Update ratio-related pattern templates

This commit intends to 1. Update the attribute_ratio DOS-DP templates. 2. Add some ratio-type trait examples to test the templates. If applied, this commit will fix #312.
obophenotype · May 21, 2024 · 229bf5f · 229bf5f
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diff --git a/src/patterns/data/default/attribute_ratio.tsv b/src/patterns/data/default/attribute_ratio.tsv
@@ -1,4 +1,7 @@
-defined_class	defined_class_name	entity	entity_name	attribute1	attribute1_name	attribute2	attribute2_name	exact_synonyms	xrefs	orcid
-OBA:2050350	urine sodium and potassium proportionality	UBERON:0001088	urine	OBA:1000949	sodium(1+) amount	OBA:1000948	potassium(1+) amount	urinary sodium to potassium ratio|urinary sodium to potassium proprotionality		https://orcid.org/0000-0001-6757-4744|https://orcid.org/0000-0001-8314-2140 
-OBA:2045455	height-adjusted body mass index	UBERON:0000468	multicellular organism	OBA:VT0001259	body mass	PATO:0000119	height	height-adjusted BMI	CMO:0000105	https://orcid.org/0000-0001-8314-2140
-OBA:2045456	body mass index	UBERON:0000468	multicellular organism	OBA:VT0001259	body mass	PATO:0001708	1-D extent	BMI	CMO:0000105	https://orcid.org/0000-0001-8314-2140
+defined_class	defined_class_name	attribute1	attribute1_name	attribute2	attribute2_name	exact_synonyms	broad_synonym	narrow_synonym	related_synonym	xrefs	orcid
+OBA:2050350	urinary sodium to potassium ratio	OBA:VT0006274	urine sodium amount	OBA:2050095	urine potassium amount						https://orcid.org/0000-0001-6757-4744|https://orcid.org/0000-0001-8314-2140 
+OBA:2045455	body mass to height ratio	OBA:VT0001259	body mass	OBA:VT0001253	body height			body mass index|BMI|height-adjusted BMI|body mass index		http://purl.obolibrary.org/obo/CMO_0000105	https://orcid.org/0000-0001-8314-2140
+OBA:2045456	body mass to body extent ratio	OBA:VT0001259	body mass	OBA:2045460	body extent	body mass to height or length ratio		body mass index|BMI		http://purl.obolibrary.org/obo/CMO_0000105	https://orcid.org/0000-0001-8314-2140
+OBA:2045457	waist to height ratio	OBA:1001085	waist circumference	OBA:VT0001253	body height	waist height ratio|waist-height ratio|WHtR					https://orcid.org/0000-0001-8314-2140
+OBA:2045458	visceral to subcutaneous adipose tissue ratio	OBA:2045224	visceral adipose tissue quantity	OBA:0004504	subcutaneous adipose tissue amount	visceral:subcutaneous adipose tissue ratio					https://orcid.org/0000-0001-8314-2140
+OBA:2045459	digit length ratio	OBA:VT0002544	digit length	OBA:VT0002544	digit length						https://orcid.org/0000-0001-8314-2140
diff --git a/src/patterns/data/default/entity_attribute.tsv b/src/patterns/data/default/entity_attribute.tsv
@@ -62,7 +62,7 @@ OBA:1000012	germ tube septin ring length	GO:0032172	germ tube septin ring	PATO:0
 OBA:1000017	mating projection tip length	GO:0043332	mating projection tip	PATO:0000122	length			
 OBA:1000018	nucleus shape	GO:0005634	nucleus	PATO:0000052	shape			
 OBA:1000021	cotyledon size	PO:0020030	cotyledon	PATO:0000117	size			
-OBA:1000024	subcutaneous adipose tissue proportionality to	UBERON:0002190	subcutaneous adipose tissue	PATO:0001470	proportionality to			
+OBA:1000024	subcutaneous adipose tissue ratio	UBERON:0002190	subcutaneous adipose tissue	PATO:0001470	ratio			
 OBA:1000025	breast size	UBERON:0000310	breast	PATO:0000117	size			
 OBA:1000027	thyroid gland volume	UBERON:0002046	thyroid gland	PATO:0000918	volume			
 OBA:1000028	membrane permeability	GO:0016020	membrane	PATO:0000970	permeability			
@@ -185,7 +185,7 @@ OBA:VT0000192	mineral amount	CHEBI:46662	mineral	PATO:0000070	amount
 OBA:VT0000217	leukocyte quantity	CL:0000738	leukocyte	PATO:0000070	amount			
 OBA:VT0000222	neutrophil quantity	CL:0000775	neutrophil	PATO:0000070	amount			
 OBA:VT0000223	monocyte quantity	CL:0000576	monocyte	PATO:0000070	amount			
-OBA:VT0000237	blood cell quantity	CL:0000988	hematopoietic cell	PATO:0001555	has number of			
+OBA:VT0000237	blood cell quantity	CL:0000081	blood cell	PATO:0000070	amount	blood cell count		
 OBA:VT0000240	hematopoiesis location trait	GO:0030097	hemopoiesis	PATO:0000140	position			
 OBA:VT0000248	erythrocyte size trait	CL:0000232	erythrocyte	PATO:0000117	size			
 OBA:VT0000254	cerebrospinal fluid amount	UBERON:0001359	cerebrospinal fluid	PATO:0000918	volume			
@@ -409,7 +409,7 @@ OBA:VT0002785	Leydig cell quantity	CL:0000178	Leydig cell	PATO:0001555	has numbe
 OBA:VT0002809	spinal cord size trait	UBERON:0002240	spinal cord	PATO:0000117	size			
 OBA:VT0002845	aorta mass	UBERON:0000947	aorta	PATO:0000125	mass			
 OBA:VT0002846	aorta capacity	UBERON:0000947	aorta	PATO:0000918	volume			
-OBA:VT0002847	glomerular filtration trait	GO:0003094	glomerular filtration	PATO:0001470	proportionality to			
+OBA:VT0002847	glomerular filtration trait	GO:0003094	glomerular filtration	PATO:0001236	process quality			
 OBA:VT0002876	thyroid gland physiology trait	UBERON:0002046	thyroid gland	PATO:0001509	functionality			
 OBA:VT0002909	adrenal gland physiology trait	UBERON:0002369	adrenal gland	PATO:0001509	functionality			
 OBA:VT0002918	paired-pulse facilitation trait	CHEBI:50459	2,5-diphenylfuran	PATO:0001629	aggregated			
@@ -4342,9 +4342,9 @@ OBA:2045295	brain connectivity attribute	UBERON:0000955	brain	PATO:0000141	struc
 OBA:2045296	defense response to other organism process attribute	GO:0098542	defense response to other organism	PATO:0001236	process quality			https://orcid.org/0000-0001-8314-2140
 OBA:2045328	DNA methylation process attribute	GO:0009008	DNA-methyltransferase activity	PATO:0001236	process quality			https://orcid.org/0000-0001-8314-2140|https://orcid.org/0000-0001-6757-4744
 OBA:2045372	gestational blood glucose level	UBERON:0009097	gravid organism	OBA:VT0000188	blood glucose amount			https://orcid.org/0000-0001-8314-2140
-OBA:2045389	leukocyte ratio	CL:0000738	leukocyte	OBA:2045457	quantity ratio			https://orcid.org/0000-0001-8314-2140
-OBA:2045390	basophil ratio	CL:0000767	basophil	OBA:2045457	quantity ratio			https://orcid.org/0000-0001-8314-2140
-OBA:2045391	eosinophil ratio	CL:0000771	eosinophil	OBA:2045457	quantity ratio			https://orcid.org/0000-0001-8314-2140
+OBA:2045389	leukocyte ratio	CL:0000738	leukocyte	PATO:0001470	ratio			https://orcid.org/0000-0001-8314-2140
+OBA:2045390	basophil ratio	CL:0000767	basophil	PATO:0001470	ratio			https://orcid.org/0000-0001-8314-2140
+OBA:2045391	eosinophil ratio	CL:0000771	eosinophil	PATO:0001470	ratio			https://orcid.org/0000-0001-8314-2140
 OBA:2045406		CL:0002535	epithelial cell of cervix	PATO:0000051	morphology			https://orcid.org/0000-0001-8314-2140
 OBA:2045407	response to bacterium process attribute	GO:0009617	response to bacterium	PATO:0001236	process quality			https://orcid.org/0000-0001-8314-2140
 OBA:2045408	amniotic fluid pH	UBERON:0000173	amniotic fluid	PATO:0001842	acidity			https://orcid.org/0000-0001-8314-2140
@@ -4386,5 +4386,4 @@ OBA:2050351	breast density	UBERON:0000310	breast	PATO:0001019	mass density	breas
 OBA:VT1000472	subcutaneous adipose mass	UBERON:0002190	subcutaneous adipose tissue	PATO:0000125	mass			https://orcid.org/0000-0001-8314-2140
 OBA:VT0010482	body fat mass	UBERON:0001013	adipose tissue	PATO:0000125	mass			https://orcid.org/0000-0001-8314-2140
 OBA:2050418	voice quality trait	UBERON:0034681	vocal organ	PATO:0001519	sound quality		PMID:37294764	https://orcid.org/0000-0001-6757-4744
-OBA:2045459	digit length ratio	UBERON:0002544	digit	OBA:2045458	length ratio	digit length proportionality		https://orcid.org/0000-0001-8314-2140
-OBA:2045460	blood cell count ratio	CL:0000081	blood cell	OBA:2045457	quantity ratio	blood cell count proportionality		https://orcid.org/0000-0001-8314-2140
+OBA:2045460	body extent	UBERON:0000468	multicellular organism	PATO:0001708	1-D extent			https://orcid.org/0000-0001-6757-4744
diff --git a/src/patterns/dosdp-patterns/attribute_ratio.yaml b/src/patterns/dosdp-patterns/attribute_ratio.yaml
@@ -1,93 +1,72 @@
-pattern_name: proportion_of_attributes
-pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/proportion_of_attributes.yaml
-
-description: 'Use this pattern for traits that that depend on the
-    proportions (ratios, or inverse ratios) of two measurable
-    attributes. Although calculating a ratio is not commutative, the
-    trait category as defined here is indifferent about the direction of
-    the ratio between the two quantifiable attributes, i.e. A:B and B:A
-    are assumed to represent reciprocal aspects of the same
-    proportionality (as an abstract biological attribute) that share the
-    same genetic determinants.
-    For example, the sodium to potassium ratio is assumed to have the
-    same genetic determinants in an organism as the potassium to sodium
-    ratio, and the resulting reciprocal values are genetically not
-    independent from each other.'
+pattern_name: attribute_ratio
+pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/attribute_ratio.yaml
+
+description: 'Use this pattern for compound attributes where the
+    magnitude of the attribute depends on the ratio of two
+    measurable characteristics.'
 
 # examples
 # http://www.ebi.ac.uk/efo/EFO_0009884	# urinary sodium to potassium ratio
 # http://www.ebi.ac.uk/efo/EFO_0005191	# waist height ratio
 # http://www.ebi.ac.uk/efo/EFO_0004767	# visceral:subcutaneous adipose tissue ratio
 
-
 contributors:
   - https://orcid.org/0000-0001-6757-4744  # Arwa Ibrahim
   - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
   - https://orcid.org/0000-0002-7356-1779  # Nicolas Matentzoglu
 
 
 classes:
-  proportionality_to: PATO:0001470
+  ratio: PATO:0001470
   quality: PATO:0000001
+  external_resource: xsd:anyURI
 
 relations:
-  has_part: BFO:0000051
+  has_numerator: RO:0020202
+  has_denominator: RO:0020203
   characteristic_of_part_of: RO:0002314
 
 annotationProperties:
   exact_synonym: oio:hasExactSynonym
+  broad_synonym: oio:hasBroadSynonym
+  narrow_synonym: oio:hasNarrowSynonym
   related_synonym: oio:hasRelatedSynonym
   xref: oio:hasDbXref
   contributor: dct:contributor
 
 vars:
-  entity: "'thing'"
   attribute1: "'quality'"
   attribute2: "'quality'"
 
 data_list_vars:
   orcid: xsd:anyURI  # ORCID of contributor
   exact_synonyms: xsd:string  # add a list of exact synonyms
-  xrefs: xsd:anyURI  # add a list of external references
+  xrefs: external_resource  # add a list of external references
 
 name:
-  text: "%s and %s proportionality in %s"
+  text: "%s to %s ratio"
   vars:
     - attribute1
     - attribute2
-    - entity
 
 def:
-  text: "A trait that affects the proportionality of %s to %s in %s."
+  text: "A compound attribute that is the ratio of %s to %s."
   vars:
     - attribute1
     - attribute2
-    - entity
   annotations:
     - annotationProperty: xref
-      text: "AUTO:patterns/patterns/proportion_of_attributes"
+      text: "AUTO:patterns/patterns/attribute_ratio"
 
 annotations:
   - annotationProperty: exact_synonym
-    text: "the proportionality of %s to %s in %s"
-    vars:
-      - attribute1
-      - attribute2
-      - entity
-    annotations:
-      - annotationProperty: xref
-        text: "AUTO:patterns/patterns/proportion_of_attributes"
-  - annotationProperty: exact_synonym
-    text: "%s to %s or %s to %s ratio in %s"
+    text: "the ratio of %s to %s"
     vars:
       - attribute1
       - attribute2
-      - attribute2
-      - attribute1
-      - entity
     annotations:
       - annotationProperty: xref
-        text: "AUTO:patterns/patterns/proportion_of_attributes"
+        text: "AUTO:patterns/patterns/attribute_ratio"
 
   - annotationProperty: contributor
     value: orcid
@@ -99,11 +78,9 @@ xref:
   value: xrefs
 
 equivalentTo:
-  text: "('proportionality_to'
-    and ('has_part' some %s)
-    and ('has_part' some %s))
-    and ('characteristic_of_part_of' some %s)"
+  text: "('ratio'
+    and ('has_numerator' some %s)
+    and ('has_denominator' some %s))"
   vars:
     - attribute1
     - attribute2
-    - entity