{"action":"created","issue":{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/118","repository_url":"https://api.github.com/repos/BgeeDB/expression-annotations","labels_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/118/labels{/name}","comments_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/118/comments","events_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/118/events","html_url":"https://github.com/BgeeDB/expression-annotations/issues/118","id":133829671,"number":118,"title":"Annotation issues in selected-samples (?)","user":{"login":"aechchiki","id":13200013,"avatar_url":"https://avatars.githubusercontent.com/u/13200013?v=3","gravatar_id":"","url":"https://api.github.com/users/aechchiki","html_url":"https://github.com/aechchiki","followers_url":"https://api.github.com/users/aechchiki/followers","following_url":"https://api.github.com/users/aechchiki/following{/other_user}","gists_url":"https://api.github.com/users/aechchiki/gists{/gist_id}","starred_url":"https://api.github.com/users/aechchiki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aechchiki/subscriptions","organizations_url":"https://api.github.com/users/aechchiki/orgs","repos_url":"https://api.github.com/users/aechchiki/repos","events_url":"https://api.github.com/users/aechchiki/events{/privacy}","received_events_url":"https://api.github.com/users/aechchiki/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/labels/GTEx","name":"GTEx","color":"fad8c7"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-02-15T22:14:30Z","updated_at":"2016-02-16T10:39:41Z","closed_at":null,"body":"I was going through (nth check) the annotations in the \"clean\"  version of selected-samples (aka the one without duplicates, and with only \"YES\" samples to be checked for quality), source for RNAseq final file. I might have noticed an imprecision in annotation for Thyroid samples (the imprecision is consistent in both selected-samples and RNAseq, this is why we haven't detected it automatically ;) ).\r\n\r\nFrom the RNAseq Library file, it seems that in Bgee we are correcting the \"universal\" Uberon (UBERON:0002046 - thyroid gland) as proposed by GTEx this way:\r\n\r\n- if both Left and Right thyroid: UBERON:0002046 - thyroid gland\r\n- if only Left thyroid: UBERON:0001120 - left lobe of thyroid gland\r\n- if only Right thyroid: UBERON:0001119 - right lobe of thyroid gland\r\n\r\nIf we only consider column SMSMPSTE (aka, tissue location), then the annotations in both selected-samples and RNAseq are correct. However, if we also consider column SMTSC (aka, free-text commentaries), then the annotations are not always correct. For example, sample `GTEX-X5EB-0726-SM-46MVR` has SMSMPSTE==\"Non-nodular region\" and SMTSC contains commentary \"Left\", which I interprete as that the sample is actually \"Left thyroid\" and not broad \"thyroid\". In this case, the annotation should be updated from current UBERON:0002046 (- thyroid gland) to UBERON:0001120 (- left lobe of thyroid gland).\r\n\r\nI ask for @ANiknejad advice on my interpretations before an eventual annotation update.\r\n"},"comment":{"url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/comments/184618297","html_url":"https://github.com/BgeeDB/expression-annotations/issues/118#issuecomment-184618297","issue_url":"https://api.github.com/repos/BgeeDB/expression-annotations/issues/118","id":184618297,"user":{"login":"aechchiki","id":13200013,"avatar_url":"https://avatars.githubusercontent.com/u/13200013?v=3","gravatar_id":"","url":"https://api.github.com/users/aechchiki","html_url":"https://github.com/aechchiki","followers_url":"https://api.github.com/users/aechchiki/followers","following_url":"https://api.github.com/users/aechchiki/following{/other_user}","gists_url":"https://api.github.com/users/aechchiki/gists{/gist_id}","starred_url":"https://api.github.com/users/aechchiki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aechchiki/subscriptions","organizations_url":"https://api.github.com/users/aechchiki/orgs","repos_url":"https://api.github.com/users/aechchiki/repos","events_url":"https://api.github.com/users/aechchiki/events{/privacy}","received_events_url":"https://api.github.com/users/aechchiki/received_events","type":"User","site_admin":false},"created_at":"2016-02-16T10:39:41Z","updated_at":"2016-02-16T10:39:41Z","body":"Awesome, thanks! I will go through the annotation in selected-samples manually to check for similar issues. I will provide a list of the eventual changes ;) "}}