{"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":1,"created_at":"2015-10-31T00:59:00Z","updated_at":"2015-11-02T11:22:54Z","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/152992501","html_url":"https://github.com/RNAcentral/rnacentral-webcode/issues/42#issuecomment-152992501","issue_url":"https://api.github.com/repos/RNAcentral/rnacentral-webcode/issues/42","id":152992501,"user":{"login":"AntonPetrov","id":432675,"avatar_url":"https://avatars.githubusercontent.com/u/432675?v=3","gravatar_id":"","url":"https://api.github.com/users/AntonPetrov","html_url":"https://github.com/AntonPetrov","followers_url":"https://api.github.com/users/AntonPetrov/followers","following_url":"https://api.github.com/users/AntonPetrov/following{/other_user}","gists_url":"https://api.github.com/users/AntonPetrov/gists{/gist_id}","starred_url":"https://api.github.com/users/AntonPetrov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AntonPetrov/subscriptions","organizations_url":"https://api.github.com/users/AntonPetrov/orgs","repos_url":"https://api.github.com/users/AntonPetrov/repos","events_url":"https://api.github.com/users/AntonPetrov/events{/privacy}","received_events_url":"https://api.github.com/users/AntonPetrov/received_events","type":"User","site_admin":false},"created_at":"2015-11-02T11:22:54Z","updated_at":"2015-11-02T11:22:54Z","body":"Hi Chris,\r\n\r\nAre you trying to get this information for all RNAcentral sequences or just a subset?\r\n\r\nIf you want to analyse the entire database, then we can look into generating a new report.\r\n\r\nAlternatively, you could consider using the API. For example, here is a description of the sequence that you mentioned in json format:\r\nhttp://rnacentral.org/api/v1/rna/URS000075EF05?flat=true\r\n\r\nIt contains a list of cross-references for each sequence with taxon id, gene name, and RNA type (not SO I am afraid).\r\n\r\nYou can download the json file from RNAcentral search. For example, if you [search for hotair gene](http://rnacentral.org/search?q=gene:%22hotair%22) you can download the json file:\r\nhttp://rnacentral.org/export/results?job=36abf470-0fd6-4b60-9547-a7fc78e8e5a4\r\n\r\nThe export works best for <10,000 entries.\r\n\r\nLet me know if the API approach suits your needs.\r\n"}}