{"action":"created","issue":{"url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/issues/6","repository_url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols","labels_url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/issues/6/comments","events_url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/issues/6/events","html_url":"https://github.com/OpenSourceMycetoma/Series-1-Fenarimols/issues/6","id":294734545,"number":6,"title":"What Codes Should MycetOS Compounds Be Given?","user":{"login":"mattodd","id":4386101,"avatar_url":"https://avatars1.githubusercontent.com/u/4386101?v=4","gravatar_id":"","url":"https://api.github.com/users/mattodd","html_url":"https://github.com/mattodd","followers_url":"https://api.github.com/users/mattodd/followers","following_url":"https://api.github.com/users/mattodd/following{/other_user}","gists_url":"https://api.github.com/users/mattodd/gists{/gist_id}","starred_url":"https://api.github.com/users/mattodd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mattodd/subscriptions","organizations_url":"https://api.github.com/users/mattodd/orgs","repos_url":"https://api.github.com/users/mattodd/repos","events_url":"https://api.github.com/users/mattodd/events{/privacy}","received_events_url":"https://api.github.com/users/mattodd/received_events","type":"User","site_admin":false},"labels":[{"id":826487050,"url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/labels/Question","name":"Question","color":"d876e3","default":false}],"state":"open","locked":false,"assignee":{"login":"mattodd","id":4386101,"avatar_url":"https://avatars1.githubusercontent.com/u/4386101?v=4","gravatar_id":"","url":"https://api.github.com/users/mattodd","html_url":"https://github.com/mattodd","followers_url":"https://api.github.com/users/mattodd/followers","following_url":"https://api.github.com/users/mattodd/following{/other_user}","gists_url":"https://api.github.com/users/mattodd/gists{/gist_id}","starred_url":"https://api.github.com/users/mattodd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mattodd/subscriptions","organizations_url":"https://api.github.com/users/mattodd/orgs","repos_url":"https://api.github.com/users/mattodd/repos","events_url":"https://api.github.com/users/mattodd/events{/privacy}","received_events_url":"https://api.github.com/users/mattodd/received_events","type":"User","site_admin":false},"assignees":[{"login":"mattodd","id":4386101,"avatar_url":"https://avatars1.githubusercontent.com/u/4386101?v=4","gravatar_id":"","url":"https://api.github.com/users/mattodd","html_url":"https://github.com/mattodd","followers_url":"https://api.github.com/users/mattodd/followers","following_url":"https://api.github.com/users/mattodd/following{/other_user}","gists_url":"https://api.github.com/users/mattodd/gists{/gist_id}","starred_url":"https://api.github.com/users/mattodd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mattodd/subscriptions","organizations_url":"https://api.github.com/users/mattodd/orgs","repos_url":"https://api.github.com/users/mattodd/repos","events_url":"https://api.github.com/users/mattodd/events{/privacy}","received_events_url":"https://api.github.com/users/mattodd/received_events","type":"User","site_admin":false}],"milestone":null,"comments":12,"created_at":"2018-02-06T12:02:17Z","updated_at":"2018-02-25T13:52:03Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"There's been [an extensive discussion on Twitter](https://twitter.com/MatToddChem/status/960120081035350017) between me and people who know a lot more about this than I do, about the syntax of codes we should give to compounds in this project. The upshot is that there are many good opinions, but no \"standard\".\r\n\r\nSince MycetOS is essentially beginning from scratch today (here's the [Master List](http://tinyurl.com/MycetomaMols) with the first column conspicuously blank) we have a clean slate and can do whatever we want.\r\n\r\nSo ... what do we want?\r\n\r\nIn Open Source Malaria we commit the sin of including hyphens. So OSM-S-5 is the 5th compound to be made in Sydney, for example. I like that we have, in the code, something of the compound's provenance. But it's going to be more important to capture, somewhere, data on i) batches (i.e. separate samples of the same molecule) and ii) whether we have a salt form or not. There's a long-standing question over at OSM (OpenSourceMalaria/OSM_To_Do_List#172) also about whether compounds of different (or even unknown) enantiomeric excess have different codes. \r\n\r\nThere will be lots of solutions used in closed organisations/projects, but we have the challenge here that MycetOS's molecules are open. We should therefore ask what opportunities there are for direct integration in public databases such as Pubchem. \r\n\r\n(It feels to me that we need a \"colloquial\" name on the one hand - something short like MyOS5, that allows us to include such numbers in discussions - as well as a longer, formal names for samples and the Master List. \r\n\r\nBut let's keep it simple. What format should we use? This Issue is intended to allow for more detailed open discussion than is possible on Twitter. \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/issues/comments/368311019","html_url":"https://github.com/OpenSourceMycetoma/Series-1-Fenarimols/issues/6#issuecomment-368311019","issue_url":"https://api.github.com/repos/OpenSourceMycetoma/Series-1-Fenarimols/issues/6","id":368311019,"user":{"login":"bendndi","id":36627399,"avatar_url":"https://avatars3.githubusercontent.com/u/36627399?v=4","gravatar_id":"","url":"https://api.github.com/users/bendndi","html_url":"https://github.com/bendndi","followers_url":"https://api.github.com/users/bendndi/followers","following_url":"https://api.github.com/users/bendndi/following{/other_user}","gists_url":"https://api.github.com/users/bendndi/gists{/gist_id}","starred_url":"https://api.github.com/users/bendndi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bendndi/subscriptions","organizations_url":"https://api.github.com/users/bendndi/orgs","repos_url":"https://api.github.com/users/bendndi/repos","events_url":"https://api.github.com/users/bendndi/events{/privacy}","received_events_url":"https://api.github.com/users/bendndi/received_events","type":"User","site_admin":false},"created_at":"2018-02-25T13:52:03Z","updated_at":"2018-02-25T13:52:03Z","author_association":"NONE","body":"We can do without the salt codes as part of the main name if people insist (some of the big pharma I work with use this approach this, others don't). What I see as essential is that if 2 (or more) samples of the same structure exist, they are both coded with the same parent code, and are then differentiated by a batch.specific identifier. If this batch aspect is part of the parent, or is a separate column in the excel that's fine. In my experience the former is more common in big pharma, but at DNDi we use the latter."}}
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