{"action":"created","issue":{"url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/36","repository_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML","labels_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/36/labels{/name}","comments_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/36/comments","events_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/36/events","html_url":"https://github.com/HUPO-PSI/mzIdentML/issues/36","id":159455421,"number":36,"title":"Validation issues for xiFDR-CrossLinkExample.mzid","user":{"login":"edeutsch","id":12707718,"avatar_url":"https://avatars.githubusercontent.com/u/12707718?v=3","gravatar_id":"","url":"https://api.github.com/users/edeutsch","html_url":"https://github.com/edeutsch","followers_url":"https://api.github.com/users/edeutsch/followers","following_url":"https://api.github.com/users/edeutsch/following{/other_user}","gists_url":"https://api.github.com/users/edeutsch/gists{/gist_id}","starred_url":"https://api.github.com/users/edeutsch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edeutsch/subscriptions","organizations_url":"https://api.github.com/users/edeutsch/orgs","repos_url":"https://api.github.com/users/edeutsch/repos","events_url":"https://api.github.com/users/edeutsch/events{/privacy}","received_events_url":"https://api.github.com/users/edeutsch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-06-09T16:44:23Z","updated_at":"2016-07-15T13:45:02Z","closed_at":null,"body":"ERROR: cvParam anchor protein should have a value, but it does not!\r\nERROR: cvParam protein-pair-level global FDR has a value, but it should not!\r\nERROR: cvParam residue-pair-level global FDR has a value, but it should not!\r\nWARNING: CV term MS:1002675 ('residue-pair-level global FDR') is not in the cv\r\nWARNING: CV term MS:1002676 ('protein-pair-level global FDR') is not in the cv\r\nWARNING: MS:1000563 should be 'Thermo RAW format' instead of 'Thermo Raw file'\r\nWARNING: MS:1002404 should be 'count of identified proteins' instead of 'count of identified protein'\r\nWARNING: MS:1002511 should be 'cross-link spectrum identification item' instead of 'Cross-linked spectrum identification item.'\r\nWARNING: MS:1002544 should be 'xi' instead of 'xiFDR'\r\nWARNING: MS:1002545 should be 'xi:score' instead of 'The xi result 'Score'.'\r\n"},"comment":{"url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/comments/232954464","html_url":"https://github.com/HUPO-PSI/mzIdentML/issues/36#issuecomment-232954464","issue_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/36","id":232954464,"user":{"login":"germa","id":3297148,"avatar_url":"https://avatars.githubusercontent.com/u/3297148?v=3","gravatar_id":"","url":"https://api.github.com/users/germa","html_url":"https://github.com/germa","followers_url":"https://api.github.com/users/germa/followers","following_url":"https://api.github.com/users/germa/following{/other_user}","gists_url":"https://api.github.com/users/germa/gists{/gist_id}","starred_url":"https://api.github.com/users/germa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/germa/subscriptions","organizations_url":"https://api.github.com/users/germa/orgs","repos_url":"https://api.github.com/users/germa/repos","events_url":"https://api.github.com/users/germa/events{/privacy}","received_events_url":"https://api.github.com/users/germa/received_events","type":"User","site_admin":false},"created_at":"2016-07-15T13:45:02Z","updated_at":"2016-07-15T13:45:02Z","body":"Should we allow also 'loop links', i.e. a cross-linking between the same peptide?\r\nLutz has some of them in his example files, but Figure 4 in the spec doc states:\r\n\r\nIn mzIdentML, they will be represented by different ProteinDetectionHypothesis(PDH) elements within different ProteinAmbiguityGroup(PAG) elements, sharing the same ID and score.\r\n"}}
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