{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12343","repository_url":"https://api.github.com/repos/geneontology/go-ontology","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12343/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12343/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12343/events","html_url":"https://github.com/geneontology/go-ontology/issues/12343","id":140731660,"number":12343,"title":"OTR: GO:0019835 cytolysis","user":{"login":"paolaroncaglia","id":4982516,"avatar_url":"https://avatars.githubusercontent.com/u/4982516?v=3","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":[{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/Apoptosis","name":"Apoptosis","color":"ededed"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/ETINE","name":"ETINE","color":"5319e7"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/obsoletion","name":"obsoletion","color":"bfe5bf"},{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/Other%20term-related%20request","name":"Other term-related request","color":"bfe5bf"}],"state":"open","locked":false,"assignee":{"login":"paolaroncaglia","id":4982516,"avatar_url":"https://avatars.githubusercontent.com/u/4982516?v=3","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":10,"created_at":"2016-03-14T16:53:02Z","updated_at":"2016-05-31T14:15:07Z","closed_at":null,"body":"The issue of ‘cytolysis’ was brought up before, and just came back again following the ETINE work: @dosumis  \r\n\r\nGO:0042268\tregulation of cytolysis\tGO:0010941\tregulation of cell death\t\r\n\r\nIn short, it is ok for the link not to be entailed any longer, and I marked it as ‘delete’. \r\n\r\n@addiehl\r\nIn more detail: ‘cytolysis’ used to be under ‘cell death’ but was removed from under there in 2013, as part of the viral work.\r\n‘Cytolysis’, describing the explosion of a cell as an uncontrollable reaction to osmotic stress (https://en.wikipedia.org/wiki/Cytolysis), is a phenotype rather than a process. As such, we shouldn’t have it in GO, and its current direct experimental annotations are suspicious. The lexical problem is that often ‘cytolysis’ stands to mean ‘cell killing by cytolysis’. In fact, we have GO:0051715 ‘cytolysis in other organism’ which means exactly that (“The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm.”). The ambiguity is confirmed when I look at the first of the papers supporting  annotations to ‘cytolysis’ in QuickGO, http://europepmc.org/abstract/MED/25876762, describing features of antimicrobial peptides in fish - it’s the fish peptides that are annotated to cytolysis.\r\n\r\nI propose to obsolete ‘cytolysis’ per se, but to keep its children. However:\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n‘cytolysis’ has two is_a children: ‘autolysis’ and ‘cytolysis in other organism’.\r\n\r\n‘autolysis’ is “The spontaneous death by lysis of bacteria in response to environmental conditions.”. It has 14 manual annotations. 2 are CACAO, 4 are EcoliWiki. @jimhu-tamu , is autolysis a true process in Bacteria? Can it be considered a form of programmed cell death? If so, the term and the bacterial annotations can stay, but ‘autolysis’ should be moved under ‘programmed cell death’ and be given a taxon constraints for bacteria. \r\n‘autolysis’ also has 7 ASPGD annotations to fungal proteins that should presumably be moved to a ‘cell killing’ term. Should this be ‘cell killing [of bacteria] by autolysis? Is that any different than ‘cytolysis in other organism’? (I’ll email someone at ASPGD to look into this)\r\n‘autolysis’ even has a UniProt mouse annotation, presumably same case as the fungal one? @mcourtot \r\n\r\n‘cytolysis in other organism’ has both parents ‘cytolysis’ and ‘killing of cells of other organism’. I suggest to remove the is_a link to ‘cytolysis’. \r\n\r\nWe need to clarify these issues, then we can make useful suggestions to rehouse annotations to cytolysis and its regulation terms.\r\n\r\nThank you all,\r\nPaola"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/222701647","html_url":"https://github.com/geneontology/go-ontology/issues/12343#issuecomment-222701647","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12343","id":222701647,"user":{"login":"paolaroncaglia","id":4982516,"avatar_url":"https://avatars.githubusercontent.com/u/4982516?v=3","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":"2016-05-31T14:15:07Z","updated_at":"2016-05-31T14:15:07Z","body":"Edited 'autolysis' as above."}}
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