Proposal for identifying ephys terms

[renaud]

Define the following as an electrophysiology trigger:

DECLARE EphysTrigger;
"(?i)((non[- ]?)?(spik(ing|e)|firing|bursting|stuttering|chattering|accomm?odating|adapting)” ->   EphysTrigger;

DECLARE NeuronProperty EphysProp;

After 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.

modifying terms:

continuous irregular regular spontaneous delay/late classical intrinsic fast non-fast

etc. More terms in the .robo file: https://www.dropbox.com/s/mncj52cme66f66g/hbp_electrophysiology_ontology.robo?dl=0

But 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).

Test cases:

[fast regular-spiking] cell [MOD] [MOD] [TRIG]

[adapting] cell []

non-accommodating cell non-accomodating cell irregular spiking cell irregular bursting cell irregularly spiking cell cell irregularly bursting slowly adapting cell

slow non-adapting spiking cell [mod][trig?][trig][neuron trigger]

[renaud]

• I did split the Ephys obo files in two, please validate them (in neuroNER/resources/bluima/neuroner/)
  • hbp_electrophysiology_ontology.robo
  • hbp_electrophysiology-triggers_ontology.robo
• 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...
• I wrote some rules to capture them
• the following tests have been implemented:
  • slow non-adapting spiking cell
  • cell irregularly bursting