EFO-OBA mapping (morphology and related traits)

[ar-ibrahim]

• will map terms from oba-efo-unreviewed.dosdp.tsv
• filtered by quality_labels: morphology, size, shape, length, circumference and thickness.

subject_id	subject_label	match_type	quality	quality_label	attribute	attribute_label
EFO:0010076	femoral neck size	Lexical	PATO:0000117	size	UBERON:0007119	femoral neck
EFO:0010949	upper face morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0001456	face
EFO:0008038	bmi-adjusted hip bone size	Lexical	PATO:0000117	size	UBERON:0001272	hip bone
EFO:0004505	telomere length	Lexical	PATO:0000122	length	GO:0005696	telomere
EFO:0007842	chin morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0008199	chin
EFO:0009286	heart relative wall thickness	Lexical	PATO:0000915	thickness	UBERON:0000948	heart
EFO:0004844	hip bone size	Lexical	PATO:0000117	size	UBERON:0001272	hip bone
EFO:0600005	ganglion cell inner plexiform layer thickness measurement	Lexical	PATO:0000915	thickness	UBERON:0000045	ganglion
EFO:0007824	hair shape measurement	Lexical	PATO:0000052	shape	UBERON:0001037	hair
EFO:0009278	cranial vault morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0004339	cranial vault
EFO:0007844	forehead morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0008200	forehead
EFO:0004577	infant head circumference	Lexical	PATO:0001648	circumference	UBERON:0000033	head
EFO:0005053	internal carotid intimal medial thickness	Lexical	PATO:0000915	thickness	UBERON:0001532	internal carotid
EFO:0007789	bmi-adjusted waist circumference	Lexical	PATO:0001648	circumference	UBERON:0037468	waist
EFO:0005852	heschl's gyrus morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0000200	gyrus
EFO:0005037	aortic root size	Lexical	PATO:0000117	size	UBERON:0010172	aortic root
EFO:0004841	digit length ratio	Lexical	PATO:0000122	length	UBERON:0002544	digit
EFO:0007821	hair morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0001037	hair
EFO:0004860	common carotid intimal medial thickness	Lexical	PATO:0000915	thickness	UBERON:0005396	carotid
EFO:0007739	left superior temporal gyrus thickness measurement	Lexical	PATO:0000915	thickness	UBERON:0002769	superior temporal gyrus
EFO:0011044	bmi-adjusted neck circumference	Lexical	PATO:0001648	circumference	UBERON:0000974	neck
EFO:0010948	lower face morphology measurement	Lexical	PATO:0000051	morphology	UBERON:0001456	face
EFO:0600002	retinal layer thickness measurement	Lexical	PATO:0000915	thickness	UBERON:0001781	retinal layer
EFO:0007117	carotid artery intima media thickness	Lexical	PATO:0000915	thickness	UBERON:0005396	carotid artery
EFO:0600004	retinal nerve fibre layer thickness measurement	Lexical	PATO:0000915	thickness	UBERON:0006134	nerve fibre
EFO:0007823	facial hair thickness measurement	Lexical	PATO:0000915	thickness	UBERON:0001037	hair
EFO:0008593	ldl particle size measurement	Lexical	PATO:0000117	size	GO:0034362	LDL particle
EFO:0004306	erythrocyte size determination	Lexical	PATO:0000117	size	CL:0000232	erythrocyte
EFO:0008594	vldl particle size measurement	Lexical	PATO:0000117	size	GO:0034361	VLDL particle
EFO:0004300	length of life	Lexical	PATO:0000122	length	UBERON:0000104	life
EFO:0008592	hdl particle size measurement	Lexical	PATO:0000117	size	GO:0034364	HDL particle

[ar-ibrahim]

Hi @rays22 and @matentzn 😊. I would like your thoughts on these 5 terms:

• The 'bmi-adjusted' terms seem to be outside the scope of OBA because they describe a change in measurement and so are not neutral. Should they be added to the efo_exclusions.sssom file?
• Not sure how to map 'digit length ratio' because the entity is described by 2 quality terms.
• The term 'erythrocyte indices' EFO:0004306 refers to red cell size, count as well as hemoglobin concentration and other blood indices like MCV etc. and so cannot be mapped to one OBA term, even as a 'skos:broadMatch'.

subject_id	subject_label	match_type	quality	quality_label	attribute	attribute_label
EFO:0008038	bmi-adjusted hip bone size	Lexical	PATO:0000117	size	UBERON:0001272	hip bone
EFO:0007789	bmi-adjusted waist circumference	Lexical	PATO:0001648	circumference	UBERON:0037468	waist
EFO:0004841	digit length ratio	Lexical	PATO:0000122	length	UBERON:0002544	digit
EFO:0011044	bmi-adjusted neck circumference	Lexical	PATO:0001648	circumference	UBERON:0000974	neck
EFO:0004306	erythrocyte size determination	Lexical	PATO:0000117	size	CL:0000232	erythrocyte