{"action":"created","comment":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/27413620","id":27413620,"diff_hunk":"@@ -353,6 +353,70 @@ record Sequence {\n }\n \n /**\n+<<<<<<< HEAD","path":"src/main/resources/avro/common.avdl","position":null,"original_position":4,"commit_id":"a578f402cbc7a86b86bbd964e5004fad40afe571","original_commit_id":"10c76c283375677af4328f87c130472f565d2567","user":{"login":"jnguyenx","id":4312088,"avatar_url":"https://avatars.githubusercontent.com/u/4312088?v=3","gravatar_id":"","url":"https://api.github.com/users/jnguyenx","html_url":"https://github.com/jnguyenx","followers_url":"https://api.github.com/users/jnguyenx/followers","following_url":"https://api.github.com/users/jnguyenx/following{/other_user}","gists_url":"https://api.github.com/users/jnguyenx/gists{/gist_id}","starred_url":"https://api.github.com/users/jnguyenx/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jnguyenx/subscriptions","organizations_url":"https://api.github.com/users/jnguyenx/orgs","repos_url":"https://api.github.com/users/jnguyenx/repos","events_url":"https://api.github.com/users/jnguyenx/events{/privacy}","received_events_url":"https://api.github.com/users/jnguyenx/received_events","type":"User","site_admin":false},"body":"Thanks for catching that, it's fixed now.","created_at":"2015-03-30T17:43:34Z","updated_at":"2015-03-30T17:43:34Z","html_url":"https://github.com/ga4gh/schemas/pull/268#discussion_r27413620","pull_request_url":"https://api.github.com/repos/ga4gh/schemas/pulls/268","_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments/27413620"},"html":{"href":"https://github.com/ga4gh/schemas/pull/268#discussion_r27413620"},"pull_request":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/268"}}},"pull_request":{"url":"https://api.github.com/repos/ga4gh/schemas/pulls/268","id":32150391,"html_url":"https://github.com/ga4gh/schemas/pull/268","diff_url":"https://github.com/ga4gh/schemas/pull/268.diff","patch_url":"https://github.com/ga4gh/schemas/pull/268.patch","issue_url":"https://api.github.com/repos/ga4gh/schemas/issues/268","number":268,"state":"open","locked":false,"title":"Genotype to phenotype","user":{"login":"jnguyenx","id":4312088,"avatar_url":"https://avatars.githubusercontent.com/u/4312088?v=3","gravatar_id":"","url":"https://api.github.com/users/jnguyenx","html_url":"https://github.com/jnguyenx","followers_url":"https://api.github.com/users/jnguyenx/followers","following_url":"https://api.github.com/users/jnguyenx/following{/other_user}","gists_url":"https://api.github.com/users/jnguyenx/gists{/gist_id}","starred_url":"https://api.github.com/users/jnguyenx/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jnguyenx/subscriptions","organizations_url":"https://api.github.com/users/jnguyenx/orgs","repos_url":"https://api.github.com/users/jnguyenx/repos","events_url":"https://api.github.com/users/jnguyenx/events{/privacy}","received_events_url":"https://api.github.com/users/jnguyenx/received_events","type":"User","site_admin":false},"body":"This protocol defines the associations between genotype and phenotype (G2P).  Associations can be made as a result of literature curation, computational modeling, inference, etc., and modeled and shared using this schema.\r\n\r\nHere, we follow the dogma of:\r\n\r\n      Genotype + Environment = Phenotype\r\n\r\nwhere a G2P association is between the G(enotype) in the context of some E(environment), which gives rise to a P(henotype). These associations have further evidence, provenance, and attribution.\r\n\r\nWe leverage the GenomicFeature in the sequenceAnnotation schema here as it can accomodate any genomic feature from a single nucleotide variation (SNV), up through a gene, and/or complex rearrangements.  Each can be modeled as genomic features, and generally linked to a phenotype.\r\nCollections of these features can represent a genotype at different levels of completeness.  Therefore, we can represent single allelic variation, allelic complement, and multiple variants in a genotype that can each or collectively be associated with a phenotype.\r\n\r\nTo enable standardized integration, this schema relies heavily on OntologyTerms, both for typing phenotype (for example, using the HPO or DO) but also genomic features (such as using SO) and levels of evidence (ECO).","created_at":"2015-03-27T22:27:31Z","updated_at":"2015-03-30T17:43:34Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c04d0784b72436ecf58d6c3fa577dfd5b770e694","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/ga4gh/schemas/pulls/268/commits","review_comments_url":"https://api.github.com/repos/ga4gh/schemas/pulls/268/comments","review_comment_url":"https://api.github.com/repos/ga4gh/schemas/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ga4gh/schemas/issues/268/comments","statuses_url":"https://api.github.com/repos/ga4gh/schemas/statuses/a578f402cbc7a86b86bbd964e5004fad40afe571","head":{"label":"jnguyenx:genotype-to-phenotype","ref":"genotype-to-phenotype","sha":"a578f402cbc7a86b86bbd964e5004fad40afe571","user":{"login":"jnguyenx","id":4312088,"avatar_url":"https://avatars.githubusercontent.com/u/4312088?v=3","gravatar_id":"","url":"https://api.github.com/users/jnguyenx","html_url":"https://github.com/jnguyenx","followers_url":"https://api.github.com/users/jnguyenx/followers","following_url":"https://api.github.com/users/jnguyenx/following{/other_user}","gists_url":"https://api.github.com/users/jnguyenx/gists{/gist_id}","starred_url":"https://api.github.com/users/jnguyenx/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jnguyenx/subscriptions","organizations_url":"https://api.github.com/users/jnguyenx/orgs","repos_url":"https://api.github.com/users/jnguyenx/repos","events_url":"https://api.github.com/users/jnguyenx/events{/privacy}","received_events_url":"https://api.github.com/users/jnguyenx/received_events","type":"User","site_admin":false},"repo":{"id":31625540,"name":"schemas","full_name":"jnguyenx/schemas","owner":{"login":"jnguyenx","id":4312088,"avatar_url":"https://avatars.githubusercontent.com/u/4312088?v=3","gravatar_id":"","url":"https://api.github.com/users/jnguyenx","html_url":"https://github.com/jnguyenx","followers_url":"https://api.github.com/users/jnguyenx/followers","following_url":"https://api.github.com/users/jnguyenx/following{/other_user}","gists_url":"https://api.github.com/users/jnguyenx/gists{/gist_id}","starred_url":"https://api.github.com/users/jnguyenx/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jnguyenx/subscriptions","organizations_url":"https://api.github.com/users/jnguyenx/orgs","repos_url":"https://api.github.com/users/jnguyenx/repos","events_url":"https://api.github.com/users/jnguyenx/events{/privacy}","received_events_url":"https://api.github.com/users/jnguyenx/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jnguyenx/schemas","description":"Work on data models and APIs for Genomic data.","fork":true,"url":"https://api.github.com/repos/jnguyenx/schemas","forks_url":"https://api.github.com/repos/jnguyenx/schemas/forks","keys_url":"https://api.github.com/repos/jnguyenx/schemas/keys{/key_id}","collaborators_url":"https://api.github.com/repos/jnguyenx/schemas/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/jnguyenx/schemas/teams","hooks_url":"https://api.github.com/repos/jnguyenx/schemas/hooks","issue_events_url":"https://api.github.com/repos/jnguyenx/schemas/issues/events{/number}","events_url":"https://api.github.com/repos/jnguyenx/schemas/events","assignees_url":"https://api.github.com/repos/jnguyenx/schemas/assignees{/user}","branches_url":"https://api.github.com/repos/jnguyenx/schemas/branches{/branch}","tags_url":"https://api.github.com/repos/jnguyenx/schemas/tags","blobs_url":"https://api.github.com/repos/jnguyenx/schemas/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/jnguyenx/schemas/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/jnguyenx/schemas/git/refs{/sha}","trees_url":"https://api.github.com/repos/jnguyenx/schemas/git/trees{/sha}","statuses_url":"https://api.github.com/repos/jnguyenx/schemas/statuses/{sha}","languages_url":"https://api.github.com/repos/jnguyenx/schemas/languages","stargazers_url":"https://api.github.com/repos/jnguyenx/schemas/stargazers","contributors_url":"https://api.github.com/repos/jnguyenx/schemas/contributors","subscribers_url":"https://api.github.com/repos/jnguyenx/schemas/subscribers","subscription_url":"https://api.github.com/repos/jnguyenx/schemas/subscription","commits_url":"https://api.github.com/repos/jnguyenx/schemas/commits{/sha}","git_commits_url":"https://api.github.com/repos/jnguyenx/schemas/git/commits{/sha}","comments_url":"https://api.github.com/repos/jnguyenx/schemas/comments{/number}","issue_comment_url":"https://api.github.com/repos/jnguyenx/schemas/issues/comments{/number}","contents_url":"https://api.github.com/repos/jnguyenx/schemas/contents/{+path}","compare_url":"https://api.github.com/repos/jnguyenx/schemas/compare/{base}...{head}","merges_url":"https://api.github.com/repos/jnguyenx/schemas/merges","archive_url":"https://api.github.com/repos/jnguyenx/schemas/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/jnguyenx/schemas/downloads","issues_url":"https://api.github.com/repos/jnguyenx/schemas/issues{/number}","pulls_url":"https://api.github.com/repos/jnguyenx/schemas/pulls{/number}","milestones_url":"https://api.github.com/repos/jnguyenx/schemas/milestones{/number}","notifications_url":"https://api.github.com/repos/jnguyenx/schemas/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/jnguyenx/schemas/labels{/name}","releases_url":"https://api.github.com/repos/jnguyenx/schemas/releases{/id}","created_at":"2015-03-03T22:43:56Z","updated_at":"2015-02-27T17:02:17Z","pushed_at":"2015-03-30T17:12:27Z","git_url":"git://github.com/jnguyenx/schemas.git","ssh_url":"git@github.com:jnguyenx/schemas.git","clone_url":"https://github.com/jnguyenx/schemas.git","svn_url":"https://github.com/jnguyenx/schemas","homepage":"http://ga4gh.org/#/api","size":606,"stargazers_count":0,"watchers_count":0,"language":null,"has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":1,"forks":0,"open_issues":1,"watchers":0,"default_branch":"master"}},"base":{"label":"ga4gh:g2p","ref":"g2p","sha":"c27178412dcc73ec55345e6c9782b75fad1c9d4e","user":{"login":"ga4gh","id":6921777,"avatar_url":"https://avatars.githubusercontent.com/u/6921777?v=3","gravatar_id":"","url":"https://api.github.com/users/ga4gh","html_url":"https://github.com/ga4gh","followers_url":"https://api.github.com/users/ga4gh/followers","following_url":"https://api.github.com/users/ga4gh/following{/other_user}","gists_url":"https://api.github.com/users/ga4gh/gists{/gist_id}","starred_url":"https://api.github.com/users/ga4gh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ga4gh/subscriptions","organizations_url":"https://api.github.com/users/ga4gh/orgs","repos_url":"https://api.github.com/users/ga4gh/repos","events_url":"https://api.github.com/users/ga4gh/events{/privacy}","received_events_url":"https://api.github.com/users/ga4gh/received_events","type":"Organization","site_admin":false},"repo":{"id":17925227,"name":"schemas","full_name":"ga4gh/schemas","owner":{"login":"ga4gh","id":6921777,"avatar_url":"https://avatars.githubusercontent.com/u/6921777?v=3","gravatar_id":"","url":"https://api.github.com/users/ga4gh","html_url":"https://github.com/ga4gh","followers_url":"https://api.github.com/users/ga4gh/followers","following_url":"https://api.github.com/users/ga4gh/following{/other_user}","gists_url":"https://api.github.com/users/ga4gh/gists{/gist_id}","starred_url":"https://api.github.com/users/ga4gh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ga4gh/subscriptions","organizations_url":"https://api.github.com/users/ga4gh/orgs","repos_url":"https://api.github.com/users/ga4gh/repos","events_url":"https://api.github.com/users/ga4gh/events{/privacy}","received_events_url":"https://api.github.com/users/ga4gh/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/ga4gh/schemas","description":"Work on data models and APIs for Genomic data.","fork":false,"url":"https://api.github.com/repos/ga4gh/schemas","forks_url":"https://api.github.com/repos/ga4gh/schemas/forks","keys_url":"https://api.github.com/repos/ga4gh/schemas/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ga4gh/schemas/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ga4gh/schemas/teams","hooks_url":"https://api.github.com/repos/ga4gh/schemas/hooks","issue_events_url":"https://api.github.com/repos/ga4gh/schemas/issues/events{/number}","events_url":"https://api.github.com/repos/ga4gh/schemas/events","assignees_url":"https://api.github.com/repos/ga4gh/schemas/assignees{/user}","branches_url":"https://api.github.com/repos/ga4gh/schemas/branches{/branch}","tags_url":"https://api.github.com/repos/ga4gh/schemas/tags","blobs_url":"https://api.github.com/repos/ga4gh/schemas/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ga4gh/schemas/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ga4gh/schemas/git/refs{/sha}","trees_url":"https://api.github.com/repos/ga4gh/schemas/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ga4gh/schemas/statuses/{sha}","languages_url":"https://api.github.com/repos/ga4gh/schemas/languages","stargazers_url":"https://api.github.com/repos/ga4gh/schemas/stargazers","contributors_url":"https://api.github.com/repos/ga4gh/schemas/contributors","subscribers_url":"https://api.github.com/repos/ga4gh/schemas/subscribers","subscription_url":"https://api.github.com/repos/ga4gh/schemas/subscription","commits_url":"https://api.github.com/repos/ga4gh/schemas/commits{/sha}","git_commits_url":"https://api.github.com/repos/ga4gh/schemas/git/commits{/sha}","comments_url":"https://api.github.com/repos/ga4gh/schemas/comments{/number}","issue_comment_url":"https://api.github.com/repos/ga4gh/schemas/issues/comments{/number}","contents_url":"https://api.github.com/repos/ga4gh/schemas/contents/{+path}","compare_url":"https://api.github.com/repos/ga4gh/schemas/compare/{base}...{head}","merges_url":"https://api.github.com/repos/ga4gh/schemas/merges","archive_url":"https://api.github.com/repos/ga4gh/schemas/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/ga4gh/schemas/downloads","issues_url":"https://api.github.com/repos/ga4gh/schemas/issues{/number}","pulls_url":"https://api.github.com/repos/ga4gh/schemas/pulls{/number}","milestones_url":"https://api.github.com/repos/ga4gh/schemas/milestones{/number}","notifications_url":"https://api.github.com/repos/ga4gh/schemas/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/ga4gh/schemas/labels{/name}","releases_url":"https://api.github.com/repos/ga4gh/schemas/releases{/id}","created_at":"2014-03-20T00:13:40Z","updated_at":"2015-03-27T17:36:06Z","pushed_at":"2015-03-30T17:12:27Z","git_url":"git://github.com/ga4gh/schemas.git","ssh_url":"git@github.com:ga4gh/schemas.git","clone_url":"https://github.com/ga4gh/schemas.git","svn_url":"https://github.com/ga4gh/schemas","homepage":"http://ga4gh.org/#/api","size":2550,"stargazers_count":128,"watchers_count":128,"language":null,"has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":54,"mirror_url":null,"open_issues_count":54,"forks":54,"open_issues":54,"watchers":128,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/268"},"html":{"href":"https://github.com/ga4gh/schemas/pull/268"},"issue":{"href":"https://api.github.com/repos/ga4gh/schemas/issues/268"},"comments":{"href":"https://api.github.com/repos/ga4gh/schemas/issues/268/comments"},"review_comments":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/268/comments"},"review_comment":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/ga4gh/schemas/pulls/268/commits"},"statuses":{"href":"https://api.github.com/repos/ga4gh/schemas/statuses/a578f402cbc7a86b86bbd964e5004fad40afe571"}}}}