{"action":"created","issue":{"url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/102","repository_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML","labels_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/102/labels{/name}","comments_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/102/comments","events_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/102/events","html_url":"https://github.com/HUPO-PSI/mzIdentML/issues/102","id":343332155,"node_id":"MDU6SXNzdWUzNDMzMzIxNTU=","number":102,"title":"Peptide <-> PeptideEvidence relationship - is this valid?","user":{"login":"colin-combe","id":977607,"node_id":"MDQ6VXNlcjk3NzYwNw==","avatar_url":"https://avatars3.githubusercontent.com/u/977607?v=4","gravatar_id":"","url":"https://api.github.com/users/colin-combe","html_url":"https://github.com/colin-combe","followers_url":"https://api.github.com/users/colin-combe/followers","following_url":"https://api.github.com/users/colin-combe/following{/other_user}","gists_url":"https://api.github.com/users/colin-combe/gists{/gist_id}","starred_url":"https://api.github.com/users/colin-combe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/colin-combe/subscriptions","organizations_url":"https://api.github.com/users/colin-combe/orgs","repos_url":"https://api.github.com/users/colin-combe/repos","events_url":"https://api.github.com/users/colin-combe/events{/privacy}","received_events_url":"https://api.github.com/users/colin-combe/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-21T14:55:17Z","updated_at":"2018-09-26T14:06:15Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nmy example refers to file /examples/1_2examples/crosslinking/xiFDR-CrossLinkExample.mzid, \r\nwhich is currently passed by the validator.\r\n\r\nIf you search for the peptide with id \"54604449_54604449_6_6_p0\",\r\nthen it seems to be missing any associated PeptideEvidence element.\r\n\r\nAlso, if you then go to its occurrence within a SpectrumIdentification (SII_3312_2),\r\nthen search for the peptideEvidence_ref of the PeptideEvidenceRef within that identification (\"pepevid_psm252621340_pep54604449_protP02768-A_decoy_576\"),\r\nthen check the peptide_ref of that PeptideEvidence,\r\nit is \"54604449_54604449_6_6_p**1**\",\r\ni.e. its not the one we started with.\r\n\r\nAssuming I'm not making some mistake, some questions:\r\n- is it valid that \"54604449_54604449_6_6_p0\" has no associated PeptideEvidence whilst most of the peptides in the file do?\r\n- is it valid that a SpectrumIdentification can contain a PeptideEvidenceRef element where the peptide_ref of the corresponding PeptideEvidence is not the peptide_ref the SpectrumIdentification identifies?\r\n\r\nI can't find anything in the specification document that's explicit about these questions. Both feel wrong to me, especially the second.\r\n\r\nIf these aren't valid then could the validator be made to detect these errors? \r\n\r\nIf they're not valid and there's nothing in the documentation about it, then could the documentation be made clearer on these points?\r\n\r\nAs an aside, aren't the PeptideEvidenceRef elements redundant if the relation between Peptides and PeptideEvidences is properly enforced? i.e. you only need the id of the peptide and you can get the associated PeptideEvidences from that?\r\n\r\nbest wishes,\r\nColin\r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/comments/424728407","html_url":"https://github.com/HUPO-PSI/mzIdentML/issues/102#issuecomment-424728407","issue_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/102","id":424728407,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNDcyODQwNw==","user":{"login":"germa","id":3297148,"node_id":"MDQ6VXNlcjMyOTcxNDg=","avatar_url":"https://avatars2.githubusercontent.com/u/3297148?v=4","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":"2018-09-26T14:06:15Z","updated_at":"2018-09-26T14:06:15Z","author_association":"CONTRIBUTOR","body":"Hi Colin,\r\n\r\nyes I too think that both cases should not occurs. I'll add a check for this in the validator.\r\n\r\nCheers,\r\nGerhard\r\n"}}
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