{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12761","repository_url":"https://api.github.com/repos/geneontology/go-ontology","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12761/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12761/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12761/events","html_url":"https://github.com/geneontology/go-ontology/issues/12761","id":184919250,"number":12761,"title":"erroneous links involving spindle pole body terms","user":{"login":"mah11","id":5196259,"avatar_url":"https://avatars.githubusercontent.com/u/5196259?v=3","gravatar_id":"","url":"https://api.github.com/users/mah11","html_url":"https://github.com/mah11","followers_url":"https://api.github.com/users/mah11/followers","following_url":"https://api.github.com/users/mah11/following{/other_user}","gists_url":"https://api.github.com/users/mah11/gists{/gist_id}","starred_url":"https://api.github.com/users/mah11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mah11/subscriptions","organizations_url":"https://api.github.com/users/mah11/orgs","repos_url":"https://api.github.com/users/mah11/repos","events_url":"https://api.github.com/users/mah11/events{/privacy}","received_events_url":"https://api.github.com/users/mah11/received_events","type":"User","site_admin":false},"labels":[{"id":240618036,"url":"https://api.github.com/repos/geneontology/go-ontology/labels/parent%20relationship%20query","name":"parent relationship query","color":"bfe5bf","default":false},{"id":240257345,"url":"https://api.github.com/repos/geneontology/go-ontology/labels/PomBase","name":"PomBase","color":"bfd4f2","default":false}],"state":"open","locked":false,"assignee":{"login":"tberardini","id":4998871,"avatar_url":"https://avatars.githubusercontent.com/u/4998871?v=3","gravatar_id":"","url":"https://api.github.com/users/tberardini","html_url":"https://github.com/tberardini","followers_url":"https://api.github.com/users/tberardini/followers","following_url":"https://api.github.com/users/tberardini/following{/other_user}","gists_url":"https://api.github.com/users/tberardini/gists{/gist_id}","starred_url":"https://api.github.com/users/tberardini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tberardini/subscriptions","organizations_url":"https://api.github.com/users/tberardini/orgs","repos_url":"https://api.github.com/users/tberardini/repos","events_url":"https://api.github.com/users/tberardini/events{/privacy}","received_events_url":"https://api.github.com/users/tberardini/received_events","type":"User","site_admin":false},"assignees":[{"login":"tberardini","id":4998871,"avatar_url":"https://avatars.githubusercontent.com/u/4998871?v=3","gravatar_id":"","url":"https://api.github.com/users/tberardini","html_url":"https://github.com/tberardini","followers_url":"https://api.github.com/users/tberardini/followers","following_url":"https://api.github.com/users/tberardini/following{/other_user}","gists_url":"https://api.github.com/users/tberardini/gists{/gist_id}","starred_url":"https://api.github.com/users/tberardini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tberardini/subscriptions","organizations_url":"https://api.github.com/users/tberardini/orgs","repos_url":"https://api.github.com/users/tberardini/repos","events_url":"https://api.github.com/users/tberardini/events{/privacy}","received_events_url":"https://api.github.com/users/tberardini/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2016-10-24T18:32:09Z","updated_at":"2016-11-01T20:27:16Z","closed_at":null,"body":"I've just noticed that GO has links that imply that the spindle pole body (SPB) is part of the spindle, but this is not always true. When a spindle exists, the SPB is indeed part of the spindle pole, and therefore part of the spindle, but the SPB is present throughout the cell cycle and therefore also exists at times when there is no spindle.\n\nSelected tags from the relevant OBO stanzas:\n\n```\nid: GO:0005816\nname: spindle pole body\ndef: \"The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.\" [ISBN:0879693568]\nis_a: GO:0005815 ! microtubule organizing center\nrelationship: part_of GO:0000922 ! spindle pole\n\nid: GO:0044732\nname: mitotic spindle pole body\ndef: \"The microtubule organizing center on a spindle that forms as part of mitosis; functionally homologous to the animal cell centrosome.\" [GOC:vw]\nis_a: GO:0005816 ! spindle pole body\nrelationship: part_of GO:0072686 ! mitotic spindle\n\nid: GO:0035974\nname: meiotic spindle pole body\ndef: \"The microtubule organizing center on a spindle that forms as part of meiosis; functionally homologous to the animal cell centrosome.\" [GOC:vw, PMID:21775631]\nis_a: GO:0005816 ! spindle pole body\nrelationship: part_of GO:0072687 ! meiotic spindle\n```\n\nTo fix, remove the asserted part_of links from all three, and change the text defs of GO:0035974 and GO:0044732 to use \"forms as part of the mitotic|meiotic cell cycle\".\n\nI'm guessing that one ore more of the CC links is/are what causes this link to be inferred in BP, which is also not always true:\n\n```\nid: GO:1902440\nname: protein localization to mitotic spindle pole body\nis_a: GO:1902480 {is_inferred=\"true\"} ! protein localization to mitotic spindle\n```\n\nIt would probably be worth checking to make sure that link is no longer inferred (or investigating where it's coming from, if not from links in CC).\n"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/257685182","html_url":"https://github.com/geneontology/go-ontology/issues/12761#issuecomment-257685182","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12761","id":257685182,"user":{"login":"tberardini","id":4998871,"avatar_url":"https://avatars.githubusercontent.com/u/4998871?v=3","gravatar_id":"","url":"https://api.github.com/users/tberardini","html_url":"https://github.com/tberardini","followers_url":"https://api.github.com/users/tberardini/followers","following_url":"https://api.github.com/users/tberardini/following{/other_user}","gists_url":"https://api.github.com/users/tberardini/gists{/gist_id}","starred_url":"https://api.github.com/users/tberardini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tberardini/subscriptions","organizations_url":"https://api.github.com/users/tberardini/orgs","repos_url":"https://api.github.com/users/tberardini/repos","events_url":"https://api.github.com/users/tberardini/events{/privacy}","received_events_url":"https://api.github.com/users/tberardini/received_events","type":"User","site_admin":false},"created_at":"2016-11-01T20:27:16Z","updated_at":"2016-11-01T20:27:16Z","body":"For spindle /spindle pole, I kept the spindle pole part_of spindle and didn't add splindle has_part spindle pole because I didnt want to muck things up with two different relationships between the same two terms.\r\n\r\n id: GO:0035974\r\n name: meiotic spindle pole body\r\n-def: \"The microtubule organizing center **on a spindle** that forms as part of meiosis; functionally homologous to the animal cell centrosome.\" [GOC:vw, PMID:21775631]\r\n+def: \"The microtubule organizing center that forms as part of t**he meiotic cell cycle**; functionally homologous to the animal cell centrosome.\" [GOC:vw, PMID:21775631]\r\n-relationship: part_of GO:0072687 ! meiotic spindle\r\n\r\n id: GO:0044732\r\n name: mitotic spindle pole body\r\n-def: \"The microtubule organizing center **on a spindle** that forms as part of mitosis; functionally homologous to the animal cell centrosome.\" [GOC:vw]\r\n+def: \"The microtubule organizing center that forms as part of **the mitotic cell cycle**; functionally homologous to the animal cell centrosome.\" [GOC:mah, GOC:vw]\r\n-relationship: part_of GO:0072686 ! mitotic spindle\r\n\r\nspindle pole body\r\n-relationship: part_of GO:0000922 ! spindle pole\r\n\r\n\r\nGoing to wait and see what happens with inferred BP link before I close this.\r\n"}}
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