{"action":"created","issue":{"url":"https://api.github.com/repos/topdownproteomics/sdk/issues/17","repository_url":"https://api.github.com/repos/topdownproteomics/sdk","labels_url":"https://api.github.com/repos/topdownproteomics/sdk/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/topdownproteomics/sdk/issues/17/comments","events_url":"https://api.github.com/repos/topdownproteomics/sdk/issues/17/events","html_url":"https://github.com/topdownproteomics/sdk/issues/17","id":294902496,"node_id":"MDU6SXNzdWUyOTQ5MDI0OTY=","number":17,"title":"Ambiguity of PTM localization","user":{"login":"acesnik","id":16342951,"node_id":"MDQ6VXNlcjE2MzQyOTUx","avatar_url":"https://avatars2.githubusercontent.com/u/16342951?v=4","gravatar_id":"","url":"https://api.github.com/users/acesnik","html_url":"https://github.com/acesnik","followers_url":"https://api.github.com/users/acesnik/followers","following_url":"https://api.github.com/users/acesnik/following{/other_user}","gists_url":"https://api.github.com/users/acesnik/gists{/gist_id}","starred_url":"https://api.github.com/users/acesnik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/acesnik/subscriptions","organizations_url":"https://api.github.com/users/acesnik/orgs","repos_url":"https://api.github.com/users/acesnik/repos","events_url":"https://api.github.com/users/acesnik/events{/privacy}","received_events_url":"https://api.github.com/users/acesnik/received_events","type":"User","site_admin":false},"labels":[{"id":890314818,"node_id":"MDU6TGFiZWw4OTAzMTQ4MTg=","url":"https://api.github.com/repos/topdownproteomics/sdk/labels/Ambiguity%20of%20Localization","name":"Ambiguity of Localization","color":"eaa179","default":false},{"id":817508174,"node_id":"MDU6TGFiZWw4MTc1MDgxNzQ=","url":"https://api.github.com/repos/topdownproteomics/sdk/labels/ProForma%20Parser","name":"ProForma Parser","color":"7f04ea","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/topdownproteomics/sdk/milestones/1","html_url":"https://github.com/topdownproteomics/sdk/milestone/1","labels_url":"https://api.github.com/repos/topdownproteomics/sdk/milestones/1/labels","id":3641904,"node_id":"MDk6TWlsZXN0b25lMzY0MTkwNA==","number":1,"title":"ProForma 2.0","description":"* TopDownSDK parses ProForma\r\n* TopDownSDK writes ProForma\r\n* TopDownSDK validates ProForma\r\n* Handles ambiguous PTM assignments\r\n* Compares ProForma terms: calculates equality or similarity of proteoforms and proteoform groups","creator":{"login":"acesnik","id":16342951,"node_id":"MDQ6VXNlcjE2MzQyOTUx","avatar_url":"https://avatars2.githubusercontent.com/u/16342951?v=4","gravatar_id":"","url":"https://api.github.com/users/acesnik","html_url":"https://github.com/acesnik","followers_url":"https://api.github.com/users/acesnik/followers","following_url":"https://api.github.com/users/acesnik/following{/other_user}","gists_url":"https://api.github.com/users/acesnik/gists{/gist_id}","starred_url":"https://api.github.com/users/acesnik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/acesnik/subscriptions","organizations_url":"https://api.github.com/users/acesnik/orgs","repos_url":"https://api.github.com/users/acesnik/repos","events_url":"https://api.github.com/users/acesnik/events{/privacy}","received_events_url":"https://api.github.com/users/acesnik/received_events","type":"User","site_admin":false},"open_issues":8,"closed_issues":0,"state":"open","created_at":"2018-09-10T22:08:01Z","updated_at":"2018-09-10T22:11:41Z","due_on":null,"closed_at":null},"comments":15,"created_at":"2018-02-06T20:28:49Z","updated_at":"2018-09-11T17:37:26Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"This issue was left unanswered in the standard. Let's come up with a proposal, implement it, and see if the committee for the standard has any issues with it."},"comment":{"url":"https://api.github.com/repos/topdownproteomics/sdk/issues/comments/420357322","html_url":"https://github.com/topdownproteomics/sdk/issues/17#issuecomment-420357322","issue_url":"https://api.github.com/repos/topdownproteomics/sdk/issues/17","id":420357322,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMDM1NzMyMg==","user":{"login":"acesnik","id":16342951,"node_id":"MDQ6VXNlcjE2MzQyOTUx","avatar_url":"https://avatars2.githubusercontent.com/u/16342951?v=4","gravatar_id":"","url":"https://api.github.com/users/acesnik","html_url":"https://github.com/acesnik","followers_url":"https://api.github.com/users/acesnik/followers","following_url":"https://api.github.com/users/acesnik/following{/other_user}","gists_url":"https://api.github.com/users/acesnik/gists{/gist_id}","starred_url":"https://api.github.com/users/acesnik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/acesnik/subscriptions","organizations_url":"https://api.github.com/users/acesnik/orgs","repos_url":"https://api.github.com/users/acesnik/repos","events_url":"https://api.github.com/users/acesnik/events{/privacy}","received_events_url":"https://api.github.com/users/acesnik/received_events","type":"User","site_admin":false},"created_at":"2018-09-11T17:37:26Z","updated_at":"2018-09-11T17:37:26Z","author_association":"CONTRIBUTOR","body":"New issues to consider from this pull request https://github.com/topdownproteomics/sdk/pull/57\r\n\r\n## On range notation:\r\n> Is the amino acid T included in the range \"A\" within `PROT[mass:19|A->]EOSFORMS[<-A]`? If so, we might want to rethink this syntax as the arrows seem to indicate otherwise. Thoughts?\"\r\n\r\n> I see your point; it does point only to the internal sequence. \r\n> \r\n> But I think this comes back to the left-right issue. Each tag pertains to the amino acid to the left in ProForma v1. I suppose we could go with one of the earlier suggestions `PROT[mass:19|start:group1]EOSFORMS[end:group1]` but that's a bit less readable.\r\n> \r\n> Or we could consider something with the exclusive/inclusive mathematical range notation (0,5] etc. Perhaps `PROT[mass:19|group1(T->]EOSFORMS[<-S)group1]`.\r\n\r\n## On unlocalized tags\r\n> The unlocalized tag on `[mass:80|Phospho|<->]PROTEOSFORMS` seems to be \"homeless\" and could be mistaken for an N-terminal modification. Maybe we should consider something that looks more like the prefix or terminal tags, e.g. `[mass:80|Phospho]?PROTEOSFORMS`. Thoughts?\r\n\r\n> The confusion with N-terminal mods could be a problem, so we should consider that. That said, I think seeming homeless is the intent. We don't know what amino acid to assign it to. The question-mark notation does do a nice job of distinguishing these from N-terminal mods."}}
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