{"action":"created","issue":{"url":"https://api.github.com/repos/biosemantics/micropie2/issues/47","repository_url":"https://api.github.com/repos/biosemantics/micropie2","labels_url":"https://api.github.com/repos/biosemantics/micropie2/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/biosemantics/micropie2/issues/47/comments","events_url":"https://api.github.com/repos/biosemantics/micropie2/issues/47/events","html_url":"https://github.com/biosemantics/micropie2/issues/47","id":157774263,"number":47,"title":"colony phenotypes","user":{"login":"carrineblank","id":11510377,"avatar_url":"https://avatars.githubusercontent.com/u/11510377?v=3","gravatar_id":"","url":"https://api.github.com/users/carrineblank","html_url":"https://github.com/carrineblank","followers_url":"https://api.github.com/users/carrineblank/followers","following_url":"https://api.github.com/users/carrineblank/following{/other_user}","gists_url":"https://api.github.com/users/carrineblank/gists{/gist_id}","starred_url":"https://api.github.com/users/carrineblank/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carrineblank/subscriptions","organizations_url":"https://api.github.com/users/carrineblank/orgs","repos_url":"https://api.github.com/users/carrineblank/repos","events_url":"https://api.github.com/users/carrineblank/events{/privacy}","received_events_url":"https://api.github.com/users/carrineblank/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-31T21:25:05Z","updated_at":"2016-06-01T20:58:10Z","closed_at":null,"body":"Hi Jin\r\n\r\nNote that optical quality terms such as \"dull\", \"shiny\", \"glistening\", \"translucent\", and \"opaque\" are being picked up by both colony texture and colony color or sometimes one but not the other.  These should be only in one column.  Perhaps the most appropriate one is colony color (thinking of the PATO structure), although you might want to ask Hong.\r\n\r\nOther issues:\r\n\r\nThe description sentence: \"Colonies on R2A agar are circular, entire, pink and not easily emulsified. \" Was extracted as:\r\nColony shape: \"not circular\" - should be \"circular\"\r\nColony margin: \"not entire\" - should be \"entire\"\r\nColony color: \"not pink\" - should be \"pink\"\r\n\r\nUnder colony color the phrase extracted for the description sentence: \"Forms orange colonies.\" was \"forms orange colonies\".  Simply the word \"orange\" would be the most preferable output.\r\n\r\nFor the description sentence: \" Colonies are circular, entirely margined, glistening, butyraceous and orange on MA and do not glide.\"  Was extracted as:\r\nColony margin: nothing extracted - should be \"entirely margined\"\r\nColony texture: nothing extracted - should be \"butyraceous\"\r\nColony color: \"not orange\" - should be \"glistening#orange\"\r\n\r\nFor the description phrase: \"circular to slightly irregular with entire to erose margins, low convex, translucent, gray, dull, smooth.\" Was extracted:\r\nColony margin: \"margins#entire\" - should be \"entire#erose\"\r\nColony texture: \"smooth#dull#translucent#stringy sediment#a smooth\" - should be \"smooth\"\r\nColony color: \"gray\" - should be \"gray#dull#translucent\"\r\n\r\nFor the description sentence: \"Colonies are circular, low convex, shiny with entire edges and 1–3 mm in diameter on marine agar 2216\".  Was extracted:\r\nColony shape: nothing extracted - should be \"circular#low convex\"\r\n\r\nFor the description sentence: \"Colonies are circular, smooth, low convex, glistening, moderately reddish-orange in colour \" Was extracted:\r\nColony color\"moderately reddish-orange\" - should be \"moderately reddish-orange#glistening\"\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/biosemantics/micropie2/issues/comments/223122561","html_url":"https://github.com/biosemantics/micropie2/issues/47#issuecomment-223122561","issue_url":"https://api.github.com/repos/biosemantics/micropie2/issues/47","id":223122561,"user":{"login":"carrineblank","id":11510377,"avatar_url":"https://avatars.githubusercontent.com/u/11510377?v=3","gravatar_id":"","url":"https://api.github.com/users/carrineblank","html_url":"https://github.com/carrineblank","followers_url":"https://api.github.com/users/carrineblank/followers","following_url":"https://api.github.com/users/carrineblank/following{/other_user}","gists_url":"https://api.github.com/users/carrineblank/gists{/gist_id}","starred_url":"https://api.github.com/users/carrineblank/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carrineblank/subscriptions","organizations_url":"https://api.github.com/users/carrineblank/orgs","repos_url":"https://api.github.com/users/carrineblank/repos","events_url":"https://api.github.com/users/carrineblank/events{/privacy}","received_events_url":"https://api.github.com/users/carrineblank/received_events","type":"User","site_admin":false},"created_at":"2016-06-01T20:58:10Z","updated_at":"2016-06-01T20:58:10Z","body":"Also.... many of the output for colony color is also picking up culture media (e.g. \"blood agar\", \"blood agar plates\", \"not  media containing hemolyzed blood\", \"anaerobic blood agar plates\", \"rabbit laked blood agar colonies\", \"blood sheep agar\", ) - this shouldn't be included under colony color.\r\n\r\n"}}
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