{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/panther-enrichment/issues/3","repository_url":"https://api.github.com/repos/geneontology/panther-enrichment","labels_url":"https://api.github.com/repos/geneontology/panther-enrichment/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/panther-enrichment/issues/3/comments","events_url":"https://api.github.com/repos/geneontology/panther-enrichment/issues/3/events","html_url":"https://github.com/geneontology/panther-enrichment/issues/3","id":210910171,"number":3,"title":"Panther slim query","user":{"login":"kltm","id":2687900,"avatar_url":"https://avatars0.githubusercontent.com/u/2687900?v=3","gravatar_id":"","url":"https://api.github.com/users/kltm","html_url":"https://github.com/kltm","followers_url":"https://api.github.com/users/kltm/followers","following_url":"https://api.github.com/users/kltm/following{/other_user}","gists_url":"https://api.github.com/users/kltm/gists{/gist_id}","starred_url":"https://api.github.com/users/kltm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kltm/subscriptions","organizations_url":"https://api.github.com/users/kltm/orgs","repos_url":"https://api.github.com/users/kltm/repos","events_url":"https://api.github.com/users/kltm/events{/privacy}","received_events_url":"https://api.github.com/users/kltm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-02-28T21:43:25Z","updated_at":"2017-02-28T21:46:23Z","closed_at":null,"body":"```\r\nFollow on from:\r\n\r\nhttp://jira.geneontology.org/browse/GO-1452\r\n\r\nI was  curious about what the slim was showing.\r\n\r\nin addition to the issues reported in the older ticket\r\n\r\nThe slim numbers for pombe seem  strange.\r\nBelow are panther reported and actual:\r\nGO:0009987  cellular process       panther(1890) actual( 3983)\r\nGO:0065007  biological regulation   panther(229) actual(1161) \r\nGO:0071840  cellular component org or bio panther(611) actual(1755)\r\nGO:0032502  developmental process panther(25) actual(157)\r\nGO:0051179  localisation panther(536) actual(1087)\r\nGO:0008152  metabolic process panther(2082) actual(3147)\r\nGO:0000003  reproduction panther(21) actual(335)\r\nGO:0050896  response to stimulus panther(271) actual(677)\r\n\r\nOther comments:\r\n\r\nShould we have a pie chart view since we discourage this?\r\nThe histogram would be better, but the link for this is broken?\r\nHow are the slim terms devised?\r\n```\r\n\r\n```\r\nValerie Wood added a comment - 31/Jan/17 5:29 PM\r\n\r\nFrom previous ticket:\r\nPie chart is very misleading for display of annotation numbers in these cases.\r\nThe legend for this pie chart is incorrect. It can't be percent of genes against total, because this would not be neatly 100% (and the total number of genes is more than the number of genes with component annotations, from the label at the top). It must be %annotations against total?\r\nValerie Wood added a comment - 31/Jan/17 5:33 PM\r\n\r\nI attached an image of what this default slim looks like for pombe (approximately).\r\nHopefully this indicates why the pie chart view doesn't work for display of Genes->annotations\r\nSeth Carbon added a comment - 31/Jan/17 5:41 PM - Restricted to go-curators\r\n\r\nI'm looking for a ticket reference, but there was a lot of discussion about this way back when. According to my email, this was a \"done\" discussion already in 2009/2010--pie charts are misleading. E.g.:\r\n\r\n```\r\nWe recommend that you avoid using pie charts because terms can have multiple parents with multiple relationships, therefore pie charts can be problematic to display your results as you invariably end up with a pie chart that adds up to more than 100%, which is nonsensical. A bar chart is a better alternative (e.g. see PMID: 12368864 fig. 3).\r\n```\r\n(Which is a 2002 ref, btw.)\r\nPie charts were removed in AmiGO fairly early on, replaced with bar charts (with the slimmer functionality removed completely later on when we moved to owltools and galaxy).\r\n\r\nCheers,\r\n\r\n-Seth\r\nValerie Wood added a comment - 31/Jan/17 5:46 PM\r\n\r\n+1.\r\n\r\nI wrote about it in a pitfalls paper\r\nhttps://www.ncbi.nlm.nih.gov/pubmed/18475267\r\nand tell undergraduates on our GO courses not to use pie charts...\r\n\r\nI'm very picky about it reviewing papers too....\r\nTanya Berardini added a comment - 31/Jan/17 8:55 PM\r\n\r\nI'd like to redirect this to the appropriate Github tracker. Which one? Or should it go to the Panther tracker instead of a GO one?\r\nValerie Wood added a comment - 01/Feb/17 6:31 AM\r\n\r\nAssigned to Huaiyu to tell us where the appropriate place is.\r\nv\r\n```\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/geneontology/panther-enrichment/issues/comments/283169987","html_url":"https://github.com/geneontology/panther-enrichment/issues/3#issuecomment-283169987","issue_url":"https://api.github.com/repos/geneontology/panther-enrichment/issues/3","id":283169987,"user":{"login":"kltm","id":2687900,"avatar_url":"https://avatars0.githubusercontent.com/u/2687900?v=3","gravatar_id":"","url":"https://api.github.com/users/kltm","html_url":"https://github.com/kltm","followers_url":"https://api.github.com/users/kltm/followers","following_url":"https://api.github.com/users/kltm/following{/other_user}","gists_url":"https://api.github.com/users/kltm/gists{/gist_id}","starred_url":"https://api.github.com/users/kltm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kltm/subscriptions","organizations_url":"https://api.github.com/users/kltm/orgs","repos_url":"https://api.github.com/users/kltm/repos","events_url":"https://api.github.com/users/kltm/events{/privacy}","received_events_url":"https://api.github.com/users/kltm/received_events","type":"User","site_admin":false},"created_at":"2017-02-28T21:46:23Z","updated_at":"2017-02-28T21:46:23Z","body":"Sorry @ValWood, I could not get your image to upload here.\r\n"}}
{"actor":{"display_login":"kltm"}}