{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12184","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12184/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12184/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12184/events","html_url":"https://github.com/geneontology/go-ontology/issues/12184","id":120388688,"number":12184,"title":"gene product specific protein phosphatase regulatory terms","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":[{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/discuss_term_specificity","name":"discuss_term_specificity","color":"eb6420"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/Other%20term-related%20request","name":"Other term-related request","color":"bfe5bf"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/PomBase","name":"PomBase","color":"bfd4f2"}],"state":"open","locked":false,"assignee":{"login":"mcourtot","id":2214135,"avatar_url":"https://avatars.githubusercontent.com/u/2214135?v=3","gravatar_id":"","url":"https://api.github.com/users/mcourtot","html_url":"https://github.com/mcourtot","followers_url":"https://api.github.com/users/mcourtot/followers","following_url":"https://api.github.com/users/mcourtot/following{/other_user}","gists_url":"https://api.github.com/users/mcourtot/gists{/gist_id}","starred_url":"https://api.github.com/users/mcourtot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcourtot/subscriptions","organizations_url":"https://api.github.com/users/mcourtot/orgs","repos_url":"https://api.github.com/users/mcourtot/repos","events_url":"https://api.github.com/users/mcourtot/events{/privacy}","received_events_url":"https://api.github.com/users/mcourtot/received_events","type":"User","site_admin":false},"milestone":null,"comments":8,"created_at":"2015-12-04T12:04:11Z","updated_at":"2016-01-26T14:19:39Z","closed_at":null,"body":"\r\nCurrently we  have terms like\r\nprotein phosphatase type 2A inhibitor activity\r\nbut for the phosphatase terms the specific gene products are synonyms\r\n\r\neg\r\nGO:0004721 phosphoprotein phosphatase activity\r\nnarrow\tprotein phosphatase-2A activity\r\nnarrow\tprotein phosphatase-2C activity\r\nnarrow\tprotein phosphatase-2B activity\r\nnarrow\tprotein phosphatase-1 activity\r\n\r\nthe regulatory terms should mirror this.\r\nAt present its confusing \r\n\r\nbecause you end up with two options\r\nprotein phosphatase type 2A inhibitor activity  \r\nprotein serine/threonine phosphatase inhibitor activity \r\nwhich aren't mutually exclusive\r\n"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/175037377","html_url":"https://github.com/geneontology/go-ontology/issues/12184#issuecomment-175037377","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12184","id":175037377,"user":{"login":"mcourtot","id":2214135,"avatar_url":"https://avatars.githubusercontent.com/u/2214135?v=3","gravatar_id":"","url":"https://api.github.com/users/mcourtot","html_url":"https://github.com/mcourtot","followers_url":"https://api.github.com/users/mcourtot/followers","following_url":"https://api.github.com/users/mcourtot/following{/other_user}","gists_url":"https://api.github.com/users/mcourtot/gists{/gist_id}","starred_url":"https://api.github.com/users/mcourtot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcourtot/subscriptions","organizations_url":"https://api.github.com/users/mcourtot/orgs","repos_url":"https://api.github.com/users/mcourtot/repos","events_url":"https://api.github.com/users/mcourtot/events{/privacy}","received_events_url":"https://api.github.com/users/mcourtot/received_events","type":"User","site_admin":false},"created_at":"2016-01-26T14:19:39Z","updated_at":"2016-01-26T14:19:39Z","body":"HI Val - so looking at the ontology again, we do have protein phosphatase type 1 complex and protein phosphatase type 2A complex being subclasses of protein serine/threonine phosphatase complex, so you're entirely right.\r\n\r\nI looked at the different relevant sections:\r\n- protein phosphatase inhibitor/regulator/activator activity\r\n- regulation of protein serine/threonine activity  (and of type1&2)\r\n- protein serine/threonine phosphatase activity (and of type1&2)\r\n- protein serine/threonine phosphatase complex (and of type1&2)\r\n\r\n2 issues:\r\n- some terms are missing, such as protein serine/threonine activator activity\r\n- It seems there ought to be propagation of the inference: if type 1 and 2 are asserted are being types of user/thr phosphatase, their activities etc ought to be propagated. Maybe this is related to the issue of transitivity over regulates.\r\n\r\nIt feels there is something fishy going on there: if \"protein phosphatase type 2A\" is a \"protein serine/threonine phosphatase\" then we should be able to automatically infer that \"protein phosphatase type 2A inhibitor activity\" is_a \"protein serine/threonine phosphatase inhibitor activity\"\r\n\r\nI will check with other editors if they know why the inferences are not made."}}