{"action":"created","issue":{"url":"https://api.github.com/repos/monarch-initiative/dipper/issues/195","labels_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/195/labels{/name}","comments_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/195/comments","events_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/195/events","html_url":"https://github.com/monarch-initiative/dipper/issues/195","id":104963672,"number":195,"title":"RO_0002600 ('causes disease') vs. RO_0002200 ('has phenotype') for G2D associations","user":{"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},"labels":[{"url":"https://api.github.com/repos/monarch-initiative/dipper/labels/blocked","name":"blocked","color":"e11d21"}],"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":{"url":"https://api.github.com/repos/monarch-initiative/dipper/milestones/7","html_url":"https://github.com/monarch-initiative/dipper/milestones/Thanksgiving%20data%20push","labels_url":"https://api.github.com/repos/monarch-initiative/dipper/milestones/7/labels","id":1338692,"number":7,"title":"Thanksgiving data push","description":"We'll have a big data release to production just prior to Thanksgiving.  This should include all the big animal data, and must necessarily include some refactoring to the phenotype and disease ontologies to be able to integrate and navigate over this data.  ","creator":{"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},"open_issues":21,"closed_issues":22,"state":"open","created_at":"2015-10-05T17:23:24Z","updated_at":"2015-11-11T19:41:37Z","due_on":"2015-11-20T08:00:00Z","closed_at":null},"comments":2,"created_at":"2015-09-04T20:22:18Z","updated_at":"2015-11-19T07:52:55Z","closed_at":null,"body":"In several data sources (ClinVar, OMIM, Orphanet), we use the RO_0002200 'has phenotype' relation for linking variants to diseases. This doesn’t seem right, and is not in line with the definition of 'has phenotype'. Since it is our practice is to use 'has phenotype' in this data only when a variant causes a disease, can we switch to use RO_0002600 ('capable of upregulating or causing pathological process')?  Seems a fit, given its alternative term 'causes disease'.\r\n\r\nOne potential issue here is the fact that this relation is under the 'causal relation between material entity and a process' branch of RO, which of course holds properties relating material entities and processes.  A variant in our modeling is not a material entity, but a generically dependent continuant that is materialized in material DNA molecules (where 'materialized in' is shorthand for 'is concretized as' o 'inheres in').  This raises the more general question of whether we can use properties like this that are defined for material entity subjects to describe both (1) the relationship between material genetic variants and a disease, and (2)  the relationship between a GDC sequence that is materialized in such genetic material and a disease.  It would  obviously be nice to have this flexibility so as to leverage existing formal relationships, and not have to create duplicative ones where needed to apply at the GDC level.  Posted a more detailed ticket in the RO tracker [here](https://github.com/oborel/obo-relations/issues/76) on this topic.  \r\n\r\n@cmungall  and @mellybelly, care to comment?"},"comment":{"url":"https://api.github.com/repos/monarch-initiative/dipper/issues/comments/157980611","html_url":"https://github.com/monarch-initiative/dipper/issues/195#issuecomment-157980611","issue_url":"https://api.github.com/repos/monarch-initiative/dipper/issues/195","id":157980611,"user":{"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},"created_at":"2015-11-19T07:52:55Z","updated_at":"2015-11-19T07:52:55Z","body":"Need one clarification here.   RO already has a 'correlated with' property (with sub-property 'is marker for') that are not specific for linking to 'conditions'.  Did we decide to use these as they are for linking variants to conditions, or did we want to create new properties specifically to be used for linking to conditions, like the causes relations (e.g. 'correlates with condition' and 'marker  for condition')?"}}