{"action":"opened","issue":{"url":"https://api.github.com/repos/WormBase/website/issues/5214","repository_url":"https://api.github.com/repos/WormBase/website","labels_url":"https://api.github.com/repos/WormBase/website/issues/5214/labels{/name}","comments_url":"https://api.github.com/repos/WormBase/website/issues/5214/comments","events_url":"https://api.github.com/repos/WormBase/website/issues/5214/events","html_url":"https://github.com/WormBase/website/issues/5214","id":187086698,"number":5214,"title":"WormMine (im-254): RNAi inhibited gene is populated with transcript names; should be gene IDs","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":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":0,"created_at":"2016-11-03T15:07:46Z","updated_at":"2016-11-03T15:07:46Z","closed_at":null,"body":"If I run the following query for all RNAi objects and their inhibited genes and transcripts:\r\n\r\n`<query name=\"\" model=\"genomic\" view=\"RNAi.primaryIdentifier RNAi.inhibitsGene.primaryIdentifier RNAi.inhibitsGene.secondaryIdentifier RNAi.inhibitsGene.symbol RNAi.inhibitsTranscript.symbol\" longDescription=\"\" sortOrder=\"RNAi.primaryIdentifier asc\">\r\n</query>`\r\n\r\nI get the following table of results:\r\n\r\n![screen shot 2016-11-03 at 10 57 57 am](https://cloud.githubusercontent.com/assets/611382/19971090/69b8917c-a1b4-11e6-8370-8579ff83b261.png)\r\n\r\nThe names listed in the \"Inhibits Gene, WormBase Gene ID\" field are actually names of transcripts, for example \"B0511.9a\", \"B0511.9b\", and \"B0511.9c\", whereas the sequence name and gene name fields are blank as is the transcript field. This may be why some duplicate/bogus gene objects are being populated in WormMine with transcript names instead of gene IDs (e.g. WBGene00000001) as reported in issue #5209 \r\n\r\nFor the rows showing \"B0511.9a\", \"B0511.9b\", and \"B0511.9c\" as the gene IDs for the inhibited gene(s), these should rather be listed as the following:\r\n\r\n`\r\nRNAi WormBase ID    WB Gene ID               Seq.Name     Gene Name     Transcript Seq.Name\r\nWBRNAi00000002     WBGene00015235     B0511.9         cdc-26            B0511.9a\r\nWBRNAi00000002     WBGene00015235     B0511.9         cdc-26            B0511.9b\r\nWBRNAi00000002     WBGene00015235     B0511.9         cdc-26            B0511.9c\r\n`\r\n\r\n"}}
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