{"action":"created","issue":{"url":"https://api.github.com/repos/renaud/neuroNER/issues/19","labels_url":"https://api.github.com/repos/renaud/neuroNER/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/renaud/neuroNER/issues/19/comments","events_url":"https://api.github.com/repos/renaud/neuroNER/issues/19/events","html_url":"https://github.com/renaud/neuroNER/issues/19","id":91166196,"number":19,"title":"Proposal for identifying ephys terms","user":{"login":"renaud","id":75369,"avatar_url":"https://avatars.githubusercontent.com/u/75369?v=3","gravatar_id":"","url":"https://api.github.com/users/renaud","html_url":"https://github.com/renaud","followers_url":"https://api.github.com/users/renaud/followers","following_url":"https://api.github.com/users/renaud/following{/other_user}","gists_url":"https://api.github.com/users/renaud/gists{/gist_id}","starred_url":"https://api.github.com/users/renaud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/renaud/subscriptions","organizations_url":"https://api.github.com/users/renaud/orgs","repos_url":"https://api.github.com/users/renaud/repos","events_url":"https://api.github.com/users/renaud/events{/privacy}","received_events_url":"https://api.github.com/users/renaud/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-26T06:10:34Z","updated_at":"2015-06-26T06:12:48Z","closed_at":null,"body":"\r\n\r\n### Define the following as an electrophysiology trigger:\r\n\r\n    DECLARE EphysTrigger;\r\n    \"(?i)((non[- ]?)?(spik(ing|e)|firing|bursting|stuttering|chattering|accomm?odating|adapting)” ->   EphysTrigger;\r\n\r\n    DECLARE NeuronProperty EphysProp;\r\n\r\nAfter defining the Ephys Trigger term, we need to find **EphysProp terms which come before or after the trigger word**, like those in the modifying terms list below.\r\n\r\n### modifying terms: \r\n\r\ncontinuous\r\nirregular\r\nregular\r\nspontaneous\r\ndelay/late\r\nclassical\r\nintrinsic\r\nfast\r\nnon-fast\r\n\r\netc.\r\nMore terms in the .robo file: https://www.dropbox.com/s/mncj52cme66f66g/hbp_electrophysiology_ontology.robo?dl=0\r\n\r\nBut unlike for Protein, we need to give an ontology id for the terms in the EphysTrigger too (if a neuron is characterized as bursting, we need to know that too).\r\n\r\n### Test cases:\r\n\r\n[fast regular-spiking] cell\r\n[MOD] [MOD] [TRIG]\r\n\r\n[adapting] cell\r\n[]\r\n\r\nnon-accommodating cell\r\nnon-accomodating cell\r\nirregular spiking cell\r\nirregular bursting cell\r\nirregularly spiking cell\r\ncell irregularly bursting\r\nslowly adapting cell\r\n\r\nslow non-adapting spiking cell\r\n[mod][trig?][trig][neuron trigger]\r\n"},"comment":{"url":"https://api.github.com/repos/renaud/neuroNER/issues/comments/115532590","html_url":"https://github.com/renaud/neuroNER/issues/19#issuecomment-115532590","issue_url":"https://api.github.com/repos/renaud/neuroNER/issues/19","id":115532590,"user":{"login":"renaud","id":75369,"avatar_url":"https://avatars.githubusercontent.com/u/75369?v=3","gravatar_id":"","url":"https://api.github.com/users/renaud","html_url":"https://github.com/renaud","followers_url":"https://api.github.com/users/renaud/followers","following_url":"https://api.github.com/users/renaud/following{/other_user}","gists_url":"https://api.github.com/users/renaud/gists{/gist_id}","starred_url":"https://api.github.com/users/renaud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/renaud/subscriptions","organizations_url":"https://api.github.com/users/renaud/orgs","repos_url":"https://api.github.com/users/renaud/repos","events_url":"https://api.github.com/users/renaud/events{/privacy}","received_events_url":"https://api.github.com/users/renaud/received_events","type":"User","site_admin":false},"created_at":"2015-06-26T06:12:48Z","updated_at":"2015-06-26T06:12:48Z","body":"\r\n\r\n* I did split the Ephys obo files in two, please validate them (in `neuroNER/resources/bluima/neuroner/`)\r\n    * `hbp_electrophysiology_ontology.robo`\r\n    * `hbp_electrophysiology-triggers_ontology.robo`\r\n* In them, I reordered the ids. *Please confirm that this is not a problem for you.** Else I will roll it back. In the future, we should avoid reordering ids...\r\n* I wrote some rules to capture them\r\n* the following tests have been implemented:\r\n\r\n\r\n"}}