{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/565","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/565/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/565/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/565/events","html_url":"https://github.com/GMOD/Apollo/issues/565","id":106059487,"number":565,"title":"Create option to export GFF3 to comply with requirements at NCBI","user":{"login":"monicacecilia","id":1714621,"avatar_url":"https://avatars.githubusercontent.com/u/1714621?v=3","gravatar_id":"","url":"https://api.github.com/users/monicacecilia","html_url":"https://github.com/monicacecilia","followers_url":"https://api.github.com/users/monicacecilia/followers","following_url":"https://api.github.com/users/monicacecilia/following{/other_user}","gists_url":"https://api.github.com/users/monicacecilia/gists{/gist_id}","starred_url":"https://api.github.com/users/monicacecilia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/monicacecilia/subscriptions","organizations_url":"https://api.github.com/users/monicacecilia/orgs","repos_url":"https://api.github.com/users/monicacecilia/repos","events_url":"https://api.github.com/users/monicacecilia/events{/privacy}","received_events_url":"https://api.github.com/users/monicacecilia/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/GMOD/Apollo/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/NAL","name":"NAL","color":"fad8c7"}],"state":"open","locked":false,"assignee":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/GMOD/Apollo/milestones/18","html_url":"https://github.com/GMOD/Apollo/milestones/2.0.2","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/18/labels","id":1245678,"number":18,"title":"2.0.2","description":"","creator":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"open_issues":28,"closed_issues":1,"state":"open","created_at":"2015-08-07T15:36:37Z","updated_at":"2015-10-06T23:30:41Z","due_on":"2015-10-16T07:00:00Z","closed_at":null},"comments":2,"created_at":"2015-09-11T17:46:14Z","updated_at":"2015-10-08T18:35:14Z","closed_at":null,"body":"These are the GFF3 formatting requirements provided by Terence Murphy from NCBI. Before submitting the official gene set (OGS), that is, the integrated GFF of predicted and manually curated models, some attributes need to be added:\r\n \r\n1. Add <code>locus_tag</code> attribute to top-level features such as gene or pseudogene (e.g., locus_tag=W904_OFAS000001; where W904 is the species accession number used in the NCBI submission system). The <code>locus_tag</code> prefix is generated when a BioProject is created, as shown here: http://www.ncbi.nlm.nih.gov/bioproject/230921\r\n\r\n2. Add <code>transcript_id</code> and <code>protein_id</code> attributes to both mRNA and CDS features (e.g., transcript_id=OFAS000001-RA;protein_id=OFAS000001-PA). **Note**: add only <code>transcript_id</code> to transcripts that are not from coding genes (e.g., <code>pseudogenic_transcript</code>, rRNA)\r\n\r\n3. Add a <code>product</code> attribute to CDS features (e.g., <code>product=prophenoloxidase</code>); this is usually the mRNA name when the name is different from ID.\r\n\r\nAdapted from email sent by Mei-Ju Chen at USDA/NAL. Mei-Ju's request: \r\n\"It will be great if WA team could help to batch processing some of the attributes. Let me know if you have questions.\""},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/146647789","html_url":"https://github.com/GMOD/Apollo/issues/565#issuecomment-146647789","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/565","id":146647789,"user":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"created_at":"2015-10-08T18:35:14Z","updated_at":"2015-10-08T18:35:14Z","body":"Should this be the default for exporting GFF3 . . or should this be another option? "}}