No phenotype information from SCKAN for CNS neuron populations.

[dbrnz]

e.g. Keast-20, Ardell-1, etc.

[tgbugs]

There aren't meaningful phenotypes for these beyond that they are projection neurons that are ascending or descending, but that information is redundant with the location phenotypes so they are not listed.

[dbrnz]

These neuron population paths are identified as cns on the current flatmap -- could SCKAN specify a phenotype indicating this? We can then flag missing phenotype information as an error.

[tgbugs]

Could you add a check for ilxtr:hasSomaLocatedIn where the object is one of the known locations for the CNS? The alternative would be to add one more cypher query that gets checks if a neuron has a soma location in the CNS and if so ignores an empty phenotype. I think that is going to be preferable on our end to minimize redundant axioms.

The quick fix is for me to get you a list of uberon ids that part of the central nervous system.

[tgbugs]

splen is missing all, should have 4, my process is broken sstom should have 4, and 7-14

[nickerso]

sstom should have 4, and 7-14

just looking into ilxtr:neuron-type-sstom-11 as an example where the phenotype doesn't make it through and found that here the check is made for predicates of ilxtr:hasPhenotype or ilxtr:hasCircuitRolePhenotype whereas ilxtr:neuron-type-sstom-11 has a predicate of ilxtr:hasFunctionalCircuitRolePhenotype - which doesn't seem to exist in interlex.

[tgbugs]

Good find. I'll submit a pr with all the phenotype predicates we use. I'm going through and adding interpretations of the phenotypes that I can.

[tgbugs]

The spleen phenotypes were all missing because the neuronTypes column was duplicated.

[tgbugs]

These are the neurons that are currently missing phenotypes now. Stomach and colon only. They are not all CNS neurons. If I can get clarification from @bdebono on sdcol l, l-prime, m, n, p and sstom 4, 5, 6 we should be able to get those wrapped up.

@bdebono I think sstom 4 is simply incorrect, maybe that phenotype was mean for 5? For sdcol l and l-prime, I think we need to refer to nitric oxide for these, because the designation of inhibitory motor may be correct for the enteric nervous system, but I can't translate that because the semantics are so radically different for those two words in particular.

[(set(), '', 'ilxtr:neuron-type-sstom-1'),
 (set(), '', 'ilxtr:neuron-type-sstom-2'),
 (set(), '', 'ilxtr:neuron-type-sstom-3'),
 (set(), 'visceral sensory neuron', 'ilxtr:neuron-type-sstom-4'),
 (set(), 'vagal afferent neuron', 'ilxtr:neuron-type-sstom-5'),
 (set(), '', 'ilxtr:neuron-type-sstom-6'),
 (set(), 'inhibitory motor neuron', 'ilxtr:neuron-type-sdcol-l'),
 (set(), 'inhibitory motor neuron', 'ilxtr:neuron-type-sdcol-l-prime'),
 (set(), 'intrinsic primary afferent neuron', 'ilxtr:neuron-type-sdcol-m'),
 (set(), 'intrinsic primary afferent neuron', 'ilxtr:neuron-type-sdcol-n'),
 (set(), 'secretomotor neuron', 'ilxtr:neuron-type-sdcol-p')]

https://github.com/SciCrunch/NIF-Ontology/commit/9d60f37fbb6b91883664e23b6ecff4282c5d6b2d

[tgbugs]

https://github.com/AnatomicMaps/map-knowledge/pull/3 should address the missing predicates issue

[tgbugs]

should be sstom-5 -> visceral sensory neuron vagal afferent neuron

[tgbugs]

sstom i - p can be enteric as well, perhaps for now we only need that designation

[tgbugs]

here is the updated report only the cns neurons in stomach are missing phenotypes at this point

[(set(), '', 'ilxtr:neuron-type-sstom-1', []),
 (set(), '', 'ilxtr:neuron-type-sstom-2', []),
 (set(), '', 'ilxtr:neuron-type-sstom-3', []),
 (set(), '', 'ilxtr:neuron-type-sstom-4', []),
 (set(), '', 'ilxtr:neuron-type-sstom-6', [])]

here are some of the bits of the type names that I am not trying to model at this time (in some cases such as the h/g connecting type we have that in the NPO representation

[(['visceral', 'vagal', 'afferent'],
  'visceral sensory vagal afferent neuron',
  'ilxtr:neuron-type-sstom-5'),
 (['intrinsic', 'afferent', 'primary'],
  'enteric intrinsic primary afferent neuron',
  'ilxtr:neuron-type-sdcol-m'),
 (['intrinsic', 'afferent', 'primary'],
  'enteric intrinsic primary afferent neuron',
  'ilxtr:neuron-type-sdcol-n'),
 (['vasodilatory'],
  'enteric vasodilatory motor neuron',
  'ilxtr:neuron-type-sdcol-o'),
 (['secretomotor'], 'enteric secretomotor neuron', 'ilxtr:neuron-type-sdcol-p'),
 (['h', 'connecting'],
  'intestinofugal neuron h connecting',
  'ilxtr:neuron-type-sdcol-q'),
 (['g', 'connecting'],
  'intestinofugal neuron g connecting',
  'ilxtr:neuron-type-sdcol-q-prime')]

[smtifahim]

@tgbugs here are the types with missing phenotypes that I found.

ilxtr:neuron-type-pancr-3   ""
ilxtr:neuron-type-pancr-5   ""
ilxtr:neuron-type-sstom-1   ""
ilxtr:neuron-type-sstom-2   ""
ilxtr:neuron-type-sstom-3   ""
ilxtr:neuron-type-sstom-4   ""
ilxtr:neuron-type-sstom-6   ""