{"action":"opened","issue":{"url":"https://api.github.com/repos/renaud/neuroNER/issues/35","labels_url":"https://api.github.com/repos/renaud/neuroNER/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/renaud/neuroNER/issues/35/comments","events_url":"https://api.github.com/repos/renaud/neuroNER/issues/35/events","html_url":"https://github.com/renaud/neuroNER/issues/35","id":101505828,"number":35,"title":"more permissive about missing terms that doesn't terminate the neuroNER prematurely","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":0,"created_at":"2015-08-17T20:41:19Z","updated_at":"2015-08-17T20:41:19Z","closed_at":null,"body":"From Shreejoy:\r\n\r\n_You can see a whole list of terms that I tried below (Based on hand-curated neuron-NER-compliant terms that I had my ugrad curator Brenna annotate based on neuroelectro articles, terms here: https://www.dropbox.com/s/npzmdfuvqpo144q/neuroelectro_neuron_long_names.txt?dl=0) . The biggest thing is that the missing terms are very often brain region terms that are being not identified since we made the switch to ABA-only terms. These examples illustrate that I think we should be more permissive when terms are missing, and not terminate the neuroNER phrase at the first instance of a missing term, like sensorimotor or prelimbic or amplitude or whatever (ideally this would be done through part of speech info and identifying coherent sentence phrases). Of course this'll lose precision, but it'll gain recall, especially in getting us longer neuroNER phrases, which is kind of what our project is all about, right?_\r\n\r\nLayer 6 sensorimotor cortexnonpyramidalVGluT1expressingneurons\r\n Layer 5primaryauditorycortexregularspikingneurons\r\nLayer 2/3 frontal pyramidalcell projecting perirhinal cortex\r\n Layer 2/3perirhinal cortexpyramidalcellprojecting to L5perirhinal cortexpyramidalcell\r\n somatosensorycortexlayer 5bpyramidalcell\r\n Layer 6somatosensorycortexpyramidalneurons\r\nLayer 5 medial prefrontal cortex prelimbic pyramidalneurons\r\n Layer 5neocortexpyramidalneuron\r\n Layer 5somatosensorycortexpyramidalneurons\r\n Layer 5visualcortexfastspikinginterneurons\r\nLayer 5 somatosensory cortex large amplitude pyramidalcells\r\n Layer 5asomatosensorybarrel cortexpyramidalneurons\r\n Regularspikinglayer Vpyramidalneuronsofsomatosensorycortex \r\nLayer 5 medial prefrontal prelimbic cortexpyramidalneurons\r\nLayer 5 medial prefrontal cortex infralimbic fastspikinginterneurons\r\nLayer 5 Fast Spikinginterneuronsexpressingparvalbuminpositive\r\nLayer 5 frontal pyramidalcells projecting perirhinal cortex \r\nLayer 2/3 sensorimotor cortexpyramidalneurons\r\nLayer 5 sensorimotor cortexpyramidalneurons\r\nLayer 4 sensorimotor cortexspinystellateneurons\r\nHypothalamus GnRH-expressing neuron\r\nneostriatum NPY-expressingSOM-expressingnNOS-expressing GABAergic plateau-depolarization low-threshold spikeinterneurons\r\n neostriatumNPY-expressingGABAergicneurogliaformcell\r\n piriform cortexpyramidalneuron\r\n piriform cortexpyramidalneurons\r\n piriform cortexpyramidalneurons\r\n piriform cortexpyramidalneurons\r\n piriform cortexpyramidalneurons\r\nLayer 4 somatosensory cortex barrel column spinystellateneurons\r\nLayer 3 somatosensory barrel column pyramidalneurons\r\n Layer 2somatosensorybarrel cortexpyramidalneurons\r\nLayer 5a somatosensory cortex barrel column small tuft pyramidalneurons\r\nLayer 5b somatosensory cortex barrel column extensive tuft pyramidalneurons\r\nLayer 6 somatosensory cortex barrel column short pyramidalneurons \r\nCA1 Oriens-Lacunosum Moleculare Interneurons\r\nCA1 Oriens-Lacunosum Moleculare Interneurons\r\nPurkinjeneurons\r\n Layer 5somatosensorybarrel cortexpyramidalneurons\r\n RapheNeuron\r\n RapheNeuron\r\n RapheNeuron\r\n RapheNeuron\r\nstratum oriens interneurons\r\nstratum oriens interneurons\r\nstratum oriens interneurons\r\nstratum oriens interneurons\r\nLayer 5 frontal pyramidal corticalthalamic projecting cell\r\nLayer 2/3perirhinal cortexpyramidalcell projecting to Corticothalamic cellpyramidalcell\r\n Layer 5perirhinal cortexpyramidalcellprojecting to Layer 2/3perirhinal cortexpyramidalcell\r\nLayer 5 somatosensory cortex small amplitude pyramidalcells\r\n Layer 6somatosensorycortexpyramidalneurons\r\nLayer 5 medial prefrontal cortex prelimbic pyramidalneurons\r\nLayer 5 medial prefrontal cortex infralimbic pyramidalneurons\r\nLayer 5 medial prefrontal cortex infralimbic non-fastspikinginterneurons\r\nLayer 6 primaryvisualcortex corticofugalneurons\r\n Layer 5primaryauditorycortexintrinsicallyburstingneurons\r\n Layer 5somatosensorycortexregularfiringpyramidalneurons\r\n Layer 5somatosensorycortexburstfiringpyramidalneurons\r\nLayer 5 somatosensory cortex weak burstfiringpyramidalneurons\r\nLayer 5 somatosensory cortex strong burstfiringpyramidalneurons\r\n Layer 5visualcortexpyramidalneurons\r\nSubstantia nigra pars reticulatadopaminergiccell\r\nTrigeminal ganglionneurons\r\nTrigeminal ganglionneurons\r\n Multipolarburstingcell\r\nFast spikingmultipolarcells \r\nMagnocellular preoptic nucleus/substantia innominatacholinergicneurons \r\nMagnocellular preoptic nucleus/substantia innominatanoncholinergicneurons\r\nNormotopic pyramidalneurons\r\nHeterotopic pyramidalneurons\r\nPFC PyramidalNeurons\r\nPFC PyramidalNeurons\r\nPFC PyramidalNeurons\r\nUrethral AfferentNeuron\r\n Dorsal raphe nucleusserotonergicneuron\r\nLayer V Barrel CorticalNeuron\r\n Dorsal raphe nucleusnon-serotonergicneuron\r\nLayer 5 Somatosensory andmotorcortex of corticothalamic projecting pyramidalneurons\r\nLayer 5 somatosensory andmotorcortex of corticotrigeminal projecting pyramidalneurons\r\nLayer 5 somatosensory andmotorcortex corticostriatal projecting neurons\r\nLayer 5 somatosensory andmotorcortex of callosal projecting pyramidalneurons\r\nHippocampus CA1 regularspikingpyramidalneurons\r\nHippocampus CA1 Burstingpyramidalneurons\r\nVentral wing serotoninreleasingneurons of dorsal raphe\r\nLateral wing ofserotoninreleasing dorsal rapheneurons\r\nPOR pyramidalneurons\r\nPOR multipolarneurons\r\nPOR bituftedneurons\r\nRegular-spiking POR neurons \r\nFast-spiking POR neurons \r\nLow-threshold spiking POR neurons \r\nLumbar flexor motoneurons \r\nLumbar extensor motoneurons \r\nStellate-like \\u201cSag\\u201d neuronsinlayer II of mEC\r\nIntermediate Sag neurons \r\nPyramidallike \\u201cNo Sag\\u201d neuronsinlayer III of mEC\r\nDorsal hippocampus CA1 pyramidalcell\r\nVentral hippocampus CA1 pyramidalcell\r\nsensorimotor cortex sideways-oriented layer 2pyramidalcells\r\n Visualcortexlayer 5regularspikingpyramidalcell\r\n Visualcortexlayer 5burstingpyramidalcell\r\nventromedial interneuron\r\nlumbar dorsal root ganglionneuron\r\nsmall dorsal root ganglioncell\r\nmedium dorsal root ganglioncell\r\nCerebral corticalneurons\r\nNon-bursting trigeminal principalsensoryneurons\r\nBursting trigeminal principalsensoryneurons\r\nsilent nucleus pontis caudalis neurons\r\nSpontaneuous firing nucleus pontis caudalis neurons\r\nTonicfiring parasympathetic preganglionic lumbosacral neurons\r\nPhasic firing parasympathetic preganglionic lumbosacral neurons\r\nPetrosal Ganglia\r\nGeniculate Ganglia\r\nLayer IV Excitatory Barrel Neurons\r\nLayer IV Excitatory Barrel Neurons\r\nintermediolateral cell column sympathetic preganglionic neurons\r\nVasomotor sympathetic preganglionic neurons\r\nthoracolumbar dorsal root ganglioncell\r\nlumbosacral dorsal root ganglioncell\r\nHippocampal Medial Septal Diagonal Band Complex GABAnergic Neuron\r\nHippocampal Medial Septal Diagonal Band Complex CholinergicNeuron\r\nPrefrontal CortexNeurons\r\nStriatal SpinyProjectionNeurons\r\n\r\n\r\n\r\n\r\n"}}