{"action":"created","issue":{"url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/328","labels_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/328/labels{/name}","comments_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/328/comments","events_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/328/events","html_url":"https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/328","id":89355909,"number":328,"title":"Request \"fingerprint contig\", to go with FPCmap (SO:0001250)","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":[{"url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/labels/question","name":"question","color":"cc317c"},{"url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/labels/Term%20Tracker","name":"Term Tracker","color":"207de5"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-18T17:53:33Z","updated_at":"2015-06-18T17:54:11Z","closed_at":null,"body":"An FPCmap (SO:0001250) is often composed of several fingerprinted contigs (FPC). Currently there is no term for FPC.\r\nMore info:\r\nThe individual contigs are composed of several BACs (SO:0000153). The FPC map is the result of analysis of restriction site (?!) markers (SO:0001645), namely RFLP fragment (SO:0000193) markers (?!)...\r\nCan you also add a term for 'restriction site' and 'restriction site marker'?\r\nSorry for overloading one request. Cheers,\r\nDan"},"comment":{"url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/comments/113236513","html_url":"https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/328#issuecomment-113236513","issue_url":"https://api.github.com/repos/The-Sequence-Ontology/SO-Ontologies/issues/328","id":113236513,"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},"created_at":"2015-06-18T17:54:11Z","updated_at":"2015-06-18T17:54:11Z","body":"Response from Dan Bolser \r\n\r\nHi Karen,\r\nYup \"restriction enzyme cleavage junction\" == \"restriction site\".\r\nA \"restriction site marker\" is a bit more complex, so I'm tempted to drop that request for now. Technically, its an \"RFLP marker\", i.e. an \"RFLP fragment\" used as a marker.\r\nNow I think about it, FPC is a bit tricky... actually FPC was originally derived from \"FingerPrinted Contigs\" named by the software called package called 'FPC'. Here is how they describe the software:\r\n\"FPC takes as input a set of clones and their restriction fragments (called Bands) and assembles the clones into contigs\"\r\nSee:\r\n* http://www.agcol.arizona.edu/software/fpc/\r\n* http://www.agcol.arizona.edu/software/fpc/summary.html\r\nHowever, on the web and in the literature, the term 'FPC contig' has become used to name the resulting 'contigs'. It is important to note that this is an overloading of the term 'contig', because they don't mean sequence contigs, they mean 'BAC contigs' or 'physical contigs'... I'm not browsing the ontology just now, but I wonder if similar terms already exist, providing a clear precedent for creating a term 'FPC Contig' or similar...\r\nYour definition of 'FPC' is accurate. Hopefully the above answers your question \"FPC is a contig?\"?\r\nThanks for taking the time to work on this.\r\nDan."}}