search

open-physiology / apinatomy-models

Working and published ApiNATOMY models
2 stars 4 forks source link

Phenotype information is missing for some connectivity paths #29

Closed dbrnz closed 1 year ago

dbrnz commented 1 year ago

The following have no phenotype:

ilxtr:neuron-type-sdcol-k
ilxtr:neuron-type-sdcol-m
ilxtr:neuron-type-sdcol-q-prime
ilxtr:neuron-type-sdcol-i
ilxtr:neuron-type-sdcol-n
ilxtr:neuron-type-sdcol-q
ilxtr:neuron-type-sdcol-p
ilxtr:neuron-type-sstom-2
ilxtr:neuron-type-sstom-11
ilxtr:neuron-type-sstom-13
ilxtr:neuron-type-sstom-3
ilxtr:neuron-type-sstom-14
ilxtr:neuron-type-sstom-4
ilxtr:neuron-type-sstom-12
ilxtr:neuron-type-sstom-6
ilxtr:neuron-type-sstom-1
dbrnz commented 1 year ago

See also issue #15

tgbugs commented 1 year ago

https://github.com/SciCrunch/NIF-Ontology/blob/78403b4895e8bbb47595c3d446c6d0d300382818/ttl/generated/neurons/apinat-pops-more.ttl#L1065

You are likely failing to handle the enteric phenotype object and the hasCircuitRolePhenotype/hasFunctionalCircuitRolePhenotype predicates.

https://github.com/AnatomicMaps/map-knowledge/pull/3 should have resolved the issue

dbrnz commented 1 year ago

Thanks.

The list of missing/unknown phenotypes is now down to:

ilxtr:neuron-type-sstom-2 phenotype [] is unknown
ilxtr:neuron-type-sstom-11 phenotype ['ILX:0105486'] is unknown
ilxtr:neuron-type-sstom-13 phenotype ['ILX:0105486'] is unknown
ilxtr:neuron-type-sstom-3 phenotype [] is unknown
ilxtr:neuron-type-sstom-14 phenotype ['ILX:0104003'] is unknown
ilxtr:neuron-type-sstom-4 phenotype [] is unknown
ilxtr:neuron-type-sstom-12 phenotype ['ILX:0104003'] is unknown
ilxtr:neuron-type-sstom-6 phenotype [] is unknown
ilxtr:neuron-type-sstom-1 phenotype [] is unknown
tgbugs commented 1 year ago

Looks like Excitatory and Inhibitory, which means hasFunctionalCircuitRolePhenotype might be missing?

tgbugs commented 1 year ago

We think that this issue is mostly resolved with the exception of the 'central nervous phenotype' cases. The hasFunctionalCircuitRolePhenotype issue should be fixed in the anatomical-maps python code if it is not then we should open an issue on that repository.

The issue with those is that we don't want to add an addition defining axiom which would be redundant with the hasSomaLocation axioms, but we also would like to be able to distinguish cases where no additional phenotype information is expected, from cases where it is incorrectly missing.

Given that all neurons currently have the data we expect them to have I am closing this issue, we can open another related to confusion between expected missing and incorrectly missing.