{"action":"created","issue":{"url":"https://api.github.com/repos/WormBase/website/issues/5385","repository_url":"https://api.github.com/repos/WormBase/website","labels_url":"https://api.github.com/repos/WormBase/website/issues/5385/labels{/name}","comments_url":"https://api.github.com/repos/WormBase/website/issues/5385/comments","events_url":"https://api.github.com/repos/WormBase/website/issues/5385/events","html_url":"https://github.com/WormBase/website/issues/5385","id":203715821,"number":5385,"title":"Gene IDs, names, and sequence names are misformatted in WormMine im-257","user":{"login":"chris-grove","id":611382,"avatar_url":"https://avatars.githubusercontent.com/u/611382?v=3","gravatar_id":"","url":"https://api.github.com/users/chris-grove","html_url":"https://github.com/chris-grove","followers_url":"https://api.github.com/users/chris-grove/followers","following_url":"https://api.github.com/users/chris-grove/following{/other_user}","gists_url":"https://api.github.com/users/chris-grove/gists{/gist_id}","starred_url":"https://api.github.com/users/chris-grove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chris-grove/subscriptions","organizations_url":"https://api.github.com/users/chris-grove/orgs","repos_url":"https://api.github.com/users/chris-grove/repos","events_url":"https://api.github.com/users/chris-grove/events{/privacy}","received_events_url":"https://api.github.com/users/chris-grove/received_events","type":"User","site_admin":false},"labels":[{"id":3567514,"url":"https://api.github.com/repos/WormBase/website/labels/data%20(problem)","name":"data (problem)","color":"207de5","default":false},{"id":220084,"url":"https://api.github.com/repos/WormBase/website/labels/Intermine","name":"Intermine","color":"0b02e1","default":false}],"state":"open","locked":false,"assignee":{"login":"nuin","id":6273,"avatar_url":"https://avatars.githubusercontent.com/u/6273?v=3","gravatar_id":"","url":"https://api.github.com/users/nuin","html_url":"https://github.com/nuin","followers_url":"https://api.github.com/users/nuin/followers","following_url":"https://api.github.com/users/nuin/following{/other_user}","gists_url":"https://api.github.com/users/nuin/gists{/gist_id}","starred_url":"https://api.github.com/users/nuin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nuin/subscriptions","organizations_url":"https://api.github.com/users/nuin/orgs","repos_url":"https://api.github.com/users/nuin/repos","events_url":"https://api.github.com/users/nuin/events{/privacy}","received_events_url":"https://api.github.com/users/nuin/received_events","type":"User","site_admin":false},"assignees":[{"login":"nuin","id":6273,"avatar_url":"https://avatars.githubusercontent.com/u/6273?v=3","gravatar_id":"","url":"https://api.github.com/users/nuin","html_url":"https://github.com/nuin","followers_url":"https://api.github.com/users/nuin/followers","following_url":"https://api.github.com/users/nuin/following{/other_user}","gists_url":"https://api.github.com/users/nuin/gists{/gist_id}","starred_url":"https://api.github.com/users/nuin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nuin/subscriptions","organizations_url":"https://api.github.com/users/nuin/orgs","repos_url":"https://api.github.com/users/nuin/repos","events_url":"https://api.github.com/users/nuin/events{/privacy}","received_events_url":"https://api.github.com/users/nuin/received_events","type":"User","site_admin":false}],"milestone":null,"comments":18,"created_at":"2017-01-27T19:12:49Z","updated_at":"2017-02-10T01:39:08Z","closed_at":null,"body":"@nuin \r\nI noticed that in the new im-257 WormMine build, the gene IDs, names, and sequence names are mostly not formatted correctly. For example, performing this query for C. elegans genes:\r\n\r\n`<query name=\"\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.secondaryIdentifier Gene.organism.name\" longDescription=\"\" sortOrder=\"Gene.primaryIdentifier asc\">\r\n  <constraint path=\"Gene.organism.name\" op=\"==\" value=\"Caenorhabditis elegans\"/>\r\n</query>`\r\n\r\nResults in the following results:\r\n\r\n![screen shot 2017-01-27 at 11 04 32 am](https://cloud.githubusercontent.com/assets/611382/22383853/7d7bf546-e480-11e6-9c8a-a165e6a39c5e.png)\r\n\r\nThe problem is that the \"WormBase Gene ID\" is of the form \"Gene:WBGene########\" when it should simply be \"WBGene########\" and the \"Gene Name\" is of the format \"WBGene########\" when it should be something like \"unc-26\" or \"dpy-3\" and the \"Sequence Name\" field is mostly empty when it should have names like \"W02C12.3\" or \"M05B5.5\".\r\n\r\nAn example of a gene entry that is formatted properly can be seen with this query:\r\n\r\n`<query name=\"\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.secondaryIdentifier Gene.organism.name\" longDescription=\"\" sortOrder=\"Gene.primaryIdentifier asc\" constraintLogic=\"A and B\">\r\n  <constraint path=\"Gene.organism.name\" code=\"A\" op=\"==\" value=\"Caenorhabditis elegans\"/>\r\n  <constraint path=\"Gene.symbol\" code=\"B\" op=\"CONTAINS\" value=\"unc\"/>\r\n</query>`\r\n\r\nThis query should return more than a hundred genes but it only returns one (unc-26), so it seems that a few genes are formatted correctly, but most are not.\r\n\r\nI hope that's clear.\r\n"},"comment":{"url":"https://api.github.com/repos/WormBase/website/issues/comments/278833174","html_url":"https://github.com/WormBase/website/issues/5385#issuecomment-278833174","issue_url":"https://api.github.com/repos/WormBase/website/issues/5385","id":278833174,"user":{"login":"nuin","id":6273,"avatar_url":"https://avatars.githubusercontent.com/u/6273?v=3","gravatar_id":"","url":"https://api.github.com/users/nuin","html_url":"https://github.com/nuin","followers_url":"https://api.github.com/users/nuin/followers","following_url":"https://api.github.com/users/nuin/following{/other_user}","gists_url":"https://api.github.com/users/nuin/gists{/gist_id}","starred_url":"https://api.github.com/users/nuin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nuin/subscriptions","organizations_url":"https://api.github.com/users/nuin/orgs","repos_url":"https://api.github.com/users/nuin/repos","events_url":"https://api.github.com/users/nuin/events{/privacy}","received_events_url":"https://api.github.com/users/nuin/received_events","type":"User","site_admin":false},"created_at":"2017-02-10T01:39:08Z","updated_at":"2017-02-10T01:39:08Z","body":"GFF3 is coming before all AceDB loads, so this info might not be loading correctly from the AceDB files. The best course of action is to try each step separately and then check what is going where."}}
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