{"action":"created","issue":{"url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/42","labels_url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/42/comments","events_url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/42/events","html_url":"https://github.com/RNAcentral/rnacentral-webcode/issues/42","id":114378738,"number":42,"title":"Which RNA central download to use to get basic metadata?","user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars.githubusercontent.com/u/50745?v=3","gravatar_id":"","url":"https://api.github.com/users/cmungall","html_url":"https://github.com/cmungall","followers_url":"https://api.github.com/users/cmungall/followers","following_url":"https://api.github.com/users/cmungall/following{/other_user}","gists_url":"https://api.github.com/users/cmungall/gists{/gist_id}","starred_url":"https://api.github.com/users/cmungall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmungall/subscriptions","organizations_url":"https://api.github.com/users/cmungall/orgs","repos_url":"https://api.github.com/users/cmungall/repos","events_url":"https://api.github.com/users/cmungall/events{/privacy}","received_events_url":"https://api.github.com/users/cmungall/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2015-10-31T00:59:00Z","updated_at":"2015-12-14T16:17:33Z","closed_at":null,"body":"I'm looking for a download that gives\r\n\r\n * RNA Central ID\r\n * Taxon ID\r\n * Symbol (eg HOTAIR)\r\n * Mappings to other IDs\r\n * RNA type (preferably SO)\r\n\r\nIt looks like this isn't possible as RNAC IDs are groupings of sequences from different species, so I would have to do the lookup myself. I'm super-lazy so looking for hints here to avoid multiple lookups.\r\n\r\nFor hotair RNAC has\r\nhttp://rnacentral.org/rna/URS000075EF05\r\n\r\nThe website has an HGNC and an NCBIGene ID which is a good start for obtaining further metadata...\r\n\r\nUnfortunately it looks like this is being stitched together from database calls. When I use the API to get the yaml or json it doesn't have any of this.\r\n\r\nThe best I can do is the id mapping file which has:\r\n\r\n```\r\nURS000075EF05   REFSEQ  NR_047518       9606\r\n```\r\n\r\nso I guess I can iterate through these, lookup the refseq in some genbank file or something like that, get the NCBI ID, and get the metadata I need that way... is there a better way?"},"comment":{"url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/comments/164481908","html_url":"https://github.com/RNAcentral/rnacentral-webcode/issues/42#issuecomment-164481908","issue_url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/42","id":164481908,"user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars.githubusercontent.com/u/50745?v=3","gravatar_id":"","url":"https://api.github.com/users/cmungall","html_url":"https://github.com/cmungall","followers_url":"https://api.github.com/users/cmungall/followers","following_url":"https://api.github.com/users/cmungall/following{/other_user}","gists_url":"https://api.github.com/users/cmungall/gists{/gist_id}","starred_url":"https://api.github.com/users/cmungall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmungall/subscriptions","organizations_url":"https://api.github.com/users/cmungall/orgs","repos_url":"https://api.github.com/users/cmungall/repos","events_url":"https://api.github.com/users/cmungall/events{/privacy}","received_events_url":"https://api.github.com/users/cmungall/received_events","type":"User","site_admin":false},"created_at":"2015-12-14T16:17:32Z","updated_at":"2015-12-14T16:17:32Z","body":"Thanks!\r\n\r\nGreat having the externally assigned gene symbols in col 6\r\n\r\nColumn 5:\r\n\r\nThe following are not in SO:\r\n\r\n * None\r\n * antisense_RNA lncRNA\r\n * lncRNA\r\n * misc_RNA\r\n * other\r\n * precursor_RNA\r\n\r\nI recommend leaving the field blank for 'None' and discarding 'other'. Or you can simply use 'RNA' if you know nothing more than it's an RNA\r\n\r\nFor the others we can coordinate with SO. Or perhaps this is a SO-INSDC coordination/mapping thing.\r\n\r\nYou might want to change your example.txt to include an example with a gene symbol, e.g\r\n\r\n```\r\nURS0000037184   VEGA    OTTHUMT00000350154      9606    antisense_RNA   HOTAIRM1\r\nURS0000037184   VEGA    OTTHUMG00000158089      9606\r\nURS0000037184   ENA     HG500100.1:1..163:ncRNA 9606    lncRNA  HOTAIRM1\r\nURS0000037184   LNCIPEDIA       lnc-EVX1-13:1   9606    lncRNA  lnc-EVX1-13\r\n```\r\n\r\nLooks great you can close this ticket on release or now"}}