{"action":"opened","issue":{"url":"https://api.github.com/repos/pombase/curation/issues/1192","repository_url":"https://api.github.com/repos/pombase/curation","labels_url":"https://api.github.com/repos/pombase/curation/issues/1192/labels{/name}","comments_url":"https://api.github.com/repos/pombase/curation/issues/1192/comments","events_url":"https://api.github.com/repos/pombase/curation/issues/1192/events","html_url":"https://github.com/pombase/curation/issues/1192","id":192592941,"number":1192,"title":"biogrid annotation check","user":{"login":"ValWood","id":7359272,"avatar_url":"https://avatars.githubusercontent.com/u/7359272?v=3","gravatar_id":"","url":"https://api.github.com/users/ValWood","html_url":"https://github.com/ValWood","followers_url":"https://api.github.com/users/ValWood/followers","following_url":"https://api.github.com/users/ValWood/following{/other_user}","gists_url":"https://api.github.com/users/ValWood/gists{/gist_id}","starred_url":"https://api.github.com/users/ValWood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ValWood/subscriptions","organizations_url":"https://api.github.com/users/ValWood/orgs","repos_url":"https://api.github.com/users/ValWood/repos","events_url":"https://api.github.com/users/ValWood/events{/privacy}","received_events_url":"https://api.github.com/users/ValWood/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-11-30T15:20:03Z","updated_at":"2016-11-30T15:20:03Z","closed_at":null,"body":"I have had this sitting in my inbox for a while.\r\nI think to know what to tell biogrid we should curate\r\n\r\nAlthough something else is odd, becasue \r\n- we are displaying  meu1-1 as the standard name on current site\r\n- there seem to be 2 features labelled 1-1  (instead of 1.1 and 1.2)\r\n- We need to deprecate the meu1-1 naming  becuase it can be cunfused with allele names.\r\n- This  will need to be resolved when we decide we have the time to begin to annotate alternative transcripts....\r\n- at present Kim's fudge of using the main ID should work OK\r\n\r\nhttp://www.pombase.org/spombe/result/SPAC1556.06\r\n\r\nHi Val.\r\n\r\nWe have this annotation from BioGRID:\r\n  958059  2538710 5802927 275294  858065  SPCC1020.12c    SPAC1556.06.1 xap5    meu1-1  SPCC14G10.06    SPAC1556.06|meu1        Positive Genetic        geneticAnver S (2014)   24957674        284812  284812 High Throughput 2.40456 -       cold sensitivity|colony size    20C, threshold: -2.5 <= S-score >= +2   -      BIOGRID\r\n\r\nhttps://thebiogrid.org/858065/summary/schizosaccharomyces-pombe/meu1-1.html?sort=evidence\r\n\r\nIt's odd because it's using the transcript IDs instead of gene IDs for\r\nmeu1.  ie. \"meu1-1\" instead of \"meu1\" and \"SPAC1556.06.1\" instead of\r\n\"SPAC1556.06\".  All the other interactions from BioGRID use gene IDs.\r\nBut the interaction above ends up in Chado as an interaction between a\r\ngene and an mRNA.\r\n\r\nI'm going to fix the loader to map the transcript ID to a gene ID but I\r\nthought I'd ask you about this in case it needs to be reported to\r\nBioGRID.\r\n\r\nI noticed it while working on the code that pulls all annotations from\r\nChado for use by the gene pages.  The new code worked for all other\r\nannotations but not for this one.\r\n\r\nKim."}}
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