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Montreal GOC meeting","description":"","creator":{"login":"pgaudet","id":4782928,"node_id":"MDQ6VXNlcjQ3ODI5Mjg=","avatar_url":"https://avatars0.githubusercontent.com/u/4782928?v=4","gravatar_id":"","url":"https://api.github.com/users/pgaudet","html_url":"https://github.com/pgaudet","followers_url":"https://api.github.com/users/pgaudet/followers","following_url":"https://api.github.com/users/pgaudet/following{/other_user}","gists_url":"https://api.github.com/users/pgaudet/gists{/gist_id}","starred_url":"https://api.github.com/users/pgaudet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgaudet/subscriptions","organizations_url":"https://api.github.com/users/pgaudet/orgs","repos_url":"https://api.github.com/users/pgaudet/repos","events_url":"https://api.github.com/users/pgaudet/events{/privacy}","received_events_url":"https://api.github.com/users/pgaudet/received_events","type":"User","site_admin":false},"open_issues":4,"closed_issues":0,"state":"open","created_at":"2018-03-19T09:09:14Z","updated_at":"2018-06-06T12:49:47Z","due_on":"2018-10-17T07:00:00Z","closed_at":null},"comments":54,"created_at":"2018-01-30T16:02:11Z","updated_at":"2018-06-18T15:18:22Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Hello, \r\n\r\nDiscussing with @amorgat about how Rhea and GO represent biochemical reactions, here are a few points to consider:\r\n\r\n- in Rhea each reaction is represented by a 'master' (undefined direction), and 3 directionalities: left to right/right to left/bi-directional \r\n- For GO right now our links are to the master (undefined direction), which is at least not wrong. This is also the reaction that corresponds to the link with EC numbers. \r\n- If we wanted to add the participants to the reactions, that might work (just using 'has participants'). Would that be informative enough? That information would be available this summer or so. \r\n- Otherwise adding the directionality would be more work. One option would use the (soon to come) mappings between Rhea (direction-specific)  and UniProt entries to pick the 'input' and 'output'. These directionalities will be manually curated. \r\n\r\nI am putting this here for discussion - @ukemi I let you decide how soon we need to discuss this. \r\n\r\nThanks, Pascale\r\n\r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/398090931","html_url":"https://github.com/geneontology/go-ontology/issues/14984#issuecomment-398090931","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/14984","id":398090931,"node_id":"MDEyOklzc3VlQ29tbWVudDM5ODA5MDkzMQ==","user":{"login":"amorgat","id":25613632,"node_id":"MDQ6VXNlcjI1NjEzNjMy","avatar_url":"https://avatars2.githubusercontent.com/u/25613632?v=4","gravatar_id":"","url":"https://api.github.com/users/amorgat","html_url":"https://github.com/amorgat","followers_url":"https://api.github.com/users/amorgat/followers","following_url":"https://api.github.com/users/amorgat/following{/other_user}","gists_url":"https://api.github.com/users/amorgat/gists{/gist_id}","starred_url":"https://api.github.com/users/amorgat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amorgat/subscriptions","organizations_url":"https://api.github.com/users/amorgat/orgs","repos_url":"https://api.github.com/users/amorgat/repos","events_url":"https://api.github.com/users/amorgat/events{/privacy}","received_events_url":"https://api.github.com/users/amorgat/received_events","type":"User","site_admin":false},"created_at":"2018-06-18T15:18:22Z","updated_at":"2018-06-18T15:18:22Z","author_association":"NONE","body":"@deustp01. To complete Alan's answer.\r\nFrom https://www.enzyme-database.org/faq.php\r\n9. Why is a reaction written in one direction even if the opposite direction is the one observed in vivo?\r\n_All reactions within a given sub-subclass are written in the same direction irrespective of the direction in which the reaction normally occurs in vitro/vivo. Many factors can influence the direction in which a reaction occurs so, by using the same direction for all reactions within a sub-subclass, we are not making any assumptions about the equilibrium of the reaction or its direction in vivo._\r\n"}}
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