{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/server/issues/1147","repository_url":"https://api.github.com/repos/ga4gh/server","labels_url":"https://api.github.com/repos/ga4gh/server/issues/1147/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/server/issues/1147/comments","events_url":"https://api.github.com/repos/ga4gh/server/issues/1147/events","html_url":"https://github.com/ga4gh/server/issues/1147","id":151070551,"number":1147,"title":"Ontology handling update required","user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/ga4gh/server/milestones/10","html_url":"https://github.com/ga4gh/server/milestones/sql%20data%20Repo","labels_url":"https://api.github.com/repos/ga4gh/server/milestones/10/labels","id":1707626,"number":10,"title":"sql data Repo","description":"This milestone covers the work required to complete the merge of the new sql data repository for the server. It includes changes to the server and the repo manager.","creator":{"login":"kozbo","id":17557555,"avatar_url":"https://avatars.githubusercontent.com/u/17557555?v=3","gravatar_id":"","url":"https://api.github.com/users/kozbo","html_url":"https://github.com/kozbo","followers_url":"https://api.github.com/users/kozbo/followers","following_url":"https://api.github.com/users/kozbo/following{/other_user}","gists_url":"https://api.github.com/users/kozbo/gists{/gist_id}","starred_url":"https://api.github.com/users/kozbo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kozbo/subscriptions","organizations_url":"https://api.github.com/users/kozbo/orgs","repos_url":"https://api.github.com/users/kozbo/repos","events_url":"https://api.github.com/users/kozbo/events{/privacy}","received_events_url":"https://api.github.com/users/kozbo/received_events","type":"User","site_admin":false},"open_issues":5,"closed_issues":24,"state":"open","created_at":"2016-04-14T20:13:50Z","updated_at":"2016-05-06T11:04:39Z","due_on":null,"closed_at":null},"comments":20,"created_at":"2016-04-26T08:11:02Z","updated_at":"2016-05-11T16:16:36Z","closed_at":null,"body":"The handling of the ontology term mapping in the sql reqo is currently quite brittle, and needs some attention. The most important issue that we need to understand is where the ontology term mapping file comes from, and how we version it. Ideally, I think it would be good if we could get rid of the intermediate text file, and create the term name -> ID mapping as a table in the DB. \r\n\r\nOnce this is done, we should set up a proper relational link between variant sets and ontologies using foreign key constraints, with a properly designed table.\r\n\r\nAny thoughts or discussion on this would be much appreciated."},"comment":{"url":"https://api.github.com/repos/ga4gh/server/issues/comments/218510301","html_url":"https://github.com/ga4gh/server/issues/1147#issuecomment-218510301","issue_url":"https://api.github.com/repos/ga4gh/server/issues/1147","id":218510301,"user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"created_at":"2016-05-11T16:16:36Z","updated_at":"2016-05-11T16:16:36Z","body":"Thanks @cmungall, I've tried it out and it works well enough to get us started. Let us know if you every get around to the heavy-duty Python ontology package --- it's badly needed!"}}