{"action":"created","issue":{"url":"https://api.github.com/repos/intermine/intermine/issues/901","labels_url":"https://api.github.com/repos/intermine/intermine/issues/901/labels{/name}","comments_url":"https://api.github.com/repos/intermine/intermine/issues/901/comments","events_url":"https://api.github.com/repos/intermine/intermine/issues/901/events","html_url":"https://github.com/intermine/intermine/issues/901","id":53389633,"number":901,"title":"OBO file contains different ontologies","user":{"login":"julie-sullivan","id":1663057,"avatar_url":"https://avatars.githubusercontent.com/u/1663057?v=3","gravatar_id":"","url":"https://api.github.com/users/julie-sullivan","html_url":"https://github.com/julie-sullivan","followers_url":"https://api.github.com/users/julie-sullivan/followers","following_url":"https://api.github.com/users/julie-sullivan/following{/other_user}","gists_url":"https://api.github.com/users/julie-sullivan/gists{/gist_id}","starred_url":"https://api.github.com/users/julie-sullivan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julie-sullivan/subscriptions","organizations_url":"https://api.github.com/users/julie-sullivan/orgs","repos_url":"https://api.github.com/users/julie-sullivan/repos","events_url":"https://api.github.com/users/julie-sullivan/events{/privacy}","received_events_url":"https://api.github.com/users/julie-sullivan/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/intermine/intermine/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/intermine/intermine/labels/data","name":"data","color":"006b75"}],"state":"open","locked":false,"assignee":{"login":"julie-sullivan","id":1663057,"avatar_url":"https://avatars.githubusercontent.com/u/1663057?v=3","gravatar_id":"","url":"https://api.github.com/users/julie-sullivan","html_url":"https://github.com/julie-sullivan","followers_url":"https://api.github.com/users/julie-sullivan/followers","following_url":"https://api.github.com/users/julie-sullivan/following{/other_user}","gists_url":"https://api.github.com/users/julie-sullivan/gists{/gist_id}","starred_url":"https://api.github.com/users/julie-sullivan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/julie-sullivan/subscriptions","organizations_url":"https://api.github.com/users/julie-sullivan/orgs","repos_url":"https://api.github.com/users/julie-sullivan/repos","events_url":"https://api.github.com/users/julie-sullivan/events{/privacy}","received_events_url":"https://api.github.com/users/julie-sullivan/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2015-01-05T12:03:34Z","updated_at":"2015-01-06T14:34:18Z","closed_at":null,"body":"FlyBase anatomy file includes some GO terms. This is creating GO terms and calling them anatomy terms. \r\n\r\nI set the priorities to be:\r\n\r\n```\r\nOntologyTerm.ontology = *, fly-anatomy-ontology\r\nOntologyTerm.namespace = *, fly-anatomy-ontology\r\n```\r\n\r\nBut this ends up with an anatomy term that is also a SO term:\r\n\r\n```\r\n\r\nflymine-1.4-2014-12-19=# select * from anatomyterm where name ='gene';\r\n identifier | obsolete | namespace |    id     | name |                                                                                                    description                                                                                                     | ontologyid |                               class                                \r\n------------+----------+-----------+-----------+------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------+--------------------------------------------------------------------\r\n SO:0000704 | f        | sequence  | 113000002 | gene | A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. |  113000000 | org.intermine.model.bio.AnatomyTerm org.intermine.model.bio.SOTerm\r\n(1 row)\r\n```\r\n\r\nOntology terms merge on name+ontology or identifier.\r\n\r\nHow to fix? \r\n\r\n@rachellyne Is this illegal? \r\n\r\nhttp://oboformat.googlecode.com/svn/trunk/doc/GO.format.obo-1_2.html\r\n\r\n```\r\ndata-version\r\n    Gives the version of the current ontology. \r\n```\r\n\r\nSo that sort of assumes there is only one ontology present. Thoughts?\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/intermine/intermine/issues/comments/68872057","html_url":"https://github.com/intermine/intermine/issues/901#issuecomment-68872057","issue_url":"https://api.github.com/repos/intermine/intermine/issues/901","id":68872057,"user":{"login":"rachellyne","id":1918045,"avatar_url":"https://avatars.githubusercontent.com/u/1918045?v=3","gravatar_id":"","url":"https://api.github.com/users/rachellyne","html_url":"https://github.com/rachellyne","followers_url":"https://api.github.com/users/rachellyne/followers","following_url":"https://api.github.com/users/rachellyne/following{/other_user}","gists_url":"https://api.github.com/users/rachellyne/gists{/gist_id}","starred_url":"https://api.github.com/users/rachellyne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rachellyne/subscriptions","organizations_url":"https://api.github.com/users/rachellyne/orgs","repos_url":"https://api.github.com/users/rachellyne/repos","events_url":"https://api.github.com/users/rachellyne/events{/privacy}","received_events_url":"https://api.github.com/users/rachellyne/received_events","type":"User","site_admin":false},"created_at":"2015-01-06T14:34:18Z","updated_at":"2015-01-06T14:34:18Z","body":"I have a feeling we had the same problem last build.  This file looks fine:\r\n\r\nhttp://flybase.org/static_pages/downloads/FB2014_06/ontologies/fly_anatomy.obo.gz"}}