{"action":"created","issue":{"url":"https://api.github.com/repos/ontodev/robot/issues/87","repository_url":"https://api.github.com/repos/ontodev/robot","labels_url":"https://api.github.com/repos/ontodev/robot/issues/87/labels{/name}","comments_url":"https://api.github.com/repos/ontodev/robot/issues/87/comments","events_url":"https://api.github.com/repos/ontodev/robot/issues/87/events","html_url":"https://github.com/ontodev/robot/issues/87","id":161821058,"number":87,"title":"URIs can become messed up when using convert to go from omn to ofn","user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars.githubusercontent.com/u/50745?v=3","gravatar_id":"","url":"https://api.github.com/users/cmungall","html_url":"https://github.com/cmungall","followers_url":"https://api.github.com/users/cmungall/followers","following_url":"https://api.github.com/users/cmungall/following{/other_user}","gists_url":"https://api.github.com/users/cmungall/gists{/gist_id}","starred_url":"https://api.github.com/users/cmungall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmungall/subscriptions","organizations_url":"https://api.github.com/users/cmungall/orgs","repos_url":"https://api.github.com/users/cmungall/repos","events_url":"https://api.github.com/users/cmungall/events{/privacy}","received_events_url":"https://api.github.com/users/cmungall/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-06-23T01:23:21Z","updated_at":"2016-06-23T13:36:46Z","closed_at":null,"body":"in.owl:\r\n\r\n```\r\nPrefix: : <http://purl.obolibrary.org/obo/>\r\nPrefix: PATO: <http://purl.obolibrary.org/obo/PATO_>\r\nPrefix: GO: <http://purl.obolibrary.org/obo/GO_>\r\nPrefix: OBA: <http://purl.obolibrary.org/obo/OBA_>\r\n\r\n ## Auto-generated\r\n\r\nOntology: <http://purl.obolibrary.org/obo/auto>\r\nObjectProperty: RO_0000052 ## inheres in\r\n## Auto-generated classes\r\n\r\nClass: PATO:0000001 ## quality\r\nClass: GO:0005575 ## cellular_component\r\n## {\"attribute\": \"PATO:0000001\", \"entity\": \"GO:0005575\"}\r\nClass: OBA:0100001\r\n EquivalentTo: PATO:0000001 and RO_0000052 some GO:0005575 ## quality and 'inheres in' some cellular_component\r\n```\r\n\r\nnow try:\r\n```\r\n$ robot convert -i in.owl -o out.ofn\r\n```\r\n\r\nThe URIs are messed up:\r\n\r\n```\r\nPrefix(:=<http://purl.obolibrary.org/obo/auto#>)\r\nPrefix(GO:=<http://purl.obolibrary.org/obo/GO_>)\r\nPrefix(dc:=<http://purl.org/dc/elements/1.1/>)\r\nPrefix(OBA:=<http://purl.obolibrary.org/obo/OBA_>)\r\nPrefix(owl:=<http://www.w3.org/2002/07/owl#>)\r\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\r\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\r\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\r\nPrefix(PATO:=<http://purl.obolibrary.org/obo/PATO_>)\r\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\r\n\r\n\r\nOntology(<http://purl.obolibrary.org/obo/auto>\r\n\r\nDeclaration(Class(:GO_0005575))\r\nDeclaration(Class(:OBA_0100001))\r\nDeclaration(Class(:PATO_0000001))\r\nDeclaration(ObjectProperty(:RO_0000052))\r\n\r\n############################\r\n#   Classes\r\n############################\r\n\r\n# Class: :OBA_0100001 (:OBA_0100001)\r\n\r\nEquivalentClasses(:OBA_0100001 ObjectIntersectionOf(:PATO_0000001 ObjectSomeValuesFrom(:RO_0000052 :GO_0005575)))\r\n\r\n\r\n)\r\n```\r\n\r\nI think this is in the OWLAPI and not ROBOT. I get exactly the same behavior in OWLTools. Want to check first if it is to do with how we are using the OWLAPI first (e.g. CURIE mappings?), then make a java test case for the owlapi tracker. Want to park it here before I forget."},"comment":{"url":"https://api.github.com/repos/ontodev/robot/issues/comments/228051874","html_url":"https://github.com/ontodev/robot/issues/87#issuecomment-228051874","issue_url":"https://api.github.com/repos/ontodev/robot/issues/87","id":228051874,"user":{"login":"jamesaoverton","id":292409,"avatar_url":"https://avatars.githubusercontent.com/u/292409?v=3","gravatar_id":"","url":"https://api.github.com/users/jamesaoverton","html_url":"https://github.com/jamesaoverton","followers_url":"https://api.github.com/users/jamesaoverton/followers","following_url":"https://api.github.com/users/jamesaoverton/following{/other_user}","gists_url":"https://api.github.com/users/jamesaoverton/gists{/gist_id}","starred_url":"https://api.github.com/users/jamesaoverton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamesaoverton/subscriptions","organizations_url":"https://api.github.com/users/jamesaoverton/orgs","repos_url":"https://api.github.com/users/jamesaoverton/repos","events_url":"https://api.github.com/users/jamesaoverton/events{/privacy}","received_events_url":"https://api.github.com/users/jamesaoverton/received_events","type":"User","site_admin":false},"created_at":"2016-06-23T13:36:46Z","updated_at":"2016-06-23T13:36:46Z","body":"Does this require a change to ROBOT? Maybe the default JSONLD context? https://github.com/ontodev/robot/blob/master/robot-core/src/main/resources/obo_context.jsonld "}}
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