{"action":"created","issue":{"url":"https://api.github.com/repos/monarch-initiative/mckb/issues/1","labels_url":"https://api.github.com/repos/monarch-initiative/mckb/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/monarch-initiative/mckb/issues/1/comments","events_url":"https://api.github.com/repos/monarch-initiative/mckb/issues/1/events","html_url":"https://github.com/monarch-initiative/mckb/issues/1","id":58036226,"number":1,"title":"convert disease-variant-drug data into triples","user":{"login":"nlwashington","id":5124411,"avatar_url":"https://avatars.githubusercontent.com/u/5124411?v=3","gravatar_id":"","url":"https://api.github.com/users/nlwashington","html_url":"https://github.com/nlwashington","followers_url":"https://api.github.com/users/nlwashington/followers","following_url":"https://api.github.com/users/nlwashington/following{/other_user}","gists_url":"https://api.github.com/users/nlwashington/gists{/gist_id}","starred_url":"https://api.github.com/users/nlwashington/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nlwashington/subscriptions","organizations_url":"https://api.github.com/users/nlwashington/orgs","repos_url":"https://api.github.com/users/nlwashington/repos","events_url":"https://api.github.com/users/nlwashington/events{/privacy}","received_events_url":"https://api.github.com/users/nlwashington/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"kshefchek","id":1467299,"avatar_url":"https://avatars.githubusercontent.com/u/1467299?v=3","gravatar_id":"","url":"https://api.github.com/users/kshefchek","html_url":"https://github.com/kshefchek","followers_url":"https://api.github.com/users/kshefchek/followers","following_url":"https://api.github.com/users/kshefchek/following{/other_user}","gists_url":"https://api.github.com/users/kshefchek/gists{/gist_id}","starred_url":"https://api.github.com/users/kshefchek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kshefchek/subscriptions","organizations_url":"https://api.github.com/users/kshefchek/orgs","repos_url":"https://api.github.com/users/kshefchek/repos","events_url":"https://api.github.com/users/kshefchek/events{/privacy}","received_events_url":"https://api.github.com/users/kshefchek/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2015-02-18T07:33:57Z","updated_at":"2015-04-02T22:23:39Z","closed_at":null,"body":"here's a first pass at design of triples, given some of oscar's data.\r\nExample1:\r\n<pre>\r\nindiv1 rdf:type glioma_of_the_brain\r\n  rdfs:label “glioma of the brain with MGMT any promoter methylation”\r\n  GENO:has_genotype gtindiv1\r\n  monarch:responds_with_increased_benefit DrugBank:DB00853\r\n\r\nDrugBank:DB00853 a owl:Class  #drugs will have to be curated.\r\nDrugBank:DB00853 rdfs:label “temozolomide” \r\n\r\ngtindiv1 rdf:type GENO:methylation  #we might need to curate these kinds of genotypes\r\n  RO:contained_in SO:promoter\r\n  RO:targets NCBIGene:4255    #need to curate gene ids/fetch from NCBI\r\n  refs:label “MGMT any promoter methylation”\r\n</pre>\r\n  \r\nExample2:\r\n<pre>\r\nindiv2 rdf:type ductal_carcinoma\r\nindiv2 rdfs:label “ductal carcinoma of the breast with ERBB2 G309A missense mutation”\r\nindiv2 GENO:has_genotype gtindiv2\r\n\r\nindiv2 monarch:reduced_sensitivity_toward CHEBI:49603      #lapatinib\r\n\r\ngtindiv2 rdf:type GENO:sequence_alteration,SO:missense_variant\r\n  rdfs:label “ERBB2 G309A missense mutation”\r\n  GENO:is_sequence_variant_of NCBIGene:ERBB2\r\n  faldo:location [ \r\n    a faldo:position,\r\n    faldo:begin 390,  #preferable to use proper genomic location\r\n    faldo:end 390 \r\n    reference: protein_id]   #if we don’t map to the genomic level, could use the protein id here for relative position\r\n  GENO:reference_nucleotide “X”  #not sure we have these relationships?\r\n  GENO:altered_nucleotide “Y”\r\n  GENO:results_in_amino_acid_change “A”\r\n\r\nannotation180 a annotation\r\n  hasSubject indiv2\r\n  hasObject gtindiv2\r\n  hasPredicate monarch:reduced_sensitivity_toward\r\n  dc:source PMID:23220880\r\n</pre>\r\nhas_genotype = GENO:0000222\r\nand the genes/labels could be defined elsewhere, if desired.\r\n\r\nbasically, we create an individual that is the combination of the cancer/disease diagnosis with the given genotype.  this is what is related to the drug via the to-be-added response relationships (we can just put these in the monarch namespace for now).  @cmungall and @mbrush please help get the right relationships for the \"genotype\".  Example1 is a tough one. (note i didn't put in the reified annotation for example1, but it should be added.) "},"comment":{"url":"https://api.github.com/repos/monarch-initiative/mckb/issues/comments/89062497","html_url":"https://github.com/monarch-initiative/mckb/issues/1#issuecomment-89062497","issue_url":"https://api.github.com/repos/monarch-initiative/mckb/issues/1","id":89062497,"user":{"login":"nlwashington","id":5124411,"avatar_url":"https://avatars.githubusercontent.com/u/5124411?v=3","gravatar_id":"","url":"https://api.github.com/users/nlwashington","html_url":"https://github.com/nlwashington","followers_url":"https://api.github.com/users/nlwashington/followers","following_url":"https://api.github.com/users/nlwashington/following{/other_user}","gists_url":"https://api.github.com/users/nlwashington/gists{/gist_id}","starred_url":"https://api.github.com/users/nlwashington/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nlwashington/subscriptions","organizations_url":"https://api.github.com/users/nlwashington/orgs","repos_url":"https://api.github.com/users/nlwashington/repos","events_url":"https://api.github.com/users/nlwashington/events{/privacy}","received_events_url":"https://api.github.com/users/nlwashington/received_events","type":"User","site_admin":false},"created_at":"2015-04-02T22:23:39Z","updated_at":"2015-04-02T22:23:39Z","body":"the only caveat might be to model it as a population of patients, rather than a single one.  i think i've done something similar for populations of mice in IMPC."}}