search

SciCrunch / NIF-Ontology

NIF Standard Ontologies (NIFSTD)
Creative Commons Attribution 4.0 International
53 stars 17 forks source link

phenotype based neurons #48

Open tgbugs opened 8 years ago

tgbugs commented 8 years ago

needed for a number of issues

tgbugs commented 8 years ago

also import fbbt.owl for this

tgbugs commented 7 years ago

Review here: https://github.com/SciCrunch/NIF-Ontology/commit/ebb80d8ecd76fb2d1c5e114c627c92d1d9fe97ff#commitcomment-19578799

tgbugs commented 7 years ago

Note. There are 3 kinds of neurons that we need to be able to deal with.

  1. Data specific neurons, e.g. rat hippocampus pyramidal neuron (using WAXHOLM or something like that)
  2. Generic neurons, e.g. hippocampus neuron (using UBERON)
  3. Definitional neurons, e.g. the current 'Neocortex pyramidal neuron' which is like the generic neurons but is a summary version (we should be able to validate these against data we collect). Essentially an assertion that 'every' pyramidal neuron will have these associated phenotypes, this is the entity that encodes the phenotypes that cooccur with P(neurotransmitter | morphology) = 1.
tgbugs commented 6 years ago

Note that we are missing a generic basket cell based on morphological classification in the ontology and interlex.

tgbugs commented 6 years ago

Integrate the curated data from https://github.com/tgbugs/nlxeol/blob/master/neuron_data_curated.csv.

tgbugs commented 5 years ago

NIFEXT:68 has a weird synonym to chopper.