{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/topiary/issues/49","repository_url":"https://api.github.com/repos/hammerlab/topiary","labels_url":"https://api.github.com/repos/hammerlab/topiary/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/topiary/issues/49/comments","events_url":"https://api.github.com/repos/hammerlab/topiary/issues/49/events","html_url":"https://github.com/hammerlab/topiary/issues/49","id":153343174,"number":49,"title":"Replace \"self-ligandome\" filtering with just search over the full proteome","user":{"login":"iskandr","id":48441,"avatar_url":"https://avatars.githubusercontent.com/u/48441?v=3","gravatar_id":"","url":"https://api.github.com/users/iskandr","html_url":"https://github.com/iskandr","followers_url":"https://api.github.com/users/iskandr/followers","following_url":"https://api.github.com/users/iskandr/following{/other_user}","gists_url":"https://api.github.com/users/iskandr/gists{/gist_id}","starred_url":"https://api.github.com/users/iskandr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iskandr/subscriptions","organizations_url":"https://api.github.com/users/iskandr/orgs","repos_url":"https://api.github.com/users/iskandr/repos","events_url":"https://api.github.com/users/iskandr/events{/privacy}","received_events_url":"https://api.github.com/users/iskandr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-05-05T22:45:17Z","updated_at":"2016-05-05T22:56:56Z","closed_at":null,"body":"I'm not sure it's worth the extra complexity to filter candidate epitopes by a \"self-ligandome\" set of peptides. No one other than Kipp ever generated these peptide sets and no one seems to use them. So, in the interest of using a more precise filter, Topiary ended up without any kind of self-filtering whatsoever. Simpler alternative: chop up the reference proteome from pyensembl and check for membership in that peptide set. \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/hammerlab/topiary/issues/comments/217303831","html_url":"https://github.com/hammerlab/topiary/issues/49#issuecomment-217303831","issue_url":"https://api.github.com/repos/hammerlab/topiary/issues/49","id":217303831,"user":{"login":"iskandr","id":48441,"avatar_url":"https://avatars.githubusercontent.com/u/48441?v=3","gravatar_id":"","url":"https://api.github.com/users/iskandr","html_url":"https://github.com/iskandr","followers_url":"https://api.github.com/users/iskandr/followers","following_url":"https://api.github.com/users/iskandr/following{/other_user}","gists_url":"https://api.github.com/users/iskandr/gists{/gist_id}","starred_url":"https://api.github.com/users/iskandr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iskandr/subscriptions","organizations_url":"https://api.github.com/users/iskandr/orgs","repos_url":"https://api.github.com/users/iskandr/repos","events_url":"https://api.github.com/users/iskandr/events{/privacy}","received_events_url":"https://api.github.com/users/iskandr/received_events","type":"User","site_admin":false},"created_at":"2016-05-05T22:56:56Z","updated_at":"2016-05-05T22:56:56Z","body":"I think all we'd be giving up is the ability to later use inexact string matches (such as looking at only interior TCR-facing residues). "}}