{"action":"created","issue":{"url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/issues/106","repository_url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM","labels_url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/issues/106/labels{/name}","comments_url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/issues/106/comments","events_url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/issues/106/events","html_url":"https://github.com/SysBioChalmers/yeast-GEM/issues/106","id":322923715,"number":106,"title":"fix: compatibility with memote","user":{"login":"BenjaSanchez","id":9384349,"avatar_url":"https://avatars1.githubusercontent.com/u/9384349?v=4","gravatar_id":"","url":"https://api.github.com/users/BenjaSanchez","html_url":"https://github.com/BenjaSanchez","followers_url":"https://api.github.com/users/BenjaSanchez/followers","following_url":"https://api.github.com/users/BenjaSanchez/following{/other_user}","gists_url":"https://api.github.com/users/BenjaSanchez/gists{/gist_id}","starred_url":"https://api.github.com/users/BenjaSanchez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenjaSanchez/subscriptions","organizations_url":"https://api.github.com/users/BenjaSanchez/orgs","repos_url":"https://api.github.com/users/BenjaSanchez/repos","events_url":"https://api.github.com/users/BenjaSanchez/events{/privacy}","received_events_url":"https://api.github.com/users/BenjaSanchez/received_events","type":"User","site_admin":false},"labels":[{"id":333637235,"url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/labels/format%20fix","name":"format fix","color":"fc2929","default":false}],"state":"open","locked":false,"assignee":{"login":"BenjaSanchez","id":9384349,"avatar_url":"https://avatars1.githubusercontent.com/u/9384349?v=4","gravatar_id":"","url":"https://api.github.com/users/BenjaSanchez","html_url":"https://github.com/BenjaSanchez","followers_url":"https://api.github.com/users/BenjaSanchez/followers","following_url":"https://api.github.com/users/BenjaSanchez/following{/other_user}","gists_url":"https://api.github.com/users/BenjaSanchez/gists{/gist_id}","starred_url":"https://api.github.com/users/BenjaSanchez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenjaSanchez/subscriptions","organizations_url":"https://api.github.com/users/BenjaSanchez/orgs","repos_url":"https://api.github.com/users/BenjaSanchez/repos","events_url":"https://api.github.com/users/BenjaSanchez/events{/privacy}","received_events_url":"https://api.github.com/users/BenjaSanchez/received_events","type":"User","site_admin":false},"assignees":[{"login":"BenjaSanchez","id":9384349,"avatar_url":"https://avatars1.githubusercontent.com/u/9384349?v=4","gravatar_id":"","url":"https://api.github.com/users/BenjaSanchez","html_url":"https://github.com/BenjaSanchez","followers_url":"https://api.github.com/users/BenjaSanchez/followers","following_url":"https://api.github.com/users/BenjaSanchez/following{/other_user}","gists_url":"https://api.github.com/users/BenjaSanchez/gists{/gist_id}","starred_url":"https://api.github.com/users/BenjaSanchez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenjaSanchez/subscriptions","organizations_url":"https://api.github.com/users/BenjaSanchez/orgs","repos_url":"https://api.github.com/users/BenjaSanchez/repos","events_url":"https://api.github.com/users/BenjaSanchez/events{/privacy}","received_events_url":"https://api.github.com/users/BenjaSanchez/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2018-05-14T18:10:42Z","updated_at":"2018-05-24T11:41:57Z","closed_at":null,"author_association":"MEMBER","body":"### Description of the issue:\r\nWe would like to include memote as provider of QC, as we are about to include many new genes/reactions/mets, and it would be best to see how the model changes as we include them. In order to do that we need to:\r\n- [x] Solve issue #19 (a requirement for memote is to have an sbml-compliant file)\r\n- [ ] As [the current report](https://github.com/SysBioChalmers/yeast-GEM/files/2001916/memote_result.zip) has several problems, the model should also be fixed in order to yield proper results. This includes:\r\n  - [ ] Scored tests: No SBO terms detected for metabolites/reactions/genes. This is probably leading to some of the other problems, so should be fixed first.\r\n  - [ ] Unscored tests:\r\n    - [ ] Basic information: \r\n      - [ ] Only 1 unique metabolite\r\n      - [ ] Several errored scores due to absence of SBO terms\r\n      - [ ] NGAM is not detected\r\n      - [ ] Model identifier is \"COBRAmodel\", should be \"yeastGEM\"\r\n    - [ ] Biomass: Need to specify with SBO term\r\n\r\nPlease comment here if anyone finds more problems using memote @hongzhonglu @feiranl @edkerk @ChristianLieven @Midnighter\r\n\r\n**I hereby confirm that I have:**\r\n- [X] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model\r\n- [X] Checked that a similar issue does not exist already\r\n"},"comment":{"url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/issues/comments/391683901","html_url":"https://github.com/SysBioChalmers/yeast-GEM/issues/106#issuecomment-391683901","issue_url":"https://api.github.com/repos/SysBioChalmers/yeast-GEM/issues/106","id":391683901,"user":{"login":"BenjaSanchez","id":9384349,"avatar_url":"https://avatars1.githubusercontent.com/u/9384349?v=4","gravatar_id":"","url":"https://api.github.com/users/BenjaSanchez","html_url":"https://github.com/BenjaSanchez","followers_url":"https://api.github.com/users/BenjaSanchez/followers","following_url":"https://api.github.com/users/BenjaSanchez/following{/other_user}","gists_url":"https://api.github.com/users/BenjaSanchez/gists{/gist_id}","starred_url":"https://api.github.com/users/BenjaSanchez/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BenjaSanchez/subscriptions","organizations_url":"https://api.github.com/users/BenjaSanchez/orgs","repos_url":"https://api.github.com/users/BenjaSanchez/repos","events_url":"https://api.github.com/users/BenjaSanchez/events{/privacy}","received_events_url":"https://api.github.com/users/BenjaSanchez/received_events","type":"User","site_admin":false},"created_at":"2018-05-24T11:41:57Z","updated_at":"2018-05-24T11:41:57Z","author_association":"MEMBER","body":"@Midnighter solving issue #19 actually solved many of the erroring tests. Commenting on some remaining ones:\r\n\r\n> only 1 unique metabolite: \r\n\r\nThe only unique metabolite is `[\"s\"]`. Might this be because of the format we have for annotating metabolites, e.g. `s_1234[c]`, `s_2345[e]`, etc? How is a unique metabolite determined by memote?\r\n\r\n> model identifier = \"COBRAmodel\":\r\n\r\nWhen looking at the 3rd line of the SBML file:\r\n\r\n```\r\n<model metaid=\"yeastGEM.xml\" id=\"COBRAModel\" name=\"Model Exported from COBRA Toolbox\" fbc:strict=\"true\">\r\n```\r\n\r\nNot sure about these distinctions, is there a reason to parse `id` instead of `metaid`? @tpfau can `writeCbModel.m` modify the model id?"}}
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