{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12437","repository_url":"https://api.github.com/repos/geneontology/go-ontology","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12437/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12437/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12437/events","html_url":"https://github.com/geneontology/go-ontology/issues/12437","id":152872005,"number":12437,"title":"GO:1990376","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":{"login":"ukemi","id":11067494,"avatar_url":"https://avatars.githubusercontent.com/u/11067494?v=3","gravatar_id":"","url":"https://api.github.com/users/ukemi","html_url":"https://github.com/ukemi","followers_url":"https://api.github.com/users/ukemi/followers","following_url":"https://api.github.com/users/ukemi/following{/other_user}","gists_url":"https://api.github.com/users/ukemi/gists{/gist_id}","starred_url":"https://api.github.com/users/ukemi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ukemi/subscriptions","organizations_url":"https://api.github.com/users/ukemi/orgs","repos_url":"https://api.github.com/users/ukemi/repos","events_url":"https://api.github.com/users/ukemi/events{/privacy}","received_events_url":"https://api.github.com/users/ukemi/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2016-05-03T20:54:29Z","updated_at":"2016-05-05T08:13:02Z","closed_at":null,"body":"GO:1990376 negative regulation of G1/S transition of mitotic cell cycle by positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation\r\n\r\ncould we obsolete this term, we wouldn't use it in annotation now(it has no exp annotations, and I don't think there is any transcriptional control of G1/S transition. I think this was probably requested in error (old annotations are deleted).\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/217100263","html_url":"https://github.com/geneontology/go-ontology/issues/12437#issuecomment-217100263","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12437","id":217100263,"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},"created_at":"2016-05-05T08:13:02Z","updated_at":"2016-05-05T08:13:02Z","body":"Hi Rob,\r\n\r\nTranscription is definitely required for passage through phases. However,  the transitions are largely  regulated by the phosphorylation state of cdc2 (I know you know this, I'm trying to describe the rationale) \r\n\r\nSo for mitotic G2/M\r\nGO:0000086 G2/M transition of mitotic cell cycle\r\nThe mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.\r\n(David, the other transition defs need updating to reflect this seems to be the only one that was refined, I'll open a ticket for this).\r\n\r\nSo, the experts (who included  Rob De Bruin, who specifically works on cell cycle transcription, and Jacky Hayles from the Nurse lab), considered that the only transcription which regulated the transition  directly, was the positive feedback loop to increase cyclin levels in G1.\r\n\r\nObviously transcription of the other participating  gene products is required, but it wasn't considered to be regulatory.\r\n\r\nSo, for the G2/M transitions, I would only annotate these pathways:\r\n\r\n![g2_m_regulation](https://cloud.githubusercontent.com/assets/7359272/15039003/d0458024-12a0-11e6-85e2-a3e51ea307a7.jpg)\r\n\r\nto regulation of the transition, but not the transcription of the genes responsible.\r\n\r\nIf the activation of a pathway is directly through transcription making the gene products available (as is often the case for metabolic pathways), I would annotate transcription as regulatory.\r\nDoes that make sense?\r\n\r\nVal\r\n\r\n\r\n"}}