{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/design_patterns/issues/5","repository_url":"https://api.github.com/repos/geneontology/design_patterns","labels_url":"https://api.github.com/repos/geneontology/design_patterns/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/design_patterns/issues/5/comments","events_url":"https://api.github.com/repos/geneontology/design_patterns/issues/5/events","html_url":"https://github.com/geneontology/design_patterns/issues/5","id":134597940,"number":5,"title":"Can we strengthen our axiomatization to have spatial disjointness work for occurs_in","user":{"login":"dosumis","id":112839,"avatar_url":"https://avatars.githubusercontent.com/u/112839?v=3","gravatar_id":"","url":"https://api.github.com/users/dosumis","html_url":"https://github.com/dosumis","followers_url":"https://api.github.com/users/dosumis/followers","following_url":"https://api.github.com/users/dosumis/following{/other_user}","gists_url":"https://api.github.com/users/dosumis/gists{/gist_id}","starred_url":"https://api.github.com/users/dosumis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dosumis/subscriptions","organizations_url":"https://api.github.com/users/dosumis/orgs","repos_url":"https://api.github.com/users/dosumis/repos","events_url":"https://api.github.com/users/dosumis/events{/privacy}","received_events_url":"https://api.github.com/users/dosumis/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"dosumis","id":112839,"avatar_url":"https://avatars.githubusercontent.com/u/112839?v=3","gravatar_id":"","url":"https://api.github.com/users/dosumis","html_url":"https://github.com/dosumis","followers_url":"https://api.github.com/users/dosumis/followers","following_url":"https://api.github.com/users/dosumis/following{/other_user}","gists_url":"https://api.github.com/users/dosumis/gists{/gist_id}","starred_url":"https://api.github.com/users/dosumis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dosumis/subscriptions","organizations_url":"https://api.github.com/users/dosumis/orgs","repos_url":"https://api.github.com/users/dosumis/repos","events_url":"https://api.github.com/users/dosumis/events{/privacy}","received_events_url":"https://api.github.com/users/dosumis/received_events","type":"User","site_admin":false},"milestone":null,"comments":0,"created_at":"2016-02-18T14:41:20Z","updated_at":"2016-02-18T14:41:21Z","closed_at":null,"body":"_From @cmungall on August 25, 2015 21:48_\n\ncc @hdietze @kltm \r\n\r\nWe currently have spatial disjointness axioms, e.g.\r\n\r\n     (partOf some nucleus) DisjointFrom (partOf some cytosol)\r\n\r\nThis will correctly identify any continuant with contradictory partOf axioms\r\n\r\nHowever, this isn't detecting some invalid biology in some of the lego models, where we have the same activity occurring in both nucleus and cytosol\r\n\r\nfor this we would need\r\n\r\n     (occursIn some nucleus) DisjointFrom (occursIn some cytosol)\r\n\r\nBut obviously we don't want to redundantly maintain parallel axioms\r\n\r\nAssigned to @dosumis to see if he has any ideas here, I feel I'm missing something, but can't think of the elegant solution. We can certainly write a script that would generate one from the other but ugh.\r\n\r\nThe other approach would be to declare a superproperty that subsumes both occursIn and partOf, and use that in the axioms, effectively doing double duty (a weaker relation inside an axiom involving negation can result in a stronger axiom). \r\n\r\nWithin FOL we would just say occursIn -> occursIn o partOf (which is valid for locally reflexive partOf) which would yield the desired inferences, but we can't say this in OWL\r\n\r\nunless I'm missing something?\n\n_Copied from original issue: geneontology/go-ontology#12028_"},"comment":{"url":"https://api.github.com/repos/geneontology/design_patterns/issues/comments/185749859","html_url":"https://github.com/geneontology/design_patterns/issues/5#issuecomment-185749859","issue_url":"https://api.github.com/repos/geneontology/design_patterns/issues/5","id":185749859,"user":{"login":"dosumis","id":112839,"avatar_url":"https://avatars.githubusercontent.com/u/112839?v=3","gravatar_id":"","url":"https://api.github.com/users/dosumis","html_url":"https://github.com/dosumis","followers_url":"https://api.github.com/users/dosumis/followers","following_url":"https://api.github.com/users/dosumis/following{/other_user}","gists_url":"https://api.github.com/users/dosumis/gists{/gist_id}","starred_url":"https://api.github.com/users/dosumis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dosumis/subscriptions","organizations_url":"https://api.github.com/users/dosumis/orgs","repos_url":"https://api.github.com/users/dosumis/repos","events_url":"https://api.github.com/users/dosumis/events{/privacy}","received_events_url":"https://api.github.com/users/dosumis/received_events","type":"User","site_admin":false},"created_at":"2016-02-18T14:41:21Z","updated_at":"2016-02-18T14:41:21Z","body":"I think i like the new, weaker OP solution. The one aspect that feels hacky is that it relies on a po relation with domain encompassing continuant and occurrent even though we would never allow occurrent po continuant.  Could fall foul of any  axiomatisation added in future to flag this this as inconsistent.  If we follow this route, new rel  should live in gorel with gorel uri and a comment on usage."}}