{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1334","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1334/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1334/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1334/events","html_url":"https://github.com/OpenMS/OpenMS/pull/1334","id":65931725,"number":1334,"title":"Feature/pep xml prophets","user":{"login":"hroest","id":464014,"avatar_url":"https://avatars.githubusercontent.com/u/464014?v=3","gravatar_id":"","url":"https://api.github.com/users/hroest","html_url":"https://github.com/hroest","followers_url":"https://api.github.com/users/hroest/followers","following_url":"https://api.github.com/users/hroest/following{/other_user}","gists_url":"https://api.github.com/users/hroest/gists{/gist_id}","starred_url":"https://api.github.com/users/hroest/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hroest/subscriptions","organizations_url":"https://api.github.com/users/hroest/orgs","repos_url":"https://api.github.com/users/hroest/repos","events_url":"https://api.github.com/users/hroest/events{/privacy}","received_events_url":"https://api.github.com/users/hroest/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":24,"created_at":"2015-04-02T13:56:06Z","updated_at":"2015-09-14T13:39:14Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1334","html_url":"https://github.com/OpenMS/OpenMS/pull/1334","diff_url":"https://github.com/OpenMS/OpenMS/pull/1334.diff","patch_url":"https://github.com/OpenMS/OpenMS/pull/1334.patch"},"body":"- improve pepXML parsing\r\n- add support for the `search_score_summary` tag\r\n- add support to store interProphet *and* peptideProphet results\r\n- support for additional attributes in `spectrum_query`\r\n- support to write out pepxml attributes"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/140078286","html_url":"https://github.com/OpenMS/OpenMS/pull/1334#issuecomment-140078286","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1334","id":140078286,"user":{"login":"hendrikweisser","id":2251068,"avatar_url":"https://avatars.githubusercontent.com/u/2251068?v=3","gravatar_id":"","url":"https://api.github.com/users/hendrikweisser","html_url":"https://github.com/hendrikweisser","followers_url":"https://api.github.com/users/hendrikweisser/followers","following_url":"https://api.github.com/users/hendrikweisser/following{/other_user}","gists_url":"https://api.github.com/users/hendrikweisser/gists{/gist_id}","starred_url":"https://api.github.com/users/hendrikweisser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hendrikweisser/subscriptions","organizations_url":"https://api.github.com/users/hendrikweisser/orgs","repos_url":"https://api.github.com/users/hendrikweisser/repos","events_url":"https://api.github.com/users/hendrikweisser/events{/privacy}","received_events_url":"https://api.github.com/users/hendrikweisser/received_events","type":"User","site_admin":false},"created_at":"2015-09-14T13:39:14Z","updated_at":"2015-09-14T13:39:14Z","body":"My opinion is that we should just model the structure that is used in mzIdentML. This would have the following advantages:\r\n- easy compatibility to mzIdentML, i.e. the main ID file format\r\n- flat hierarchy makes it easier to find specific scores\r\n- score orientation is stored only once, with the score type\r\n- \"main score\" is ill-defined, may depend on the application (not for PeptideProphet, but for Mascot, Percolator, MS-GF+, ...)\r\n\r\nIn the mzIdentML structure, the hierarchical grouping is implicitly given by the CV terms. There are pros and cons for a flat or a hierarchical implementation, but in case of doubt I would prefer to go with the way it's done in mzIdentML. (I'm pretty sure the pepXML scoring case is covered there, too.)\r\n"}}