renaud / neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules
GNU Lesser General Public License v3.0
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combining EphysProp and EpyhsTrigger #20

Closed stripathy closed 9 years ago

stripathy commented 9 years ago

EphysProps and EphysTriggers should be combined into a neuroNER if they are conjoined by a hyphen: fast-spiking cell // fast not part of neuroNER, but identified as EphysProp non-fast-spiking cell // non-fast not part of neuroNER, but identified as EphysProp spiking cell //

See example below:

screenshot from 2015-07-01 18 07 46

stripathy commented 9 years ago

make these as tests and then close issue

stripathy commented 9 years ago

Here's a test for 'fast-spiking basket cell'

{
"EphysTrigger": [
    {
      "begin": 5,
      "end": 12
    }
],
"Morphology": [
    {
      "begin": 13,
      "end": 19
    }
  ],
  "EphysProp": [
    {
      "begin": 0,
      "end": 4
    }
  ],
  "Electrophysiology": [
    {
      "begin": 0,
      "end": 12
    },
  ]
}
renaud commented 9 years ago

The test will be as below, it's the same as your json:

{
  "Morphology": [
    {
      "begin": 13,
      "end": 19,
      "properties": {
        "ontologyId": "HBP_MORPHOLOGY:0000019"
      }
    }
  ],
  "EphysTrigger": [
    {
      "begin": 5,
      "end": 12,
      "properties": {
        "ontologyId": "HBP_EPHYS_TRIGGER:0000003"
      }
    }
  ],
  "Electrophysiology": [
    {
      "begin": 0,
      "end": 12
    }
  ],
  "EphysProp": [
    {
      "begin": 0,
      "end": 4,
      "properties": {
        "ontologyId": "HBP_EPHYS:0000080"
      }
    }
  ],
  "Neuron": [
    {
      "begin": 0,
      "end": 24
    }
  ]
}