{"action":"created","issue":{"url":"https://api.github.com/repos/WormBase/website/issues/4221","labels_url":"https://api.github.com/repos/WormBase/website/issues/4221/labels{/name}","comments_url":"https://api.github.com/repos/WormBase/website/issues/4221/comments","events_url":"https://api.github.com/repos/WormBase/website/issues/4221/events","html_url":"https://github.com/WormBase/website/issues/4221","id":108964754,"number":4221,"title":"Display of entity-quality phenotype annotations","user":{"login":"chris-grove","id":611382,"avatar_url":"https://avatars.githubusercontent.com/u/611382?v=3","gravatar_id":"","url":"https://api.github.com/users/chris-grove","html_url":"https://github.com/chris-grove","followers_url":"https://api.github.com/users/chris-grove/followers","following_url":"https://api.github.com/users/chris-grove/following{/other_user}","gists_url":"https://api.github.com/users/chris-grove/gists{/gist_id}","starred_url":"https://api.github.com/users/chris-grove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chris-grove/subscriptions","organizations_url":"https://api.github.com/users/chris-grove/orgs","repos_url":"https://api.github.com/users/chris-grove/repos","events_url":"https://api.github.com/users/chris-grove/events{/privacy}","received_events_url":"https://api.github.com/users/chris-grove/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/WormBase/website/labels/feature%20request","name":"feature request","color":"02d7e1"},{"url":"https://api.github.com/repos/WormBase/website/labels/UI-data%20display","name":"UI-data display","color":"02e10c"},{"url":"https://api.github.com/repos/WormBase/website/labels/Webteam","name":"Webteam","color":"a369e7"}],"state":"open","locked":false,"assignee":{"login":"sibyl229","id":1753893,"avatar_url":"https://avatars.githubusercontent.com/u/1753893?v=3","gravatar_id":"","url":"https://api.github.com/users/sibyl229","html_url":"https://github.com/sibyl229","followers_url":"https://api.github.com/users/sibyl229/followers","following_url":"https://api.github.com/users/sibyl229/following{/other_user}","gists_url":"https://api.github.com/users/sibyl229/gists{/gist_id}","starred_url":"https://api.github.com/users/sibyl229/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sibyl229/subscriptions","organizations_url":"https://api.github.com/users/sibyl229/orgs","repos_url":"https://api.github.com/users/sibyl229/repos","events_url":"https://api.github.com/users/sibyl229/events{/privacy}","received_events_url":"https://api.github.com/users/sibyl229/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/WormBase/website/milestones/27","html_url":"https://github.com/WormBase/website/milestones/WS251","labels_url":"https://api.github.com/repos/WormBase/website/milestones/27/labels","id":1329995,"number":27,"title":"WS251","description":null,"creator":{"login":"chris-grove","id":611382,"avatar_url":"https://avatars.githubusercontent.com/u/611382?v=3","gravatar_id":"","url":"https://api.github.com/users/chris-grove","html_url":"https://github.com/chris-grove","followers_url":"https://api.github.com/users/chris-grove/followers","following_url":"https://api.github.com/users/chris-grove/following{/other_user}","gists_url":"https://api.github.com/users/chris-grove/gists{/gist_id}","starred_url":"https://api.github.com/users/chris-grove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chris-grove/subscriptions","organizations_url":"https://api.github.com/users/chris-grove/orgs","repos_url":"https://api.github.com/users/chris-grove/repos","events_url":"https://api.github.com/users/chris-grove/events{/privacy}","received_events_url":"https://api.github.com/users/chris-grove/received_events","type":"User","site_admin":false},"open_issues":13,"closed_issues":1,"state":"open","created_at":"2015-09-29T21:34:05Z","updated_at":"2015-12-17T16:28:13Z","due_on":null,"closed_at":null},"comments":18,"created_at":"2015-09-29T21:34:28Z","updated_at":"2016-01-04T20:07:08Z","closed_at":null,"body":"@sibyl229  @tharris \r\nI'd like to start the discussion about how to best display the new phenotype annotation style that we've added. As a reminder, the ?Phenotype_info model, usually used as a hash in phenotype annotations, has recently had some tags added to allow phenotype curators to annotate entities and associated qualities to phenotype annotations, in addition to the existing WBPhenotype term. The WS250 ?Phenotype_info model had:\r\n\r\n?Phenotype_info\r\n    Anatomy_term  ?Anatomy_term  #Evidence\r\n    Phenotype_assay  Life_stage  ?Life_stage  #Evidence \r\n\r\nand WS251 now has:\r\n\r\n?Phenotype_info\r\n    EQ_annotations  Anatomy_term  ?Anatomy_term  ?PATO_term   #Evidence\r\n                                Life_stage  ?Life_stage  ?PATO_term   #Evidence\r\n                                GO_term  ?GO_term  ?PATO_term  #Evidence\r\n                                Molecule_affected   ?Molecule   ?PATO_term   #Evidence\r\n\r\nThe point of this is to allow us to specifically annotate to various entities affected as part of the phenotype without having to create all permutations of phenotype terms. Currently, anatomy and life stage terms are displayed on gene page \"Phenotypes\" widgets. For an anatomy example see the ced-12 distal tip cell migration variant phenotype:\r\n\r\nhttp://www.wormbase.org/species/c_elegans/gene/WBGene00000426#0-b-3\r\n\r\nIt would be good if we could somehow extend the existing anatomy term display to include the PATO  term (generally defaults to \"abnormal\") and similar displays for life stage, GO term, and molecule affected.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/WormBase/website/issues/comments/168790669","html_url":"https://github.com/WormBase/website/issues/4221#issuecomment-168790669","issue_url":"https://api.github.com/repos/WormBase/website/issues/4221","id":168790669,"user":{"login":"chris-grove","id":611382,"avatar_url":"https://avatars.githubusercontent.com/u/611382?v=3","gravatar_id":"","url":"https://api.github.com/users/chris-grove","html_url":"https://github.com/chris-grove","followers_url":"https://api.github.com/users/chris-grove/followers","following_url":"https://api.github.com/users/chris-grove/following{/other_user}","gists_url":"https://api.github.com/users/chris-grove/gists{/gist_id}","starred_url":"https://api.github.com/users/chris-grove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chris-grove/subscriptions","organizations_url":"https://api.github.com/users/chris-grove/orgs","repos_url":"https://api.github.com/users/chris-grove/repos","events_url":"https://api.github.com/users/chris-grove/events{/privacy}","received_events_url":"https://api.github.com/users/chris-grove/received_events","type":"User","site_admin":false},"created_at":"2016-01-04T20:07:08Z","updated_at":"2016-01-04T20:07:08Z","body":"@sibyl229 \r\nIt seems the PATO name reference has reverted to a PATO ID, which is unreadable to users:\r\n\r\n![screen shot 2016-01-04 at 12 05 10 pm](https://cloud.githubusercontent.com/assets/611382/12099140/7604b99c-b2db-11e5-867f-83fc1ec696cd.png)\r\n\r\nPerhaps you're in the middle of working on it.\r\n\r\nAlso, can we change \"Entity\" to \"Entities affected\"?\r\n"}}