{"action":"created","issue":{"url":"https://api.github.com/repos/genome/civic-server/issues/88","labels_url":"https://api.github.com/repos/genome/civic-server/issues/88/labels{/name}","comments_url":"https://api.github.com/repos/genome/civic-server/issues/88/comments","events_url":"https://api.github.com/repos/genome/civic-server/issues/88/events","html_url":"https://github.com/genome/civic-server/issues/88","id":103817786,"number":88,"title":"Unable to merge or otherwise fix a duplicate variant for a gene","user":{"login":"malachig","id":856728,"avatar_url":"https://avatars.githubusercontent.com/u/856728?v=3","gravatar_id":"","url":"https://api.github.com/users/malachig","html_url":"https://github.com/malachig","followers_url":"https://api.github.com/users/malachig/followers","following_url":"https://api.github.com/users/malachig/following{/other_user}","gists_url":"https://api.github.com/users/malachig/gists{/gist_id}","starred_url":"https://api.github.com/users/malachig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/malachig/subscriptions","organizations_url":"https://api.github.com/users/malachig/orgs","repos_url":"https://api.github.com/users/malachig/repos","events_url":"https://api.github.com/users/malachig/events{/privacy}","received_events_url":"https://api.github.com/users/malachig/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":8,"created_at":"2015-08-29T00:46:05Z","updated_at":"2015-11-22T00:24:36Z","closed_at":"2015-11-22T00:24:36Z","body":"While Cody was adding coordinates for variants he noted that two variants had been created for KRAS, one called 'EXON 1 MUTATIONS' the other called 'EXON 2 MUTATIONS'.  \r\n\r\n'EXON 1 MUTATIONS' is a labeling ambiguity and is actually referring to the same mutations as 'EXON 2 MUTATIONS'.  \r\n\r\nCody renamed the exon 1 variant to exon 2.  But of course merging is not that simple as these are just names not the actual variant IDs.  Should such a rename have been allowed?  Anyway, to fix this ...\r\n\r\nI would like to move this evidence item:\r\nhttps://civic.genome.wustl.edu/#/events/genes/30/summary/variants/74/summary/evidence/250/summary\r\n\r\nFrom this variant:\r\nhttps://civic.genome.wustl.edu/#/events/genes/30/summary/variants/74/summary\r\n\r\nTo this variant:\r\nhttps://civic.genome.wustl.edu/#/events/genes/30/summary/variants/75/summary\r\n\r\nAnd then delete variant `74`.  There are various barriers to doing so.  For one thing, in the admin interface:\r\n- It would be helpful if you could filter down to a specific evidence item, in this case `250`\r\n- If you filter to KRAS, this helps but now you have three evidence items that now say `EXON 2 MUTATIONS`, two of which are associated with variant `75` and one with variant `74`.  But you can't see this in the interface directly.\r\n- If I figure out which is associated with variant `74` and edit it I see this:\r\n \r\nhttps://civic.genome.wustl.edu/admin/evidence_items/250/edit\r\n\r\n- In this view I can not change the evidence item to variant `74` because I only have a drop down list of variant names that are non-unique.  `EXON 2 MUTATIONS` appears three times in this list.  `EXPRESSION` appears 9 times.\r\n\r\nMy next strategy was to attempt to just create an entirely new evidence item that duplicated the content of the one I want to merge and then just associate that with the correct variant `75`.  That attempt failed and can be seen here:\r\nhttps://civic.genome.wustl.edu/admin/evidence_items/530\r\n\r\nI guess that is related to the issue @obigriffith reported recently.  This is a reminder to clean up these KRAS mutations when we have a way to do this either in the admin interface or civic-client interface.\r\n\r\nIn general I think we should talk about how we want to handle duplicate variant names within a gene and across genes.  As a starting point we could disallow the former? There may be places where we want to scope variant queries to within the gene. \r\n\r\nFinally, in general in the admin interface I think it would be helpful to display the unique civic database IDs for variants, genes, evidence items, etc."},"comment":{"url":"https://api.github.com/repos/genome/civic-server/issues/comments/158693880","html_url":"https://github.com/genome/civic-server/issues/88#issuecomment-158693880","issue_url":"https://api.github.com/repos/genome/civic-server/issues/88","id":158693880,"user":{"login":"kkrysiak","id":8527125,"avatar_url":"https://avatars.githubusercontent.com/u/8527125?v=3","gravatar_id":"","url":"https://api.github.com/users/kkrysiak","html_url":"https://github.com/kkrysiak","followers_url":"https://api.github.com/users/kkrysiak/followers","following_url":"https://api.github.com/users/kkrysiak/following{/other_user}","gists_url":"https://api.github.com/users/kkrysiak/gists{/gist_id}","starred_url":"https://api.github.com/users/kkrysiak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kkrysiak/subscriptions","organizations_url":"https://api.github.com/users/kkrysiak/orgs","repos_url":"https://api.github.com/users/kkrysiak/repos","events_url":"https://api.github.com/users/kkrysiak/events{/privacy}","received_events_url":"https://api.github.com/users/kkrysiak/received_events","type":"User","site_admin":false},"created_at":"2015-11-22T00:24:35Z","updated_at":"2015-11-22T00:24:35Z","body":"I've addressed the KRAS (variant 74), TP53 (variant 123) and CEBPA (variant 188) variants.\r\n\r\nWe tried to address the FGFR3-TACC3 but problems with the merge led to opening issue #110.\r\n\r\nThe EGFR variants are being addressed by https://github.com/genome/civic-client/issues/233 unless we choose to rename and merge them as discussed in the issue.\r\n\r\n@acoffman, unless you want to re-open this to remind you of additional utilities, for the reasons above, I am closing this issue."}}