{"action":"created","issue":{"url":"https://api.github.com/repos/intermine/intermine/issues/1259","labels_url":"https://api.github.com/repos/intermine/intermine/issues/1259/labels{/name}","comments_url":"https://api.github.com/repos/intermine/intermine/issues/1259/comments","events_url":"https://api.github.com/repos/intermine/intermine/issues/1259/events","html_url":"https://github.com/intermine/intermine/issues/1259","id":121196401,"number":1259,"title":"NCBI GFF - create parser","user":{"login":"julie-sullivan","id":1663057,"avatar_url":"https://avatars.githubusercontent.com/u/1663057?v=3","gravatar_id":"","url":"https://api.github.com/users/julie-sullivan","html_url":"https://github.com/julie-sullivan","followers_url":"https://api.github.com/users/julie-sullivan/followers","following_url":"https://api.github.com/users/julie-sullivan/following{/other_user}","gists_url":"https://api.github.com/users/julie-sullivan/gists{/gist_id}","starred_url":"https://api.github.com/users/julie-sullivan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julie-sullivan/subscriptions","organizations_url":"https://api.github.com/users/julie-sullivan/orgs","repos_url":"https://api.github.com/users/julie-sullivan/repos","events_url":"https://api.github.com/users/julie-sullivan/events{/privacy}","received_events_url":"https://api.github.com/users/julie-sullivan/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/intermine/intermine/labels/data","name":"data","color":"006b75"},{"url":"https://api.github.com/repos/intermine/intermine/labels/enhancement","name":"enhancement","color":"02d7e1"}],"state":"open","locked":false,"assignee":{"login":"julie-sullivan","id":1663057,"avatar_url":"https://avatars.githubusercontent.com/u/1663057?v=3","gravatar_id":"","url":"https://api.github.com/users/julie-sullivan","html_url":"https://github.com/julie-sullivan","followers_url":"https://api.github.com/users/julie-sullivan/followers","following_url":"https://api.github.com/users/julie-sullivan/following{/other_user}","gists_url":"https://api.github.com/users/julie-sullivan/gists{/gist_id}","starred_url":"https://api.github.com/users/julie-sullivan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julie-sullivan/subscriptions","organizations_url":"https://api.github.com/users/julie-sullivan/orgs","repos_url":"https://api.github.com/users/julie-sullivan/repos","events_url":"https://api.github.com/users/julie-sullivan/events{/privacy}","received_events_url":"https://api.github.com/users/julie-sullivan/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/intermine/intermine/milestones/9","html_url":"https://github.com/intermine/intermine/milestones/Future%20InterMine%20release","labels_url":"https://api.github.com/repos/intermine/intermine/milestones/9/labels","id":558446,"number":9,"title":"Future InterMine release","description":"The release after the next release.","creator":{"login":"julie-sullivan","id":1663057,"avatar_url":"https://avatars.githubusercontent.com/u/1663057?v=3","gravatar_id":"","url":"https://api.github.com/users/julie-sullivan","html_url":"https://github.com/julie-sullivan","followers_url":"https://api.github.com/users/julie-sullivan/followers","following_url":"https://api.github.com/users/julie-sullivan/following{/other_user}","gists_url":"https://api.github.com/users/julie-sullivan/gists{/gist_id}","starred_url":"https://api.github.com/users/julie-sullivan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julie-sullivan/subscriptions","organizations_url":"https://api.github.com/users/julie-sullivan/orgs","repos_url":"https://api.github.com/users/julie-sullivan/repos","events_url":"https://api.github.com/users/julie-sullivan/events{/privacy}","received_events_url":"https://api.github.com/users/julie-sullivan/received_events","type":"User","site_admin":false},"open_issues":23,"closed_issues":8,"state":"open","created_at":"2014-02-04T13:39:12Z","updated_at":"2015-12-11T11:12:53Z","due_on":null,"closed_at":null},"comments":15,"created_at":"2015-12-09T09:39:47Z","updated_at":"2015-12-11T14:36:15Z","closed_at":null,"body":"@rachellyne there are some more issues with the GFF parser.\r\n\r\n* Chromosome is set to be `NC_000001.11` instead of just 1. It's in the name though:\r\n\r\n```\r\nNC_000001.11    RefSeq  region  1       248956422       .       +       .       ID=id0;Dbxref=taxon:9606;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA\r\n```\r\n\r\nMight leave for the next build as will need to rewrite the parser.\r\n\r\n* Transcript is marked with the term [`primary_transcript`](http://www.sequenceontology.org/browser/current_svn/term/SO:0000185) which is a child of transcript but not something we have in our model right now. There are transcripts as well.\r\n\r\n```\r\nNC_000001.11    BestRefSeq      primary_transcript      17369   17436   .       -       .       ID=rna2;Parent=gene2;Dbxref=GeneID:102466751,Genbank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705;Name=NR_106918.1;gbkey=precursor_RNA;gene=MIR6859-1;product=microRNA 6859-1;transcript_id=NR_106918.1\r\n```\r\n\r\nGoing to add to the model.\r\n\r\n\r\nIgnoring:\r\n\r\n> 9606.excludes=region,match,cDNA_match,C_gene_segment,D_loop,J_gene_segment,V_gene_segment,D_gene_segment,long_terminal_repeat\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/intermine/intermine/issues/comments/163950496","html_url":"https://github.com/intermine/intermine/issues/1259#issuecomment-163950496","issue_url":"https://api.github.com/repos/intermine/intermine/issues/1259","id":163950496,"user":{"login":"julie-sullivan","id":1663057,"avatar_url":"https://avatars.githubusercontent.com/u/1663057?v=3","gravatar_id":"","url":"https://api.github.com/users/julie-sullivan","html_url":"https://github.com/julie-sullivan","followers_url":"https://api.github.com/users/julie-sullivan/followers","following_url":"https://api.github.com/users/julie-sullivan/following{/other_user}","gists_url":"https://api.github.com/users/julie-sullivan/gists{/gist_id}","starred_url":"https://api.github.com/users/julie-sullivan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julie-sullivan/subscriptions","organizations_url":"https://api.github.com/users/julie-sullivan/orgs","repos_url":"https://api.github.com/users/julie-sullivan/repos","events_url":"https://api.github.com/users/julie-sullivan/events{/privacy}","received_events_url":"https://api.github.com/users/julie-sullivan/received_events","type":"User","site_admin":false},"created_at":"2015-12-11T14:36:15Z","updated_at":"2015-12-11T14:36:15Z","body":"See 0915ca46ee4d9b82107f8114c7cb0a82e016b2b7\r\n\r\n* Deletes synonyms when we skip a feature\r\n* Only parses features that start with `NC_`\r\n  * This will break next release, I am sure. Maybe okay for first try\r\n* Resolves chromosome IDs\r\n  * This will break next release too, I am sure. Maybe okay for now.\r\n\r\n```\r\n        CHROMOSOMES.put(\"NC_000001.11\", \"1\");\r\n        CHROMOSOMES.put(\"NC_000002.12\", \"2\");\r\n        CHROMOSOMES.put(\"NC_000003.12\", \"3\");\r\n        CHROMOSOMES.put(\"NC_000004.12\", \"4\");\r\n        CHROMOSOMES.put(\"NC_000005.10\", \"5\");\r\n        CHROMOSOMES.put(\"NC_000006.12\", \"6\");\r\n        CHROMOSOMES.put(\"NC_000007.14\", \"7\");\r\n        CHROMOSOMES.put(\"NC_000008.11\", \"8\");\r\n        CHROMOSOMES.put(\"NC_000009.12\", \"9\");\r\n        CHROMOSOMES.put(\"NC_000010.11\", \"10\");\r\n\r\n        CHROMOSOMES.put(\"NC_000011.10\", \"11\");\r\n        CHROMOSOMES.put(\"NC_000012.12\", \"12\");\r\n        CHROMOSOMES.put(\"NC_000013.11\", \"13\");\r\n        CHROMOSOMES.put(\"NC_000014.9\", \"14\");\r\n        CHROMOSOMES.put(\"NC_000015.10\", \"15\");\r\n        CHROMOSOMES.put(\"NC_000016.10\", \"16\");\r\n        CHROMOSOMES.put(\"NC_000017.11\", \"17\");\r\n        CHROMOSOMES.put(\"NC_000018.10\", \"18\");\r\n        CHROMOSOMES.put(\"NC_000019.10\", \"19\");\r\n        CHROMOSOMES.put(\"NC_000020.11\", \"20\");\r\n\r\n        CHROMOSOMES.put(\"NC_000021.9\", \"21\");\r\n        CHROMOSOMES.put(\"NC_000022.11\", \"22\");\r\n        CHROMOSOMES.put(\"NC_000023.11\", \"X\");\r\n        CHROMOSOMES.put(\"NC_000024.10\", \"Y\");\r\n```\r\n"}}