How to handle non diseases in EFO?

[dhimmel]

explodes #35 (comment)

We currently ignore non-diseases, by only training and predicting on terms that are diseases as per get_disease_nodes.

Our training labels only apply to diseases. Therefore, I think it makes sense to continue training only on diseases. However, there is the possibility that we could:

1. create an is_disease marker column that is part of the output
2. compute features for non-diseases
3. compute predictions for non-diseases

While predictions on non-diseases would likely be of lower quality due to the lack of training coverage, many of the same concepts of grouping terms versus more specific terms would still apply. Users could then decide to discard all predictions when is_disease is False to continue with the current behavior.

There could be a benefit to having precision predictions for non-diseases. For example, classifications of symptoms (one example being pain) would make sense along a precision axis:

@yonromai: I'll bring this up with the data team at our next meeting, so no need to do anything until then. CC @eric-czech

[dhimmel]

We were missing injury, poisoning or other complication as a non-disease TA (fixed in 1b59233). However, this does let us see what some classifications are like on non-disease terms:

Expand for table

efo_otar_slim_id	efo_label	class_new
EFO:0010686	muscle strain	02-disease-root
EFO:0010725	aseptic loosening	02-disease-root
EFO:0010581	organophosphate poisoning	02-disease-root
EFO:0011061	toxicity	03-disease-area
EFO:0020910	thermal burn	02-disease-root
EFO:0020930	immune-mediated adverse reaction	02-disease-root
EFO:0600078	Achilles tendon injury	01-disease-subtype
EFO:0000546	injury	03-disease-area
EFO:0002687	ischemia reperfusion injury	02-disease-root
MONDO:0037747	spinal injury	01-disease-subtype
MONDO:0700220	disease related to transplantation	03-disease-area
MONDO:0700222	disease related to hematopoietic stem cell transplant	03-disease-area
OTAR:0000009	injury, poisoning or other complication	03-disease-area
MONDO:0800373	carbon monoxide poisoning	03-disease-area
EFO:0007430	persian gulf syndrome	02-disease-root
EFO:0009485	eye injury	01-disease-subtype
EFO:0009518	complication	03-disease-area
EFO:0009582	sprain	02-disease-root
EFO:0009508	leg injury	02-disease-root
EFO:0009574	intoxication	02-disease-root
EFO:0009503	caustic injury	02-disease-root
EFO:0009565	radiation-induced disorder	03-disease-area
EFO:0009504	crush injury	02-disease-root
EFO:0009816	perineal laceration during delivery	02-disease-root
EFO:0009516	burn	03-disease-area
EFO:0009509	limb injury	03-disease-area
EFO:0009658	adverse effect	01-disease-subtype
EFO:0009434	death by undetermined cause	01-disease-subtype
EFO:0009521	dislocation	02-disease-root
EFO:0009887	intrathoracic organ injury	02-disease-root
EFO:0009506	heart injury	02-disease-root
EFO:0008546	poisoning	03-disease-area
EFO:0009507	knee injury	02-disease-root
EFO:0009527	frostbite	02-disease-root
EFO:0009888	trauma complication	01-disease-subtype
EFO:0009623	nose injury	02-disease-root
EFO:0009502	abdominal injury	02-disease-root
EFO:0009525	foreign body	03-disease-area
EFO:0009476	neck injury	02-disease-root
EFO:0009519	device complication	02-disease-root
EFO:0009833	kidney injury	02-disease-root
EFO:0009505	head injury	02-disease-root
MONDO:0019088	post-transplant lymphoproliferative disease	01-disease-subtype
EFO:1001291	ciguatera poisoning	02-disease-root
EFO:1001788	Eye Burns	02-disease-root
EFO:1001328	fluoride poisoning	02-disease-root
EFO:1001518	heavy metal poisoning	03-disease-area
EFO:1001756	Acrodynia	02-disease-root
EFO:1001373	Multiple Organ Failure	02-disease-root
EFO:1001768	cadmium poisoning	02-disease-root
​

Many make sense, but some seem off like "spinal injury" and "adverse effect" as high precision. So this makes me reconsider whether it entirely makes sense to apply the model outside of its trained domain.