{"action":"created","issue":{"url":"https://api.github.com/repos/monarch-initiative/dipper/issues/374","repository_url":"https://api.github.com/repos/monarch-initiative/dipper","labels_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/374/labels{/name}","comments_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/374/comments","events_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/374/events","html_url":"https://github.com/monarch-initiative/dipper/issues/374","id":178202011,"number":374,"title":"Replace BFO 'part-of' and 'has-part'","user":{"login":"TomConlin","id":1911895,"avatar_url":"https://avatars.githubusercontent.com/u/1911895?v=3","gravatar_id":"","url":"https://api.github.com/users/TomConlin","html_url":"https://github.com/TomConlin","followers_url":"https://api.github.com/users/TomConlin/followers","following_url":"https://api.github.com/users/TomConlin/following{/other_user}","gists_url":"https://api.github.com/users/TomConlin/gists{/gist_id}","starred_url":"https://api.github.com/users/TomConlin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TomConlin/subscriptions","organizations_url":"https://api.github.com/users/TomConlin/orgs","repos_url":"https://api.github.com/users/TomConlin/repos","events_url":"https://api.github.com/users/TomConlin/events{/privacy}","received_events_url":"https://api.github.com/users/TomConlin/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-09-20T22:56:34Z","updated_at":"2016-09-21T00:27:41Z","closed_at":"2016-09-21T00:27:41Z","body":"@cmungall @mbrush \r\n\r\nBFO_0000050  ! part of\r\nBFO_0000051  ! has part \r\n\r\nThese terms have not been welcome in the basic formal ontology \r\nfor several years now, we should replace them with well supported terms.  \r\n\r\nWe use them in across all ingests from here: \r\nhttps://github.com/monarch-initiative/dipper/blob/c2f379fea90ca3d40b844f3f3a8ffefbbc24a260/dipper/utils/GraphUtils.py#L56\r\n\r\n\r\nFor \"has part\"  there is a single obvious choice.\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0000057 ! has part\r\n\r\n\r\nFor \"part of\" it is not as clear.  Ontobee still  referenced BFO_0000050  but as part of RO\r\n<http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/BFO_0000050>\r\ntechnically this works, but if the Basic Formal Ontology does not support the terms we(?) should not continue using their namespace BFO for what is now a RO term.\r\n\r\nother related terms\r\n\r\n http://purl.obolibrary.org/obo/RO_0002287\r\n    part of developmental precursor of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002329\r\n    part of structure that is capable of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002350\r\n    member part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002331\r\n    enables part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002225\r\n    develops from part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002314\r\n    inheres in part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002216\r\n    capable of part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002380\r\n    branching part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002177\r\n    attached to part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002509\r\n    determined by part of\r\n\r\nhttp://purl.obolibrary.org/obo/RO_0002012 \r\n    occurent part of\r\n\r\n\r\nreference\r\nhttps://github.com/BFO-ontology/BFO/issues/46.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/monarch-initiative/dipper/issues/comments/248476167","html_url":"https://github.com/monarch-initiative/dipper/issues/374#issuecomment-248476167","issue_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/374","id":248476167,"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},"created_at":"2016-09-21T00:27:41Z","updated_at":"2016-09-21T00:27:41Z","body":"> http://purl.obolibrary.org/obo/RO_0000057 ! has part\r\n\r\nhas participant. Different relation.\r\n\r\nhttps://github.com/oborel/obo-relations/wiki/ROAndBFO"}}
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