife.org/v2/taxonomy/subtree --data '{\"ott_id\": 776728}' \r\n\r\ngives a subset:\r\n\r\n    {\r\n      \"subtree\" : \"(Halicnemia_sp._BELUM<GBR>_Mc5427_ott4939607,Halicnemia_sp._BELUM<GBR>_Mc4307_ott4939608,Halicnemia_papillosa_ott2835824,Halicnemia_diazae_ott2835823,Halicnemia_geniculata_ott2835822,Halicnemia_salomonensis_ott2835821,Halicnemia_arcuata_ott2835820,Halicnemia_patera_ott776726,Halicnemia_sp._A_CM-2010_ott145568)Halicnemia_ott776728;\"\r\n    }\r\n\r\nof what you get when you ask for the synth tree:\r\n\r\n    $ curl -X POST -H \"Content-Type\":\"application/json\" -H \"Accept\":\"application/json\" http://api.opentreeoflife.org/v2/tree_f_life/subtree --data '{\"node_id\": \"860705\", \"tree_id\": \"otol.draft.22\"}'\r\n\r\n. Note the `newick` field and its root label:\r\n\r\n    {\r\n      \"newick\" : \"((Parahigginsia_phakelloides_ott2835918,Parahigginsia_phakellioides_ott2835865)Parahigginsia_ott2835866,(Alloscleria_tenuispinosa_ott2835914)Alloscleria_ott2835915,(Negombo_kellyae_ott2835911,Negombo_jogashimensis_ott2835936,Negombo_acanthosanidastera_ott2835862,Negombo_tenuistellata_ott2835858)Negombo_ott2835859,(Acanthoclada_prostrata_ott2835939)Acanthoclada_ott2835931,(Julavis_jamaicensis_ott2835881,Julavis_levis_ott2835880)Julavis_ott2835854,(Microxistyla_petrina_ott2835896)Microxistyla_ott2835867,(Heteroxya_corticata_ott2835861,Heteroxya_sp_1_CM-2013_ott5223187)Heteroxya_ott2835860,(Desmoxya_lunata_ott2835932,Desmoxya_pelagiae_ott2835917)Desmoxya_ott2835871,Halicnemia_arcuata_ott2835820,Halicnemia_sp_A_CM-2010_ott145568,Halicnemia_salomonensis_ott2835821,Halicnemia_sp_BELUM_GBR_Mc4307_ott4939608,Halicnemia_sp_BELUM_GBR_Mc5427_ott4939607,Halicnemia_geniculata_ott2835822,Halicnemia_patera_ott776726,Halicnemia_papillosa_ott2835824,Halicnemia_diazae_ott2835823)Halicnemia_ott776728;\",\r\n      \"tree_id\" : \"otol.draft.22\"\r\n    }\r\n\r\nThat tree is the same tree structure as the parent taxon\r\n\r\n    $ curl -X POST -H \"Content-Type\":\"application/json\" -H \"Accept\":\"application/json\" http://api.opentreeoflife.org/v2/taxonmy/subtree --data '{\"ott_id\": 668403}'\r\n\r\nwhich results: \r\n\r\n    {\r\n      \"subtree\" : \"((Heteroxya_sp._1_CM-2013_ott5223187,Heteroxya_corticata_ott2835861)Heteroxya_ott2835860,(Negombo_acanthosanidastera_ott2835862,Negombo_tenuistellata_ott2835858,Negombo_jogashimensis_ott2835936,Negombo_kellyae_ott2835911)Negombo_ott2835859,(Desmoxya_lunata_ott2835932,Desmoxya_pelagiae_ott2835917)Desmoxya_ott2835871,(Microxistyla_petrina_ott2835896)Microxistyla_ott2835867,(Parahigginsia_phakellioides_ott2835865,Parahigginsia_phakelloides_ott2835918)Parahigginsia_ott2835866,(Julavis_levis_ott2835880,Julavis_jamaicensis_ott2835881)Julavis_ott2835854,(Acanthoclada_prostrata_ott2835939)Acanthoclada_ott2835931,(Alloscleria_tenuispinosa_ott2835914)Alloscleria_ott2835915,(Halicnemia_sp._BELUM<GBR>_Mc5427_ott4939607,Halicnemia_sp._BELUM<GBR>_Mc4307_ott4939608,Halicnemia_papillosa_ott2835824,Halicnemia_diazae_ott2835823,Halicnemia_geniculata_ott2835822,Halicnemia_salomonensis_ott2835821,Halicnemia_arcuata_ott2835820,Halicnemia_patera_ott776726,Halicnemia_sp._A_CM-2010_ott145568)Halicnemia_ott776728)Heteroxyidae_ott668403;\"\r\n      }\r\n"},"comment":{"url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/comments/103889292","html_url":"https://github.com/OpenTreeOfLife/treemachine/issues/154#issuecomment-103889292","issue_url":"https://api.github.com/repos/OpenTreeOfLife/treemachine/issues/154","id":103889292,"user":{"login":"chinchliff","id":1258397,"avatar_url":"https://avatars.githubusercontent.com/u/1258397?v=3","gravatar_id":"","url":"https://api.github.com/users/chinchliff","html_url":"https://github.com/chinchliff","followers_url":"https://api.github.com/users/chinchliff/followers","following_url":"https://api.github.com/users/chinchliff/following{/other_user}","gists_url":"https://api.github.com/users/chinchliff/gists{/gist_id}","starred_url":"https://api.github.com/users/chinchliff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chinchliff/subscriptions","organizations_url":"https://api.github.com/users/chinchliff/orgs","repos_url":"https://api.github.com/users/chinchliff/repos","events_url":"https://api.github.com/users/chinchliff/events{/privacy}","received_events_url":"https://api.github.com/users/chinchliff/received_events","type":"User","site_admin":false},"created_at":"2015-05-20T13:29:44Z","updated_at":"2015-05-20T13:29:44Z","body":"Actually, I suppose not, since the issue with Cottioideae remains. We know\nit isn't missing children. I wonder what else could be happening that would\naffect taxonomic composition like that?\n\nOn Wed, May 20, 2015 at 9:27 AM Cody Hinchliff <cody.hinchliff@gmail.com>\nwrote:\n\n> Oh. Well that's good. So maybe we can resolve this issue and remove the\n> associated disclaimer from the manuscript?\n>\n> On Wed, May 20, 2015 at 9:07 AM Joseph W. Brown <notifications@github.com>\n> wrote:\n>\n>> I implemented my missing-children fix for \"Limnothrix redekei ott704052\"\n>> and re-ran synthesis. The problem went away (and didn't generate new\n>> ones!). The \"Cottioidei ott237343\" issue remains (as do the 9 unsupported\n>> nodes).\n>>\n>> —\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/OpenTreeOfLife/treemachine/issues/154#issuecomment-103877619>\n>> .\n>>\n>\n"}}