{"action":"created","issue":{"url":"https://api.github.com/repos/monarch-initiative/dipper/issues/54","labels_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/54/labels{/name}","comments_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/54/comments","events_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/54/events","html_url":"https://github.com/monarch-initiative/dipper/issues/54","id":57507904,"number":54,"title":"Phenotype modeling for IMPC","user":{"login":"bryanlaraway","id":5770358,"avatar_url":"https://avatars.githubusercontent.com/u/5770358?v=3","gravatar_id":"","url":"https://api.github.com/users/bryanlaraway","html_url":"https://github.com/bryanlaraway","followers_url":"https://api.github.com/users/bryanlaraway/followers","following_url":"https://api.github.com/users/bryanlaraway/following{/other_user}","gists_url":"https://api.github.com/users/bryanlaraway/gists{/gist_id}","starred_url":"https://api.github.com/users/bryanlaraway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bryanlaraway/subscriptions","organizations_url":"https://api.github.com/users/bryanlaraway/orgs","repos_url":"https://api.github.com/users/bryanlaraway/repos","events_url":"https://api.github.com/users/bryanlaraway/events{/privacy}","received_events_url":"https://api.github.com/users/bryanlaraway/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/monarch-initiative/dipper/labels/help%20wanted","name":"help wanted","color":"159818"},{"url":"https://api.github.com/repos/monarch-initiative/dipper/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":{"login":"mbrush","id":5184212,"avatar_url":"https://avatars.githubusercontent.com/u/5184212?v=3","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},"milestone":null,"comments":3,"created_at":"2015-02-12T19:33:02Z","updated_at":"2015-02-18T20:52:19Z","closed_at":null,"body":"References #14 .\r\n\r\nHave a question regarding the modeling of additional phenotype data in IMPC. I have created the genotype to phenotype associations, but I'm unsure exactly how I should proceed in creating the phenotype node and where to hang the additional phenotype testing data.\r\n\r\nFor the genotype to phenotype association, I'm currently using the MP term as the phenotype ID, same as we are using for the [NIF view](http://beta.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151660-3), although the ID is hidden in the interface. However, I think we don't want to hang the additional phenotype data available from IMPC, such as a phenotype free text description (includes phenotype center, testing procedure, testing parameter, effect size, and p-value), from the phenotype ID, as this would result in a single phenotype associated with multiple genotypes and multiple measurements attached to the phenotype that are associated with multiple genotypes.\r\n\r\nUpdate: Talked with Matt and it sounds appropriate to hang this data to the association between the genotype and the phenotype. He has created GENO_0000612 - 'phenotype description' for the phenotype description free text. Will work on creating additional entries for other phenotype parts as needed."},"comment":{"url":"https://api.github.com/repos/monarch-initiative/dipper/issues/comments/74945431","html_url":"https://github.com/monarch-initiative/dipper/issues/54#issuecomment-74945431","issue_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/54","id":74945431,"user":{"login":"bryanlaraway","id":5770358,"avatar_url":"https://avatars.githubusercontent.com/u/5770358?v=3","gravatar_id":"","url":"https://api.github.com/users/bryanlaraway","html_url":"https://github.com/bryanlaraway","followers_url":"https://api.github.com/users/bryanlaraway/followers","following_url":"https://api.github.com/users/bryanlaraway/following{/other_user}","gists_url":"https://api.github.com/users/bryanlaraway/gists{/gist_id}","starred_url":"https://api.github.com/users/bryanlaraway/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bryanlaraway/subscriptions","organizations_url":"https://api.github.com/users/bryanlaraway/orgs","repos_url":"https://api.github.com/users/bryanlaraway/repos","events_url":"https://api.github.com/users/bryanlaraway/events{/privacy}","received_events_url":"https://api.github.com/users/bryanlaraway/received_events","type":"User","site_admin":false},"created_at":"2015-02-18T20:52:19Z","updated_at":"2015-02-18T20:52:19Z","body":"@mbrush One additional item in regards to genotype and phenotype modeling is in regard to the sex of the organism. In the views we created for NIF, the sex was not incorporated into the [MouseGenotypes view](http://beta.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151660-2), and the underlying data stopped at the creation of the intrinsic genotype, while the [MousePhenotypes view](http://beta.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151660-3) included the sex, and the genotype partonomy was extended to the effective genotype, which in the case of IMPC was the intrinsic genotype + sex. The question then is whether it would be more appropriate to have the sex be part of the intrinsic genotype, allowing for the consideration of how the differences in sex chromosomes apply to the intrinsic genotype, or whether it should stay attached to the effective genotype."}}