{"action":"created","issue":{"url":"https://api.github.com/repos/monarch-initiative/monarch-app/issues/1251","repository_url":"https://api.github.com/repos/monarch-initiative/monarch-app","labels_url":"https://api.github.com/repos/monarch-initiative/monarch-app/issues/1251/labels{/name}","comments_url":"https://api.github.com/repos/monarch-initiative/monarch-app/issues/1251/comments","events_url":"https://api.github.com/repos/monarch-initiative/monarch-app/issues/1251/events","html_url":"https://github.com/monarch-initiative/monarch-app/issues/1251","id":155828861,"number":1251,"title":"Gene-disease lists are sometimes perplexing in multiple ways","user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars.githubusercontent.com/u/50745?v=3","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":null,"milestone":null,"comments":3,"created_at":"2016-05-19T20:35:28Z","updated_at":"2016-05-23T14:15:42Z","closed_at":null,"body":"E.g. https://monarchinitiative.org/gene/NCBIGene%3A2263, diseases tab\r\n\r\nThis is confusing for anyone coming to the system and confusing to me too.\r\n\r\nFirst of all, the reference is the same for all associations (\"Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin\"). This is surely irrelevant.\r\n\r\nThe relationship for all of them is \"inferred\", with no explanation of what inferred means.\r\n\r\nThe source for all of them is the tuple (biogrid,omim)\r\n\r\nWhat does this even mean? The user might be lead to believe this is inferred from interaction data. I don't think this is the case.\r\n\r\nThe evidence type is the pair (sequencing assay, imaging) which is kind of bonkers\r\n\r\nIt should be possible to easily discern relationships that come from OMIM (see http://omim.org/entry/176943). And these should not be marked inferred. Instead we have a melange of OMIM associations, plus associations to MESH and DOID. The ones to MESH and DOID are marked as coming from OMIM, but this is obviously not correct.\r\n\r\nIt's not clear what needs fixed here: dipper, scigraph clique merging, golr export queries, UI - or all of these. But we need to deobfuscate."},"comment":{"url":"https://api.github.com/repos/monarch-initiative/monarch-app/issues/comments/220992570","html_url":"https://github.com/monarch-initiative/monarch-app/issues/1251#issuecomment-220992570","issue_url":"https://api.github.com/repos/monarch-initiative/monarch-app/issues/1251","id":220992570,"user":{"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},"created_at":"2016-05-23T14:15:42Z","updated_at":"2016-05-23T14:15:42Z","body":"I would like to remove direct/inferred from the relationship column, or at least add some documentation of what this means.  This value comes from the qualifier property in solr and moves to the relation column in cases where this is empty (as an attempt to contextualize rows with no relation), but causes confusion.\r\n\r\nAs far as the overmodeling, you can see the various ways we link genes to diseases from omim here:\r\nhttps://github.com/kshefchek/dipper/blob/64c77c3c963f7a58cd5ba832befb7c2d989c6edb/scripts/stats/omim-gene-disease.py\r\n\r\nThe idea is that a gene cannot be directly linked to a disease, but rather inferred through an allele or variant.  But the term inferred is ambiguous to the user, it could mean we inferred through joining sources or inferred biologically.\r\n\r\nWe could easily remove the anonymous variant used to connect genes to diseases without a reference allele or variant if that would be useful."}}
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