{"action":"created","issue":{"url":"https://api.github.com/repos/SBRG/BIGG2/issues/145","labels_url":"https://api.github.com/repos/SBRG/BIGG2/issues/145/labels{/name}","comments_url":"https://api.github.com/repos/SBRG/BIGG2/issues/145/comments","events_url":"https://api.github.com/repos/SBRG/BIGG2/issues/145/events","html_url":"https://github.com/SBRG/BIGG2/issues/145","id":100626919,"number":145,"title":"add subsystems to reaction objects","user":{"login":"jonm4024","id":3847808,"avatar_url":"https://avatars.githubusercontent.com/u/3847808?v=3","gravatar_id":"","url":"https://api.github.com/users/jonm4024","html_url":"https://github.com/jonm4024","followers_url":"https://api.github.com/users/jonm4024/followers","following_url":"https://api.github.com/users/jonm4024/following{/other_user}","gists_url":"https://api.github.com/users/jonm4024/gists{/gist_id}","starred_url":"https://api.github.com/users/jonm4024/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jonm4024/subscriptions","organizations_url":"https://api.github.com/users/jonm4024/orgs","repos_url":"https://api.github.com/users/jonm4024/repos","events_url":"https://api.github.com/users/jonm4024/events{/privacy}","received_events_url":"https://api.github.com/users/jonm4024/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/SBRG/BIGG2/milestones/5","html_url":"https://github.com/SBRG/BIGG2/milestones/Final%20BiGG%202%20release","labels_url":"https://api.github.com/repos/SBRG/BIGG2/milestones/5/labels","id":1136857,"number":5,"title":"Final BiGG 2 release","description":"","creator":{"login":"zakandrewking","id":1250400,"avatar_url":"https://avatars.githubusercontent.com/u/1250400?v=3","gravatar_id":"","url":"https://api.github.com/users/zakandrewking","html_url":"https://github.com/zakandrewking","followers_url":"https://api.github.com/users/zakandrewking/followers","following_url":"https://api.github.com/users/zakandrewking/following{/other_user}","gists_url":"https://api.github.com/users/zakandrewking/gists{/gist_id}","starred_url":"https://api.github.com/users/zakandrewking/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zakandrewking/subscriptions","organizations_url":"https://api.github.com/users/zakandrewking/orgs","repos_url":"https://api.github.com/users/zakandrewking/repos","events_url":"https://api.github.com/users/zakandrewking/events{/privacy}","received_events_url":"https://api.github.com/users/zakandrewking/received_events","type":"User","site_admin":false},"open_issues":20,"closed_issues":14,"state":"open","created_at":"2015-05-27T20:54:06Z","updated_at":"2015-08-12T20:58:35Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2015-08-12T20:22:59Z","updated_at":"2015-08-12T21:22:45Z","closed_at":null,"body":"I noticed that models exported as sbml from BIGG2 do not contain reaction subsystems - could we add this feature back to the models?"},"comment":{"url":"https://api.github.com/repos/SBRG/BIGG2/issues/comments/130452803","html_url":"https://github.com/SBRG/BIGG2/issues/145#issuecomment-130452803","issue_url":"https://api.github.com/repos/SBRG/BIGG2/issues/145","id":130452803,"user":{"login":"nel3","id":3577516,"avatar_url":"https://avatars.githubusercontent.com/u/3577516?v=3","gravatar_id":"","url":"https://api.github.com/users/nel3","html_url":"https://github.com/nel3","followers_url":"https://api.github.com/users/nel3/followers","following_url":"https://api.github.com/users/nel3/following{/other_user}","gists_url":"https://api.github.com/users/nel3/gists{/gist_id}","starred_url":"https://api.github.com/users/nel3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nel3/subscriptions","organizations_url":"https://api.github.com/users/nel3/orgs","repos_url":"https://api.github.com/users/nel3/repos","events_url":"https://api.github.com/users/nel3/events{/privacy}","received_events_url":"https://api.github.com/users/nel3/received_events","type":"User","site_admin":false},"created_at":"2015-08-12T21:22:45Z","updated_at":"2015-08-12T21:22:45Z","body":"1. Is straightforward and necessary.\n\n2. A nice addition, using GO or KEGG, but will get complicated with\nmultiple term or pathway assignments\n\n3. A good idea, but as you mentioned, maps need to be completed for it.\n\nSent from my Android phone.\nOn Aug 12, 2015 4:58 PM, \"Zachary A. King\" <notifications@github.com> wrote:\n\n> We have been discussing this. There are a few ways we could add subsystems:\n>\n>    1.\n>\n>    Just use the subsystems from the published models. This retains the\n>    existing annotations, but it will require manual curation if we ever want\n>    to fix things or add subsystems to models that do not already have them.\n>    2.\n>\n>    Use an ontology (e.g. GO terms <http://geneontology.org/>) for more\n>    extensive subsystem information.\n>    3.\n>\n>    Use the Escher maps that are defined for an organism as the\n>    definitions of subsystems. With this approach, improving the Escher\n>    coverage also improves subsystem info.\n>\n> And a combination of these is possible. At the very least, we should do\n> (1).\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/SBRG/BIGG2/issues/145#issuecomment-130446273>.\n>\n"}}