{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/gemini/issues/571","labels_url":"https://api.github.com/repos/arq5x/gemini/issues/571/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/gemini/issues/571/comments","events_url":"https://api.github.com/repos/arq5x/gemini/issues/571/events","html_url":"https://github.com/arq5x/gemini/issues/571","id":113374283,"number":571,"title":"gene :: disease lookup.","user":{"login":"brentp","id":1739,"avatar_url":"https://avatars.githubusercontent.com/u/1739?v=3","gravatar_id":"","url":"https://api.github.com/users/brentp","html_url":"https://github.com/brentp","followers_url":"https://api.github.com/users/brentp/followers","following_url":"https://api.github.com/users/brentp/following{/other_user}","gists_url":"https://api.github.com/users/brentp/gists{/gist_id}","starred_url":"https://api.github.com/users/brentp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brentp/subscriptions","organizations_url":"https://api.github.com/users/brentp/orgs","repos_url":"https://api.github.com/users/brentp/repos","events_url":"https://api.github.com/users/brentp/events{/privacy}","received_events_url":"https://api.github.com/users/brentp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-10-26T14:57:32Z","updated_at":"2015-11-03T21:20:32Z","closed_at":null,"body":"via @jxchong cc @arq5x \r\nA user may find a variant that is not itself associated with disease, but is in a gene known to be associated with the disease. There is no way to store or query this info in gemini at this time.\r\n\r\nclinvar is an obvious choice and omim seems to be available to download for academic (http://omim.org/downloads). \r\n\r\nDesign\r\n======\r\n+ need a way to do this in a relatively generic fashion as we think about switching to support any organism.\r\n+ need a simple query to do this even though we'd probably be storing in a table that's many-to-1 relative to gene_detailed (?)\r\n+ could provide an example where user can use gemini annotate and smash all associations into a single \"|\" delimited string for every variant in that gene and it would be a single column in the variants table.\r\n+ likely better to have a \"|\" delimited string associated with each gene and require a join on gene_name."},"comment":{"url":"https://api.github.com/repos/arq5x/gemini/issues/comments/153492991","html_url":"https://github.com/arq5x/gemini/issues/571#issuecomment-153492991","issue_url":"https://api.github.com/repos/arq5x/gemini/issues/571","id":153492991,"user":{"login":"jxchong","id":1133838,"avatar_url":"https://avatars.githubusercontent.com/u/1133838?v=3","gravatar_id":"","url":"https://api.github.com/users/jxchong","html_url":"https://github.com/jxchong","followers_url":"https://api.github.com/users/jxchong/followers","following_url":"https://api.github.com/users/jxchong/following{/other_user}","gists_url":"https://api.github.com/users/jxchong/gists{/gist_id}","starred_url":"https://api.github.com/users/jxchong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jxchong/subscriptions","organizations_url":"https://api.github.com/users/jxchong/orgs","repos_url":"https://api.github.com/users/jxchong/repos","events_url":"https://api.github.com/users/jxchong/events{/privacy}","received_events_url":"https://api.github.com/users/jxchong/received_events","type":"User","site_admin":false},"created_at":"2015-11-03T21:20:32Z","updated_at":"2015-11-03T21:20:32Z","body":"Oh hey! I think this appears to be implemented in VEP v82 with the VEP option \r\n`--gene_phenotype   Indicates if the overlapped gene is associated with a phenotype, disease or trait. See list of phenotype sources. Not used by default`\r\n\r\nThis appears to be multi-species. List of phenotype sources: http://uswest.ensembl.org/info/genome/variation/sources_phenotype_documentation.html\r\n\r\nI have not had time to test yet though."}}