synonyms for neuron degeneration (MP:0003224)

[slaulederkind]

It would be nice if you could add the narrow synonyms entered below for neuron degeneration (MP:0003224). Similar synonyms for children terms of neuron degeneration (MP:0003224) would also be nice.

2. Synonyms (e.g., absent spleen)

1. neuron loss
2. loss of neurons

[sbello]

We have loss of X for some neuron types as independent terms with the definition:
"loss of the [X], commonly due to an apoptotic event"
These are typically siblings of degeneration terms when both terms exist (see: loss of hippocampal neurons (MP:0003240) and hippocampal neuron degeneration (MP:0000811). So I don't think 'narrow' is the correct synonym type.

Questions:
Should 'X neuron loss' be a parent to 'X neuron degeneration'? Then we could add 'X neuron loss' as a broad synonym when the loss term does not exist. Note, neuron apoptosis is in the physiology branch so loss could not be a parent to both.

I think neuron loss is typically used when the cause of the loss is unclear but need to review the annotations. Do we really need both loss and degeneration terms?

Additionally, degeneration is frequently defined in the MP as 'retrogressive impairment of function or destruction' but the terms are placed under morphology so 'impairment of function' seems wrong. In PATO, degeneration is under structure on the morphology branch. So based on that the placement is okay but the text definition is misleading. We need to review these terms in general.

Looking at annotations to MP:0003224 (neuron degeneration) there are 1945 annotations + notes and in this result set there are 592 mentions of 'loss'

loss of dopaminergic neurons (MP:0003244) - has a couple of notes that mention degeneration of cells
loss of hippocampal neurons (MP:0003240) - single annotation that mentions degeneration

[sbello]

change loss of motor neuron to be a related synonym to motor neuron degeneration

[anna-anagnostop]

abnormalDegenerationOfAnatomicalEntity.yaml

https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormalDegenerationOfAnatomicalEntity.yaml

[sbello]

To do:

• collect the various core definitions of 'degeneration'
• develop a standard definition for degeneration that is clearly morphology based and modifies but does not fundamentally change the meaning
• review the eqs for degeneration terms - most using degenerate from PATO (see https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormalDegenerationOfAnatomicalEntity.yaml)
• review annotations - should loss and degeneration terms be combined? If not is a sibling relation correct?
• [ ]

[sbello]

Also we have the term decreased hippocampus cell number but decreased hippocampus pyramidal cell number is not a child of this term