{"action":"opened","issue":{"url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/205","labels_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/205/labels{/name}","comments_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/205/comments","events_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/205/events","html_url":"https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/205","id":84641562,"number":205,"title":"Designating core promoter elements","user":{"login":"srynobio","id":1106139,"avatar_url":"https://avatars.githubusercontent.com/u/1106139?v=3","gravatar_id":"","url":"https://api.github.com/users/srynobio","html_url":"https://github.com/srynobio","followers_url":"https://api.github.com/users/srynobio/followers","following_url":"https://api.github.com/users/srynobio/following{/other_user}","gists_url":"https://api.github.com/users/srynobio/gists{/gist_id}","starred_url":"https://api.github.com/users/srynobio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/srynobio/subscriptions","organizations_url":"https://api.github.com/users/srynobio/orgs","repos_url":"https://api.github.com/users/srynobio/repos","events_url":"https://api.github.com/users/srynobio/events{/privacy}","received_events_url":"https://api.github.com/users/srynobio/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-06-03T16:08:06Z","updated_at":"2015-06-03T16:08:06Z","closed_at":null,"body":"**Reported by kchris on 2010-06-11 23:46 UTC**\nHi\r\n\r\n\\* I'd like to be able to specifically designate core promoter elements for RNA polymerase II, that are recognized by basal txn factors. A good source is this Thomas and Chiang review.\r\n\\* So, I'd like a grouping term for core promoter elements, something like below. This one is specific for RNAP II, but a parent term that would be generally applicable would be appropriate since I think this distinction is also relevant for E. coli.\r\n\r\n&gt; id: tmp:0001001 \r\n&gt; name: RNApol\\_II\\_promoter\\_core\\_element \r\n&gt; def: \"Characteristic DNA sequences required for proper assembly and orientation of the RNA polymerase II transcription preinitiation complex \\(PIC\\) and recognized by basal RNA polymerase II transcription factors.\" \\[GOC:krc, PMID:16858867 \"Thomas & Chiang 2006\"\\] \r\n&gt; relationship: part\\_of SO:0000170 \\! RNApol\\_II\\_promoter \r\nI just realized that I've phrased this term as \"core promoter element\", but given the child terms \"part\\_of\" relationships. If this term contains the word \"element\", then the child terms should probably get is\\_a relations; alternately, if this term is phrased something like \"RNApol\\_II\\_core\\_promoter\" without the word element, then the \"part\\_of\" relationship probably holds. Not sure which is better or more consistent with SO practice. \r\n\r\n\\* Some of the existing motifs currently directly under \"RNApol\\_II\\_promoter\" are these core elements, so I'd like to move them to be direct children of a new term for \"RNApol\\_II\\_core\\_promoter\", or something similar. One, \"BRE motif\" may merit some changes, since the Thomas & Chiang review \\(PMID: 16858867\\) specifies two different BRE motifs \\(upstream and downstream\\) that are both core elements. There would also be two more elements \\(BREd and DCE\\) to add. \r\n\r\nThe SO file I mailed to Karen E has my efforts on RNAP II core promoter elements, as listed in the Thomas & Chiang review.\r\n\r\nIn addition, all of the elements specifically listed for types 1, 2, and 3 RNAP III promoters would be core elements.\r\n\r\nI'll check with Jim Hu about whether we'd want to do something similar for E. coli promoters.\r\n\r\nthanks\r\n\r\n-Karen C"}}