{"action":"created","issue":{"url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition/issues/11","repository_url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition","labels_url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition/issues/11/comments","events_url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition/issues/11/events","html_url":"https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/11","id":256344157,"number":11,"title":"Ideas for exemplar queries","user":{"login":"mbrush","id":5184212,"avatar_url":"https://avatars1.githubusercontent.com/u/5184212?v=4","gravatar_id":"","url":"https://api.github.com/users/mbrush","html_url":"https://github.com/mbrush","followers_url":"https://api.github.com/users/mbrush/followers","following_url":"https://api.github.com/users/mbrush/following{/other_user}","gists_url":"https://api.github.com/users/mbrush/gists{/gist_id}","starred_url":"https://api.github.com/users/mbrush/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbrush/subscriptions","organizations_url":"https://api.github.com/users/mbrush/orgs","repos_url":"https://api.github.com/users/mbrush/repos","events_url":"https://api.github.com/users/mbrush/events{/privacy}","received_events_url":"https://api.github.com/users/mbrush/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"krobasky","id":413166,"avatar_url":"https://avatars0.githubusercontent.com/u/413166?v=4","gravatar_id":"","url":"https://api.github.com/users/krobasky","html_url":"https://github.com/krobasky","followers_url":"https://api.github.com/users/krobasky/followers","following_url":"https://api.github.com/users/krobasky/following{/other_user}","gists_url":"https://api.github.com/users/krobasky/gists{/gist_id}","starred_url":"https://api.github.com/users/krobasky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/krobasky/subscriptions","organizations_url":"https://api.github.com/users/krobasky/orgs","repos_url":"https://api.github.com/users/krobasky/repos","events_url":"https://api.github.com/users/krobasky/events{/privacy}","received_events_url":"https://api.github.com/users/krobasky/received_events","type":"User","site_admin":false},"assignees":[{"login":"krobasky","id":413166,"avatar_url":"https://avatars0.githubusercontent.com/u/413166?v=4","gravatar_id":"","url":"https://api.github.com/users/krobasky","html_url":"https://github.com/krobasky","followers_url":"https://api.github.com/users/krobasky/followers","following_url":"https://api.github.com/users/krobasky/following{/other_user}","gists_url":"https://api.github.com/users/krobasky/gists{/gist_id}","starred_url":"https://api.github.com/users/krobasky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/krobasky/subscriptions","organizations_url":"https://api.github.com/users/krobasky/orgs","repos_url":"https://api.github.com/users/krobasky/repos","events_url":"https://api.github.com/users/krobasky/events{/privacy}","received_events_url":"https://api.github.com/users/krobasky/received_events","type":"User","site_admin":false}],"milestone":null,"comments":9,"created_at":"2017-09-08T19:05:36Z","updated_at":"2017-09-25T17:57:10Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"For coming up with queries, it may help to use the cmap [here](https://github.com/NCI-Thesaurus/thesaurus-obo-edition/blob/master/docs/NCIT-Diagram.jpg) that shows all paths through the data. Below are a few examples of queries we can see should be supported, along with the path the query would take through top-level types in NCIt.  Queries get more complex as you go down the list.\r\n\r\n**What genes are targeted by drugs used to treat cancer x?**\r\nQuery path: `Disease or Disorder -> Chemotherapy Regimen or Agent Combination -> Drug, Food, Chemical or Biomedical Material  -> Gene`\r\n\r\n**What pathways are targeted by drugs used to treat cancer x?**\r\nQuery path: `Disease or Disorder -> Gene -> Biochemical Pathway`   \r\n\r\n**What signaling pathways are affected in cancer x?**\r\nQuery path: `Disease or Disorder -> Molecular Abnormality -> Gene ->  Biochemical Pathway `\r\n\r\n**What drugs target the highest number of pathways?**\r\nQuery path:` Drug, Food, Chemical or Biomedical Material -> Gene -> COUNT(Biochemical Pathway) `\r\n\r\n**What other drugs target genes in the same signaling pathway as drug X?**\r\nQuery path: `Drug, Food, Chemical or Biomedical Material  -> Gene Product -> Gene  -> Biochemical Pathway -> Gene -> Gene Product ->  Drug, Food, Chemical or Biomedical Material `\r\n\r\n**A possible drug re-purposing query (based on WD example [here](https://www.wikidata.org/wiki/User:ProteinBoxBot/SPARQL_Examples#Drug_Repurposing))**\r\nFind cancers that may be treated by drugs used to treat non-cancers (based on fact that the one or more of the genes known to be targeted by the drug are associated with the cancer)\r\nQuery path: `Disease or Disorder -> Drug, Food, Chemical or Biomedical Material  -> Gene Product -> Gene -> Drug, Food, Chemical or Biomedical Material  -> Disease or Disorder `\r\n\r\n**A drug re-purposing query extension:**\r\nCan go further and constrain results to include only matches based on shared genes annotated to apoptosis or cell proliferation GO terms.\r\nQuery path:  `Disease or Disorder -> Drug, Food, Chemical or Biomedical Material  -> Gene Product -> Gene (filter by GO annotation) -> Drug, Food, Chemical or Biomedical Material  -> Disease or Disorder `\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition/issues/comments/331962119","html_url":"https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/11#issuecomment-331962119","issue_url":"https://api.github.com/repos/NCI-Thesaurus/thesaurus-obo-edition/issues/11","id":331962119,"user":{"login":"decorons","id":7051504,"avatar_url":"https://avatars2.githubusercontent.com/u/7051504?v=4","gravatar_id":"","url":"https://api.github.com/users/decorons","html_url":"https://github.com/decorons","followers_url":"https://api.github.com/users/decorons/followers","following_url":"https://api.github.com/users/decorons/following{/other_user}","gists_url":"https://api.github.com/users/decorons/gists{/gist_id}","starred_url":"https://api.github.com/users/decorons/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/decorons/subscriptions","organizations_url":"https://api.github.com/users/decorons/orgs","repos_url":"https://api.github.com/users/decorons/repos","events_url":"https://api.github.com/users/decorons/events{/privacy}","received_events_url":"https://api.github.com/users/decorons/received_events","type":"User","site_admin":false},"created_at":"2017-09-25T17:57:10Z","updated_at":"2017-09-25T17:57:10Z","author_association":"NONE","body":"How about a query like All the Diseases that 'may have molecular abnormality' RB1 gene inactivation?\r\nThat shows a long list in the regular NCIt browser."}}
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