{"action":"created","issue":{"url":"https://api.github.com/repos/EBISPOT/efo/issues/292","repository_url":"https://api.github.com/repos/EBISPOT/efo","labels_url":"https://api.github.com/repos/EBISPOT/efo/issues/292/labels{/name}","comments_url":"https://api.github.com/repos/EBISPOT/efo/issues/292/comments","events_url":"https://api.github.com/repos/EBISPOT/efo/issues/292/events","html_url":"https://github.com/EBISPOT/efo/issues/292","id":380250305,"node_id":"MDU6SXNzdWUzODAyNTAzMDU=","number":292,"title":"Niemann-Pick disease is not a neoplasm","user":{"login":"paolaroncaglia","id":4982516,"node_id":"MDQ6VXNlcjQ5ODI1MTY=","avatar_url":"https://avatars0.githubusercontent.com/u/4982516?v=4","gravatar_id":"","url":"https://api.github.com/users/paolaroncaglia","html_url":"https://github.com/paolaroncaglia","followers_url":"https://api.github.com/users/paolaroncaglia/followers","following_url":"https://api.github.com/users/paolaroncaglia/following{/other_user}","gists_url":"https://api.github.com/users/paolaroncaglia/gists{/gist_id}","starred_url":"https://api.github.com/users/paolaroncaglia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolaroncaglia/subscriptions","organizations_url":"https://api.github.com/users/paolaroncaglia/orgs","repos_url":"https://api.github.com/users/paolaroncaglia/repos","events_url":"https://api.github.com/users/paolaroncaglia/events{/privacy}","received_events_url":"https://api.github.com/users/paolaroncaglia/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"paolaroncaglia","id":4982516,"node_id":"MDQ6VXNlcjQ5ODI1MTY=","avatar_url":"https://avatars0.githubusercontent.com/u/4982516?v=4","gravatar_id":"","url":"https://api.github.com/users/paolaroncaglia","html_url":"https://github.com/paolaroncaglia","followers_url":"https://api.github.com/users/paolaroncaglia/followers","following_url":"https://api.github.com/users/paolaroncaglia/following{/other_user}","gists_url":"https://api.github.com/users/paolaroncaglia/gists{/gist_id}","starred_url":"https://api.github.com/users/paolaroncaglia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolaroncaglia/subscriptions","organizations_url":"https://api.github.com/users/paolaroncaglia/orgs","repos_url":"https://api.github.com/users/paolaroncaglia/repos","events_url":"https://api.github.com/users/paolaroncaglia/events{/privacy}","received_events_url":"https://api.github.com/users/paolaroncaglia/received_events","type":"User","site_admin":false},"assignees":[{"login":"paolaroncaglia","id":4982516,"node_id":"MDQ6VXNlcjQ5ODI1MTY=","avatar_url":"https://avatars0.githubusercontent.com/u/4982516?v=4","gravatar_id":"","url":"https://api.github.com/users/paolaroncaglia","html_url":"https://github.com/paolaroncaglia","followers_url":"https://api.github.com/users/paolaroncaglia/followers","following_url":"https://api.github.com/users/paolaroncaglia/following{/other_user}","gists_url":"https://api.github.com/users/paolaroncaglia/gists{/gist_id}","starred_url":"https://api.github.com/users/paolaroncaglia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolaroncaglia/subscriptions","organizations_url":"https://api.github.com/users/paolaroncaglia/orgs","repos_url":"https://api.github.com/users/paolaroncaglia/repos","events_url":"https://api.github.com/users/paolaroncaglia/events{/privacy}","received_events_url":"https://api.github.com/users/paolaroncaglia/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-11-13T14:24:42Z","updated_at":"2018-11-26T14:30:55Z","closed_at":null,"author_association":"COLLABORATOR","body":"EFO:1001380 ‘Niemann-Pick disease’ is currently classified as a neoplasm (see https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_1001380), but it’s a metabolic disorder instead (see https://en.wikipedia.org/wiki/Niemann–Pick_disease). No idea where that parentage came from - not from the DOID or the NCIt equivalents, at least as they are now (I haven’t checked ICD10, MSH and MedRA yet).\r\n\r\nMONDO’s classification looks better (see http://www.ontobee.org/ontology/MONDO?iri=http://purl.obolibrary.org/obo/MONDO_0001982). We should classify as subclass of sphingolipidosis (as indeed all 4 children of the terms are already) or other metabolic disorder (need to look more closely).\r\n\r\nWe also need to check and, if necessary, fix axioms for the child EFO Orphanet:646 ‘Niemann-Pick disease type C’ (now subclass of, among others, eye neoplasm, brain neoplasm, and a couple other axioms that may be better represented by different relations). \r\n\r\nLastly, the definition of EFO:1001380 ‘Niemann-Pick disease’ now reads “_The classic infantile form of Niemann-Pick Disease_, caused by mutation in SPHINGOMYELIN PHOSPHODIESTERASE...” which sounds more like a subclass of the disease than its generic form; check."},"comment":{"url":"https://api.github.com/repos/EBISPOT/efo/issues/comments/441657986","html_url":"https://github.com/EBISPOT/efo/issues/292#issuecomment-441657986","issue_url":"https://api.github.com/repos/EBISPOT/efo/issues/292","id":441657986,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTY1Nzk4Ng==","user":{"login":"paolaroncaglia","id":4982516,"node_id":"MDQ6VXNlcjQ5ODI1MTY=","avatar_url":"https://avatars0.githubusercontent.com/u/4982516?v=4","gravatar_id":"","url":"https://api.github.com/users/paolaroncaglia","html_url":"https://github.com/paolaroncaglia","followers_url":"https://api.github.com/users/paolaroncaglia/followers","following_url":"https://api.github.com/users/paolaroncaglia/following{/other_user}","gists_url":"https://api.github.com/users/paolaroncaglia/gists{/gist_id}","starred_url":"https://api.github.com/users/paolaroncaglia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolaroncaglia/subscriptions","organizations_url":"https://api.github.com/users/paolaroncaglia/orgs","repos_url":"https://api.github.com/users/paolaroncaglia/repos","events_url":"https://api.github.com/users/paolaroncaglia/events{/privacy}","received_events_url":"https://api.github.com/users/paolaroncaglia/received_events","type":"User","site_admin":false},"created_at":"2018-11-26T14:30:55Z","updated_at":"2018-11-26T14:30:55Z","author_association":"COLLABORATOR","body":"Note for self/EFO editor:\r\n\r\n- [ ] Edit EFO:1001380 ‘Niemann-Pick disease’:\r\nMake it subclass of EFO Orphanet:79225 ‘Sphingolipidosis’ instead of ‘neoplasm’;\r\nClassify its 4 children (Niemann-Pick disease type A/B/C/E) under it rather than under EFO Orphanet:79225 ‘Sphingolipidosis’;\r\nModify definition to read: “A group of inherited, severe metabolic disorders in which sphingomyelin accumulates in lysosomes in cells. The lysosomes normally transport material through and out of the cell.”;\r\nAdd definition citations MONDO:0001982, https://en.wikipedia.org/wiki/Niemann–Pick_disease;\r\nEdit synonyms: remove the ones referring to types A/B/C.\r\n\r\n- [ ] Edit EFO Orphanet:646 ‘Niemann-Pick disease type C’:\r\nRemove subclasses ‘eye neoplasm’, ‘tauopathy’, ‘brain neoplasm’, ‘supranuclear oculomotor palsy’, ‘Unclassified primitive or secondary maculopathy’, and check https://en.wikipedia.org/wiki/Niemann–Pick_disease,_type_C to see if those disorders should be captured by other axioms instead (has disease feature?)."}}
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