{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12587","repository_url":"https://api.github.com/repos/geneontology/go-ontology","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12587/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12587/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12587/events","html_url":"https://github.com/geneontology/go-ontology/issues/12587","id":171926363,"number":12587,"title":"inconsistencies in TM  transport function term names","user":{"login":"ValWood","id":7359272,"avatar_url":"https://avatars.githubusercontent.com/u/7359272?v=3","gravatar_id":"","url":"https://api.github.com/users/ValWood","html_url":"https://github.com/ValWood","followers_url":"https://api.github.com/users/ValWood/followers","following_url":"https://api.github.com/users/ValWood/following{/other_user}","gists_url":"https://api.github.com/users/ValWood/gists{/gist_id}","starred_url":"https://api.github.com/users/ValWood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ValWood/subscriptions","organizations_url":"https://api.github.com/users/ValWood/orgs","repos_url":"https://api.github.com/users/ValWood/repos","events_url":"https://api.github.com/users/ValWood/events{/privacy}","received_events_url":"https://api.github.com/users/ValWood/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/Other%20term-related%20request","name":"Other 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transporting ATPase activity\r\ndoes not return in top hits\r\noligopeptide-transporting ATPase activity\r\n\r\nThere is a lot if inconsistency as to how these are named, and I’m not sure which hyphenation is correct but I see:\r\n\r\nhyphen after substrate\r\nGO:0015446\tarsenite-transmembrane transporting ATPase activity\t\r\nGO:0005388\tcalcium-transporting ATPase activity\t\r\n\t\tprotein-transmembrane transporting ATPase activity\t\r\n\r\nhyphen after transmembrane\r\nGO:0015414 nitrate transmembrane-transporting ATPase activity\r\n\t   sulfate transmembrane-transporting ATPase activity\r\n\r\nno hyphen\r\nGO:0033225\t2-aminoethylphosphonate transporting ATPase activity\r\n\t\toligogalacturonide transporting ATPase activity\r\nGO:0035673\toligopeptide transmembrane transporter activity\r\n\r\netc\r\n\r\ncould these all  be standardised so we know what to search on (no hyphen seems correct to me?)\r\n"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/244928583","html_url":"https://github.com/geneontology/go-ontology/issues/12587#issuecomment-244928583","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12587","id":244928583,"user":{"login":"paolaroncaglia","id":4982516,"avatar_url":"https://avatars.githubusercontent.com/u/4982516?v=3","gravatar_id":"","url":"https://api.github.com/users/paolaroncaglia","html_url":"https://github.com/paolaroncaglia","followers_url":"https://api.github.com/users/paolaroncaglia/followers","following_url":"https://api.github.com/users/paolaroncaglia/following{/other_user}","gists_url":"https://api.github.com/users/paolaroncaglia/gists{/gist_id}","starred_url":"https://api.github.com/users/paolaroncaglia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paolaroncaglia/subscriptions","organizations_url":"https://api.github.com/users/paolaroncaglia/orgs","repos_url":"https://api.github.com/users/paolaroncaglia/repos","events_url":"https://api.github.com/users/paolaroncaglia/events{/privacy}","received_events_url":"https://api.github.com/users/paolaroncaglia/received_events","type":"User","site_admin":false},"created_at":"2016-09-06T11:58:44Z","updated_at":"2016-09-06T11:58:44Z","body":"@ValWood, @mah11\r\nSumming up:\r\n\r\n- Let’s limit to the ATPase activity branch\r\n\r\n- Wrt ‘x-transporting ATPase activity’ terms, we resolved that the correct syntax contains the hyphen, i.e. ‘oligopeptide-transporting ATPase activity’ (in fact, most terms in this branch conform to that)\r\n\r\n- Searching GO term labels for ‘transporting ATPase activity’ (using OBO-Edit) retrieves 86 matches. All of the ‘non-transmembrane’ labels are already correctly hyphenated, except for the following ones, which I’ll fix:\r\n\r\nGO:0033225\t2-aminoethylphosphonate transporting ATPase activity\r\nGO:0033154\toligogalacturonide transporting ATPase activity\r\nGO:0015633\tzinc transporting ATPase activity\r\n\r\n- Within the same branch, the following labels contain the problematic ‘transmembrane’ string:\r\n\r\nGO:0102017\talkylphosphonate transmembrane-transporting ATPase activity\r\nGO:0043225\tanion transmembrane-transporting ATPase activity\r\nGO:0015446\tarsenite-transmembrane transporting ATPase activity\r\nGO:1901242\tdoxorubicin transmembrane-transporting ATPase activity\r\nGO:1901514\tlipo-chitin oligosaccharide transmembrane-transporting ATPase activity\r\nGO:1901243\tmethionine transmembrane-transporting ATPase activity\r\nGO:0015412\tmolybdate transmembrane-transporting ATPase activity\r\nGO:0015414\tnitrate transmembrane-transporting ATPase activity\r\nGO:0015416\torganic phosphonate transmembrane-transporting ATPase activity\r\nGO:0015415\tphosphate ion transmembrane-transporting ATPase activity\r\nGO:0015462\tprotein-transmembrane transporting ATPase activity\r\nGO:0015419\tsulfate transmembrane-transporting ATPase activity\r\nGO:0032146\tthiosulfate transmembrane-transporting ATPase activity\r\nGO:1901238\ttungstate transmembrane-transporting ATPase activity\r\n\r\nAll these labels follow the pattern ‘x transmembrane-transporting ATPase activity’ except for one (arsenite-transmembrane transporting ATPase activity). I agree that for these cases the current hyphenation is unsatisfactory. I agree with Midori’s proposal to rename them all as ‘ATPase-coupled xxx transmembrane transporter activity’, and retain the original labels as (related) synonyms. \r\n\r\nPlease confirm that this is good with you both before I do the edits. Thanks!"}}
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