{"action":"created","issue":{"url":"https://api.github.com/repos/OpenTreeOfLife/feedback/issues/293","repository_url":"https://api.github.com/repos/OpenTreeOfLife/feedback","labels_url":"https://api.github.com/repos/OpenTreeOfLife/feedback/issues/293/labels{/name}","comments_url":"https://api.github.com/repos/OpenTreeOfLife/feedback/issues/293/comments","events_url":"https://api.github.com/repos/OpenTreeOfLife/feedback/issues/293/events","html_url":"https://github.com/OpenTreeOfLife/feedback/issues/293","id":163749385,"number":293,"title":"Freshwater Ichthyosporeans 1 & 2, and Marine Ichthyosporeans 1 have no descendants","user":{"login":"hyanwong","id":4699014,"avatar_url":"https://avatars.githubusercontent.com/u/4699014?v=3","gravatar_id":"","url":"https://api.github.com/users/hyanwong","html_url":"https://github.com/hyanwong","followers_url":"https://api.github.com/users/hyanwong/followers","following_url":"https://api.github.com/users/hyanwong/following{/other_user}","gists_url":"https://api.github.com/users/hyanwong/gists{/gist_id}","starred_url":"https://api.github.com/users/hyanwong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hyanwong/subscriptions","organizations_url":"https://api.github.com/users/hyanwong/orgs","repos_url":"https://api.github.com/users/hyanwong/repos","events_url":"https://api.github.com/users/hyanwong/events{/privacy}","received_events_url":"https://api.github.com/users/hyanwong/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-07-04T22:51:34Z","updated_at":"2016-07-05T21:15:42Z","closed_at":null,"body":"These are from SILVA, but seem to have no subtaxa, and may simply be RNA sequence clusters. Not sure if anything need to be done about this or not, to if it is symptomatic of a general SILVA issue\n\n================================================\nMetadata   |   Do not edit below this line\n:------------|:----------\nAuthor   |   [Yan Wong](https://github.com/hyanwong) \nUpvotes   |   0 \nURL   |   [tree.opentreeoflife.org/opentree/argus/opentree5.0@ott5251365/Freshwater-Ichthyosporeans-1](https://tree.opentreeoflife.org/opentree/argus/opentree5.0@ott5251365/Freshwater-Ichthyosporeans-1) \nTarget node label   |   Freshwater Ichthyosporeans 1 \nSynthetic tree id   |   opentree5.0 \nSynthetic tree node id   |   ott5251365 \nSource tree id(s)   |    \nOpen Tree Taxonomy id   |    \nSupporting reference   |   N/A \n"},"comment":{"url":"https://api.github.com/repos/OpenTreeOfLife/feedback/issues/comments/230605528","html_url":"https://github.com/OpenTreeOfLife/feedback/issues/293#issuecomment-230605528","issue_url":"https://api.github.com/repos/OpenTreeOfLife/feedback/issues/293","id":230605528,"user":{"login":"jar398","id":2035858,"avatar_url":"https://avatars.githubusercontent.com/u/2035858?v=3","gravatar_id":"","url":"https://api.github.com/users/jar398","html_url":"https://github.com/jar398","followers_url":"https://api.github.com/users/jar398/followers","following_url":"https://api.github.com/users/jar398/following{/other_user}","gists_url":"https://api.github.com/users/jar398/gists{/gist_id}","starred_url":"https://api.github.com/users/jar398/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jar398/subscriptions","organizations_url":"https://api.github.com/users/jar398/orgs","repos_url":"https://api.github.com/users/jar398/repos","events_url":"https://api.github.com/users/jar398/events{/privacy}","received_events_url":"https://api.github.com/users/jar398/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T21:15:42Z","updated_at":"2016-07-05T21:15:42Z","body":"This group does have a member, as you can see in the SILVA taxonomy\nbrowser. NCBI gives it a name with the word 'uncultured' in it.  Uncultured\ntaxa from NCBI only are filtered out as 'unclassified,' but since SILVA\nclassifies them they occur unflagged in the taxonomy - not in 2.9, which\nhas a bug, but it will appear in 2.10.\n\nFor 'microbes' we use the taxonomy from SILVA (on the advice of Laura\nKatz), which, as I say, is the work of one or a small number of people.\nSILVA made a big phylogenetic tree based on 16S sequences organized into\nclusters, and then, partly based on known groups, gave names to internal\nnodes that were well supported.  But there were a lot of groups left over\nfor which there was phylogenetic signal but no name.  So they just made up\nnames, as you say.  Since Open Tree is about phylogenetic relationships and\nnomenclature is not a primary concern, SILVA seems a good match to the\nproject.\n\nI suppose that if the SILVA team cared a lot about proper description they\nwould research each group to figure out its biology so that it could be\ndescribed and given a 'respectable' name. That sounds really really hard to\nme. The phylogeny is way ahead of taxonomy and I doubt they are funded to\ndo anything other than sequence-based taxonomy.\n\nI can't say anything about the quality of the phylogeny, but I think they\nare being conservative; many nodes in the taxonomy are big polytomies,\nwhich to me says they're being conservative in saying which nodes are well\nenough supported to deserve names.\n"}}
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