{"action":"created","issue":{"url":"https://api.github.com/repos/ontodev/robot/issues/175","repository_url":"https://api.github.com/repos/ontodev/robot","labels_url":"https://api.github.com/repos/ontodev/robot/issues/175/labels{/name}","comments_url":"https://api.github.com/repos/ontodev/robot/issues/175/comments","events_url":"https://api.github.com/repos/ontodev/robot/issues/175/events","html_url":"https://github.com/ontodev/robot/issues/175","id":244455752,"node_id":"MDU6SXNzdWUyNDQ0NTU3NTI=","number":175,"title":"Performing extract using ROBOT excludes GCIs","user":{"login":"cmungall","id":50745,"node_id":"MDQ6VXNlcjUwNzQ1","avatar_url":"https://avatars1.githubusercontent.com/u/50745?v=4","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":{"login":"cmungall","id":50745,"node_id":"MDQ6VXNlcjUwNzQ1","avatar_url":"https://avatars1.githubusercontent.com/u/50745?v=4","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},"assignees":[{"login":"cmungall","id":50745,"node_id":"MDQ6VXNlcjUwNzQ1","avatar_url":"https://avatars1.githubusercontent.com/u/50745?v=4","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}],"milestone":null,"comments":6,"created_at":"2017-07-20T18:29:24Z","updated_at":"2018-08-14T15:37:45Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Reference (mostly for me): https://github.com/geneontology/go-ontology/issues/13725\r\n\r\nWe're stuck using owltools for module extraction in GO for bio-chebi for now. It's weird as both owltools and robot use SLME under the hood here.\r\n\r\nMostly for my own reference:\r\n\r\n```\r\nROBOT_JAVA_ARGS=-Xmx8G robot extract -i bio-chebi.owl -T imports/chebi_terms_combined.txt --method BOT -O http://purl.obolibrary.org/obo/go/imports/chebi_import.owl annotate -V http://purl.obolibrary.org/obo/go/releases/`date +%Y-%m-%d`/imports/chebi_import.owl -o imports/chebi_import.owl\r\n```\r\n\r\nthis should produce 1000s of GCIs, as seen here: http://purl.obolibrary.org/obo/go/imports/chebi_import.owl\r\n\r\nHowever, robot produces a single lonely GCI:\r\n\r\n```\r\n    <!-- \r\n    ///////////////////////////////////////////////////////////////////////////////////////\r\n    //\r\n    // General axioms\r\n    //\r\n    ///////////////////////////////////////////////////////////////////////////////////////\r\n     -->\r\n\r\n    <owl:Restriction>\r\n        <owl:onProperty rdf:resource=\"http://purl.obolibrary.org/obo/RO_0000087\"/>\r\n        <owl:someValuesFrom rdf:resource=\"http://purl.obolibrary.org/obo/CHEBI_37527\"/>\r\n        <rdfs:subClassOf>\r\n            <owl:Restriction>\r\n                <owl:onProperty rdf:resource=\"http://purl.obolibrary.org/obo/GOCHEREL_0000004\"/>\r\n                <owl:someValuesFrom rdf:resource=\"http://purl.obolibrary.org/obo/CHEBI_37527\"/>\r\n            </owl:Restriction>\r\n        </rdfs:subClassOf>\r\n    </owl:Restriction>\r\n```\r\n\r\nAssigning to myself to make a better test case"},"comment":{"url":"https://api.github.com/repos/ontodev/robot/issues/comments/412916115","html_url":"https://github.com/ontodev/robot/issues/175#issuecomment-412916115","issue_url":"https://api.github.com/repos/ontodev/robot/issues/175","id":412916115,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMjkxNjExNQ==","user":{"login":"rctauber","id":16750150,"node_id":"MDQ6VXNlcjE2NzUwMTUw","avatar_url":"https://avatars1.githubusercontent.com/u/16750150?v=4","gravatar_id":"","url":"https://api.github.com/users/rctauber","html_url":"https://github.com/rctauber","followers_url":"https://api.github.com/users/rctauber/followers","following_url":"https://api.github.com/users/rctauber/following{/other_user}","gists_url":"https://api.github.com/users/rctauber/gists{/gist_id}","starred_url":"https://api.github.com/users/rctauber/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rctauber/subscriptions","organizations_url":"https://api.github.com/users/rctauber/orgs","repos_url":"https://api.github.com/users/rctauber/repos","events_url":"https://api.github.com/users/rctauber/events{/privacy}","received_events_url":"https://api.github.com/users/rctauber/received_events","type":"User","site_admin":false},"created_at":"2018-08-14T15:37:45Z","updated_at":"2018-08-14T15:37:45Z","author_association":"CONTRIBUTOR","body":"Are you still having problems with this?"}}
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