{"action":"created","issue":{"url":"https://api.github.com/repos/dictyBase/Modware-Loader/issues/149","labels_url":"https://api.github.com/repos/dictyBase/Modware-Loader/issues/149/labels{/name}","comments_url":"https://api.github.com/repos/dictyBase/Modware-Loader/issues/149/comments","events_url":"https://api.github.com/repos/dictyBase/Modware-Loader/issues/149/events","html_url":"https://github.com/dictyBase/Modware-Loader/issues/149","id":54627961,"number":149,"title":"Representing multiple assemblies of the same organism","user":{"login":"cybersiddhu","id":48740,"avatar_url":"https://avatars.githubusercontent.com/u/48740?v=3","gravatar_id":"","url":"https://api.github.com/users/cybersiddhu","html_url":"https://github.com/cybersiddhu","followers_url":"https://api.github.com/users/cybersiddhu/followers","following_url":"https://api.github.com/users/cybersiddhu/following{/other_user}","gists_url":"https://api.github.com/users/cybersiddhu/gists{/gist_id}","starred_url":"https://api.github.com/users/cybersiddhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cybersiddhu/subscriptions","organizations_url":"https://api.github.com/users/cybersiddhu/orgs","repos_url":"https://api.github.com/users/cybersiddhu/repos","events_url":"https://api.github.com/users/cybersiddhu/events{/privacy}","received_events_url":"https://api.github.com/users/cybersiddhu/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/dictyBase/Modware-Loader/labels/Data+import","name":"Data import","color":"5319e7"},{"url":"https://api.github.com/repos/dictyBase/Modware-Loader/labels/in+progress","name":"in progress","color":"ededed"},{"url":"https://api.github.com/repos/dictyBase/Modware-Loader/labels/overhaul","name":"overhaul","color":"d4c5f9"}],"state":"open","locked":false,"assignee":{"login":"cybersiddhu","id":48740,"avatar_url":"https://avatars.githubusercontent.com/u/48740?v=3","gravatar_id":"","url":"https://api.github.com/users/cybersiddhu","html_url":"https://github.com/cybersiddhu","followers_url":"https://api.github.com/users/cybersiddhu/followers","following_url":"https://api.github.com/users/cybersiddhu/following{/other_user}","gists_url":"https://api.github.com/users/cybersiddhu/gists{/gist_id}","starred_url":"https://api.github.com/users/cybersiddhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cybersiddhu/subscriptions","organizations_url":"https://api.github.com/users/cybersiddhu/orgs","repos_url":"https://api.github.com/users/cybersiddhu/repos","events_url":"https://api.github.com/users/cybersiddhu/events{/privacy}","received_events_url":"https://api.github.com/users/cybersiddhu/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/dictyBase/Modware-Loader/milestones/14","labels_url":"https://api.github.com/repos/dictyBase/Modware-Loader/milestones/14/labels","id":876435,"number":14,"title":"Sprint #6","description":"","creator":{"login":"cybersiddhu","id":48740,"avatar_url":"https://avatars.githubusercontent.com/u/48740?v=3","gravatar_id":"","url":"https://api.github.com/users/cybersiddhu","html_url":"https://github.com/cybersiddhu","followers_url":"https://api.github.com/users/cybersiddhu/followers","following_url":"https://api.github.com/users/cybersiddhu/following{/other_user}","gists_url":"https://api.github.com/users/cybersiddhu/gists{/gist_id}","starred_url":"https://api.github.com/users/cybersiddhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cybersiddhu/subscriptions","organizations_url":"https://api.github.com/users/cybersiddhu/orgs","repos_url":"https://api.github.com/users/cybersiddhu/repos","events_url":"https://api.github.com/users/cybersiddhu/events{/privacy}","received_events_url":"https://api.github.com/users/cybersiddhu/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":2,"state":"open","created_at":"2014-11-21T22:43:34Z","updated_at":"2015-01-16T21:48:35Z","due_on":"2015-01-21T06:00:00Z","closed_at":null},"comments":3,"created_at":"2015-01-16T21:36:42Z","updated_at":"2015-01-20T22:52:22Z","closed_at":null,"body":"## Context\r\nThis is the case when the same organism is sequenced multiple times, then there has to be a way to capture the information. Once we have the information we will be able to figure out which particular build this genome belongs or this is the canonical build etc.\r\nAt dictybase, this will happen in case the strain is sequenced multiple times. This will be seldom but it is definitely possible, for example, multiple research group has sequenced the canonical AX4 strain. It's wise to have the provision in the data model.\r\n\r\n\r\n## Data model for implementation\r\nAs discussed in the chado mailing list, there are few options with their ups and downs.\r\n* Each assembly has its own organism entry. It could be done by appending assembly id to the species value. However, it creates fake organism entries that is less desirable. You also have to do extra work to get all information for a particular organism with different assembly. \r\n* Create an assembly feature for grouping. It will modeled around the concept of GenBank and Ensembl handling of assemblies where you create a chado feature to represent the assembly. An example genome assembly [page](http://www.ncbi.nlm.nih.gov/assembly/GCA_000004695) from NCBI. The information gather from this could easily be turned into an chado feature for assembly. The assembled features like chromosomes and contigs will be its biological descendants.\r\n__Representing the entry:__  Use ```assembly``` cvterm to type the feature and feature relation ```member_of``` to relate the chromosomes and contigs.\r\n__Notes:__ The downside would be to have that fake grouping feature, this will be always hacky. The other solution is to plug in the chado group module, however it is still not in final shape to be released.\r\n* Use ```analysis``` and ```analysis_feature``` tables to model the assembly. Represent the assembly as an ```analysis``` entry and then link the required feature through ```analysis_feature```. This is quite clear, straightforward, less hacky and chado centric. So, lets __stick__ with this model.\r\n\r\n## Other avenues to explore\r\n* As mentioned before ```chado group module```, have been discussed and being actively or planned to be used in few places.\r\n* Karl Pinc's data model about storing genomes from different population of the same organism."},"comment":{"url":"https://api.github.com/repos/dictyBase/Modware-Loader/issues/comments/70751352","html_url":"https://github.com/dictyBase/Modware-Loader/issues/149#issuecomment-70751352","issue_url":"https://api.github.com/repos/dictyBase/Modware-Loader/issues/149","id":70751352,"user":{"login":"cybersiddhu","id":48740,"avatar_url":"https://avatars.githubusercontent.com/u/48740?v=3","gravatar_id":"","url":"https://api.github.com/users/cybersiddhu","html_url":"https://github.com/cybersiddhu","followers_url":"https://api.github.com/users/cybersiddhu/followers","following_url":"https://api.github.com/users/cybersiddhu/following{/other_user}","gists_url":"https://api.github.com/users/cybersiddhu/gists{/gist_id}","starred_url":"https://api.github.com/users/cybersiddhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cybersiddhu/subscriptions","organizations_url":"https://api.github.com/users/cybersiddhu/orgs","repos_url":"https://api.github.com/users/cybersiddhu/repos","events_url":"https://api.github.com/users/cybersiddhu/events{/privacy}","received_events_url":"https://api.github.com/users/cybersiddhu/received_events","type":"User","site_admin":false},"created_at":"2015-01-20T22:52:22Z","updated_at":"2015-01-20T22:52:22Z","body":"[Asked](http://generic-model-organism-system-database.450254.n5.nabble.com/Multiple-assemblies-and-chado-group-module-td5713034.html) chado schema group for ideas."}}