{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/11977","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/11977/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/11977/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/11977/events","html_url":"https://github.com/geneontology/go-ontology/issues/11977","id":97271374,"number":11977,"title":"APC complexed with inhibitor","user":{"login":"gocentral","id":12972975,"avatar_url":"https://avatars.githubusercontent.com/u/12972975?v=3","gravatar_id":"","url":"https://api.github.com/users/gocentral","html_url":"https://github.com/gocentral","followers_url":"https://api.github.com/users/gocentral/followers","following_url":"https://api.github.com/users/gocentral/following{/other_user}","gists_url":"https://api.github.com/users/gocentral/gists{/gist_id}","starred_url":"https://api.github.com/users/gocentral/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gocentral/subscriptions","organizations_url":"https://api.github.com/users/gocentral/orgs","repos_url":"https://api.github.com/users/gocentral/repos","events_url":"https://api.github.com/users/gocentral/events{/privacy}","received_events_url":"https://api.github.com/users/gocentral/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/auto-migrated","name":"auto-migrated","color":"ededed"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/PomBase","name":"PomBase","color":"bfd4f2"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/protein%20complex","name":"protein complex","color":"ededed"}],"state":"open","locked":false,"assignee":{"login":"tberardini","id":4998871,"avatar_url":"https://avatars.githubusercontent.com/u/4998871?v=3","gravatar_id":"","url":"https://api.github.com/users/tberardini","html_url":"https://github.com/tberardini","followers_url":"https://api.github.com/users/tberardini/followers","following_url":"https://api.github.com/users/tberardini/following{/other_user}","gists_url":"https://api.github.com/users/tberardini/gists{/gist_id}","starred_url":"https://api.github.com/users/tberardini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tberardini/subscriptions","organizations_url":"https://api.github.com/users/tberardini/orgs","repos_url":"https://api.github.com/users/tberardini/repos","events_url":"https://api.github.com/users/tberardini/events{/privacy}","received_events_url":"https://api.github.com/users/tberardini/received_events","type":"User","site_admin":false},"milestone":null,"comments":15,"created_at":"2015-07-22T10:10:38Z","updated_at":"2015-09-16T08:35:16Z","closed_at":null,"body":"\r\nFollowing on from a discussion with Tanya and Antonia....\r\n\r\nThe APC is inhibited by various CDC20/fizzy family inhibitors at various cell cycle phases (not clear cut, sometimes overlapping).\r\n\r\nOur first question is how to represent these complexes.\r\n\r\n1. Do we request a complex\r\n\r\nAPC-Cdc20\r\nAPC-fizzy related (there is a precedent for this, but there are various fizzy related proteins so it is difficult to establish each complex version without using the gene names\r\nAPC-Srw1 complex, APC-Mfr1 etc)\r\n\r\n2. Alternatively as this is a complex inhibitor, we could annotate this as \r\nAPC -complex binding.\r\n\r\n(IN which case we would obsolete the existing APC-inhibitor complex terms)\r\n\r\n\r\nOne advantage of 2 is that we would not need to ensure that all 15 APC subunits were annotated to all complexes, and we would not have the difficulties defining the complexes which do not seem to be exactly conserved in their role between species.\r\n\r\nHowever, if people would expect to see these annotated as a complex in their own right we should do 1.\r\nIf we decide to do 1. we will need a better way to describe the various permutations (I can't think of anything easily without including gene product names we would not easily be able to  distinguish the specific variations.\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\n\nReported by: ValWood\n\nOriginal Ticket: [geneontology/ontology-requests/11816](https://sourceforge.net/p/geneontology/ontology-requests/11816)"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/140670386","html_url":"https://github.com/geneontology/go-ontology/issues/11977#issuecomment-140670386","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/11977","id":140670386,"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":"2015-09-16T08:35:16Z","updated_at":"2015-09-16T08:35:16Z","body":"We would need to allow Intact complex IDs in extensions. I think this could  work. However, I think APC_fizzy is probably a bit of a borderline case. There are  broadly conserved APC variants which I think should be in GO, and species specific variants which maybe should not. The complex Antonia is requesting is one of the conserved complexes I believe, although probably not studied yet in other species.  I prefer establishing the complex with pombe gene names in the term name, but defined according to functional role. If human ends up giving this complex a different name, we are happy to change it (we often go with the cerevisiae complex names for conserved complexes with the pombe names as synonyms. Our community are not particularly imaginative with their complex names!)\r\n\r\nI'm not fond of the name \"APC fizzy related\"  term I think it was chosen because APC-Cdc20 has the exact synonym APC-fizzy http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0090620, but the APC-fizzy  is only an arbitrary lumping term for  all of the APC complexes which are not APC-Cdc20. I would abolish that term and establish \"APC-gene family name\" for each conserved instance of APC as  they are characterized (as this is how they are referred to). We can converge on the name which becomes most commonly used (which is usually the first characterised).\r\n\r\nTo be consistent, we need the \"APC-gene family name\" terms, otherwise, why have APC-Cdc20? The only difference is that APC-Cdc20 is well characterized, and the others are not.\r\n\r\n\r\n"}}