{"action":"created","issue":{"url":"https://api.github.com/repos/PlantReactome/data-management/issues/1","repository_url":"https://api.github.com/repos/PlantReactome/data-management","labels_url":"https://api.github.com/repos/PlantReactome/data-management/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/PlantReactome/data-management/issues/1/comments","events_url":"https://api.github.com/repos/PlantReactome/data-management/issues/1/events","html_url":"https://github.com/PlantReactome/data-management/issues/1","id":301215300,"number":1,"title":"Fixes to plant regulation instances in which CatalystActivity is specified as regulatedEntity","user":{"login":"preecej","id":7563737,"avatar_url":"https://avatars1.githubusercontent.com/u/7563737?v=4","gravatar_id":"","url":"https://api.github.com/users/preecej","html_url":"https://github.com/preecej","followers_url":"https://api.github.com/users/preecej/followers","following_url":"https://api.github.com/users/preecej/following{/other_user}","gists_url":"https://api.github.com/users/preecej/gists{/gist_id}","starred_url":"https://api.github.com/users/preecej/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/preecej/subscriptions","organizations_url":"https://api.github.com/users/preecej/orgs","repos_url":"https://api.github.com/users/preecej/repos","events_url":"https://api.github.com/users/preecej/events{/privacy}","received_events_url":"https://api.github.com/users/preecej/received_events","type":"User","site_admin":false},"labels":[{"id":852002160,"url":"https://api.github.com/repos/PlantReactome/data-management/labels/enhancement","name":"enhancement","color":"a2eeef","default":true}],"state":"open","locked":false,"assignee":{"login":"preecej","id":7563737,"avatar_url":"https://avatars1.githubusercontent.com/u/7563737?v=4","gravatar_id":"","url":"https://api.github.com/users/preecej","html_url":"https://github.com/preecej","followers_url":"https://api.github.com/users/preecej/followers","following_url":"https://api.github.com/users/preecej/following{/other_user}","gists_url":"https://api.github.com/users/preecej/gists{/gist_id}","starred_url":"https://api.github.com/users/preecej/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/preecej/subscriptions","organizations_url":"https://api.github.com/users/preecej/orgs","repos_url":"https://api.github.com/users/preecej/repos","events_url":"https://api.github.com/users/preecej/events{/privacy}","received_events_url":"https://api.github.com/users/preecej/received_events","type":"User","site_admin":false},"assignees":[{"login":"preecej","id":7563737,"avatar_url":"https://avatars1.githubusercontent.com/u/7563737?v=4","gravatar_id":"","url":"https://api.github.com/users/preecej","html_url":"https://github.com/preecej","followers_url":"https://api.github.com/users/preecej/followers","following_url":"https://api.github.com/users/preecej/following{/other_user}","gists_url":"https://api.github.com/users/preecej/gists{/gist_id}","starred_url":"https://api.github.com/users/preecej/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/preecej/subscriptions","organizations_url":"https://api.github.com/users/preecej/orgs","repos_url":"https://api.github.com/users/preecej/repos","events_url":"https://api.github.com/users/preecej/events{/privacy}","received_events_url":"https://api.github.com/users/preecej/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2018-02-28T22:53:43Z","updated_at":"2018-02-28T22:54:27Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Per Lisa Matthews:\r\nReactome is changing the way we represent regulation of catalysts in Reactome. Instead of showing the catalyst as the regulatedEntity in a regulation instances, we will be assigning the ReactionLikeEvent that contains the catalyst as the regulatedEntity.\r\n\r\nFor manually curated regulation instances that have been laid out in pathway diagrams, a bit of fixing will be required. The procedure for this fix is described below.  We suspect, however,  that most of the plant instances on the list came in from the original data import and likely haven't been laid out in actual diagrams. For all of these instances, Guanming suggested that there could be an automated fix.  We would be interested in for your feedback on this when you have time to think about it. We realize you are quite busy now!\r\n\r\nHere is the [list of affected instances](https://docs.google.com/spreadsheets/d/13cfD0Aa1G2rGmxcr8viddHZu1zu1tuS-JMeb_oQ_nz8/edit#gid=1925862972) (plant instances are listed in a separate tab).\r\n\r\nFix for regulation instances drawn in pathway diagrams:\r\nFor manually curated instances (in which the regulation instance has been drawn out in a diagram):\r\n1.  Create a NEW regulation instance in which the ReactionLikeEvent   (not catalyst)  is specified as the regulatedEntity.\r\n2.  Delete the the old regulation instance (creating a \"deleted\" instance when prompted by the curator tool). \r\n3. In the \"deleted\" instance,  enter the new regulation instance in the \"replacement\" attribute\r\n4. In the \"deleted\" instance  \"reason\"  attribute  specify \"killed and not replaced\" "},"comment":{"url":"https://api.github.com/repos/PlantReactome/data-management/issues/comments/369412470","html_url":"https://github.com/PlantReactome/data-management/issues/1#issuecomment-369412470","issue_url":"https://api.github.com/repos/PlantReactome/data-management/issues/1","id":369412470,"user":{"login":"preecej","id":7563737,"avatar_url":"https://avatars1.githubusercontent.com/u/7563737?v=4","gravatar_id":"","url":"https://api.github.com/users/preecej","html_url":"https://github.com/preecej","followers_url":"https://api.github.com/users/preecej/followers","following_url":"https://api.github.com/users/preecej/following{/other_user}","gists_url":"https://api.github.com/users/preecej/gists{/gist_id}","starred_url":"https://api.github.com/users/preecej/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/preecej/subscriptions","organizations_url":"https://api.github.com/users/preecej/orgs","repos_url":"https://api.github.com/users/preecej/repos","events_url":"https://api.github.com/users/preecej/events{/privacy}","received_events_url":"https://api.github.com/users/preecej/received_events","type":"User","site_admin":false},"created_at":"2018-02-28T22:54:27Z","updated_at":"2018-02-28T22:54:27Z","author_association":"CONTRIBUTOR","body":"A sampling of the instances referenced by Lisa suggests that only Arabidopsis imports from AraCyc are affected. If that proves to be the case for all of these instances, I recommend that we fix it with a script, as outlined in the steps below.\r\n"}}
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