{"action":"created","issue":{"url":"https://api.github.com/repos/TeselaGen/ve/issues/1267","labels_url":"https://api.github.com/repos/TeselaGen/ve/issues/1267/labels{/name}","comments_url":"https://api.github.com/repos/TeselaGen/ve/issues/1267/comments","events_url":"https://api.github.com/repos/TeselaGen/ve/issues/1267/events","html_url":"https://github.com/TeselaGen/ve/issues/1267","id":102261426,"number":1267,"title":"TAP: Tox/Allergy/Pathogen Screen","user":{"login":"sampearl","id":348837,"avatar_url":"https://avatars.githubusercontent.com/u/348837?v=3","gravatar_id":"","url":"https://api.github.com/users/sampearl","html_url":"https://github.com/sampearl","followers_url":"https://api.github.com/users/sampearl/followers","following_url":"https://api.github.com/users/sampearl/following{/other_user}","gists_url":"https://api.github.com/users/sampearl/gists{/gist_id}","starred_url":"https://api.github.com/users/sampearl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sampearl/subscriptions","organizations_url":"https://api.github.com/users/sampearl/orgs","repos_url":"https://api.github.com/users/sampearl/repos","events_url":"https://api.github.com/users/sampearl/events{/privacy}","received_events_url":"https://api.github.com/users/sampearl/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/TeselaGen/ve/labels/Customer:%20DAS%20Phase%20I","name":"Customer: DAS Phase I","color":"e11d21"},{"url":"https://api.github.com/repos/TeselaGen/ve/labels/Priority:%20Medium","name":"Priority: Medium","color":"F39C12"},{"url":"https://api.github.com/repos/TeselaGen/ve/labels/Type:%20Feature","name":"Type: Feature","color":"8B2E5F"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-20T23:43:29Z","updated_at":"2015-11-06T16:35:17Z","closed_at":null,"body":"In-app functionality to check genes for pathogenicity/allergenicity/toxicity using existing resources.\r\n* High importance to DAS\r\n* Results and the detail folder link currently are emailed to the submitter and cc the mailing list .DL BIOS DLBIOS@dow.com \r\n* Primary input is a FASTA file containing AA sequence. Should allow for DNA sequence input in the future.\r\n* Log files currently associate run information with Project / Project Leader / Project Description / Assessment Purpose (Biosafety or Regulatory)\r\n* Pathogenicity check (not yet required at DAS)\r\n  * Check against synthesis of pathogenic sequences. This is not required at DAS, but a review of current practices as gene synthesis companies and recommendation for future checks should be made.\r\n* Allergenicity check\r\n  * FASTA search against internal instance of the Nebraska Allergenicity Database\r\n  * Returns hit value of 0 or 1, positive hits have associated information on Allergen source / type / group\r\n  * Interesting note: sucrose binding proteins are often allergens\r\n* Toxicity check\r\n  * FASTA search against internally curated list of AA sequences cited in literature containing keywords such as “toxic” or “toxicity”\r\n  * Returns AA sequence if there is a DB hit (otherwise null) and an xls file containing a table of accession numbers, FASTA statistics, and URLs to a amino acid profiles on uniprot.org where the publication can be found, users are then required to read the publications to assess the toxicity risk(s) of the protein in question.\r\n  * Internally curated DB has not been updated in a few years, unclear what the curation/update for this DB is.\r\n"},"comment":{"url":"https://api.github.com/repos/TeselaGen/ve/issues/comments/154461977","html_url":"https://github.com/TeselaGen/ve/issues/1267#issuecomment-154461977","issue_url":"https://api.github.com/repos/TeselaGen/ve/issues/1267","id":154461977,"user":{"login":"craftjk","id":4167907,"avatar_url":"https://avatars.githubusercontent.com/u/4167907?v=3","gravatar_id":"","url":"https://api.github.com/users/craftjk","html_url":"https://github.com/craftjk","followers_url":"https://api.github.com/users/craftjk/followers","following_url":"https://api.github.com/users/craftjk/following{/other_user}","gists_url":"https://api.github.com/users/craftjk/gists{/gist_id}","starred_url":"https://api.github.com/users/craftjk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/craftjk/subscriptions","organizations_url":"https://api.github.com/users/craftjk/orgs","repos_url":"https://api.github.com/users/craftjk/repos","events_url":"https://api.github.com/users/craftjk/events{/privacy}","received_events_url":"https://api.github.com/users/craftjk/received_events","type":"User","site_admin":false},"created_at":"2015-11-06T16:35:16Z","updated_at":"2015-11-06T16:35:16Z","body":"This issue was moved to TeselaGen/Peony-Issue-Tracking#80"}}