add harrison subset (#8553)

* add harrison subset * Create harrison-view.sparql Run this with ``` robot --catalog catalog-v001.xml reason -i mondo-edit.obo query --use-graphs true -f tsv --query ../sparql/reports/harrison-view.sparql reports/report-reason-harrison-view.tsv ``` * add to harrison_subset --------- Co-authored-by: Nico Matentzoglu <[email protected]> Co-authored-by: katiermullen <[email protected]>
monarch-initiative · Jan 10, 2025 · 77ada1d · 77ada1d
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diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo
@@ -33650,6 +33650,7 @@ replaced_by: MONDO:0015766
 id: MONDO:0002025
 name: psychiatric disorder
 def: "A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia." [NCIT:C2893]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of mental health" NARROW []
@@ -34265,6 +34266,7 @@ id: MONDO:0002051
 name: integumentary system disorder
 alt_id: MONDO:0045027
 def: "A disease involving the integumental system." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of integumental system" EXACT [MONDO:patterns/location_top]
@@ -34856,6 +34858,7 @@ replaced_by: MONDO:0019306
 id: MONDO:0002081
 name: musculoskeletal system disorder
 def: "A disease involving the musculoskeletal system." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of musculoskeletal system" EXACT [MONDO:patterns/location_top]
@@ -35713,6 +35716,7 @@ intersection_of: disease_has_location UBERON:0001264 ! pancreas
 id: MONDO:0002118
 name: urinary system disorder
 def: "A disease involving the renal system." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of renal system" EXACT [MONDO:patterns/location_top]
@@ -41855,6 +41859,7 @@ relationship: has_characteristic MONDO:0021152 {source="OMIMPS:237450"} ! inheri
 id: MONDO:0002409
 name: auditory system disorder
 def: "A disease involving the auditory system." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "auditory disease" EXACT []
@@ -47307,6 +47312,7 @@ intersection_of: disease_has_location UBERON:0000014 ! zone of skin
 id: MONDO:0002657
 name: breast disorder
 def: "A disease involving the breast." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 synonym: "breast disease" EXACT [DOID:3463, MONDO:patterns/location, NCIT:C26709]
 synonym: "breast disease or disorder" EXACT [MONDO:design_pattern, MONDO:patterns/location]
@@ -71994,6 +72000,7 @@ id: MONDO:0003900
 name: connective tissue disorder
 def: "A disease involving the connective tissue." [https://orcid.org/0000-0002-6601-2165]
 comment: Following clinical usage of the term 'connective tissue disorder' this grouping excludes some diseases affecting tissues classically considered to be connective tissue, such as bone.
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "connective tissue disease" EXACT [DOID:65, MONDO:patterns/location, NCIT:C26729]
@@ -80007,6 +80014,7 @@ property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/4002/non-fun
 id: MONDO:0004335
 name: digestive system disorder
 def: "A disease or disorder that involves the digestive system." [MONDO:design_pattern]
+subset: harrisons_view
 subset: rare_grouping
 synonym: "alimentary system disease" EXACT [DOID:77]
 synonym: "digestive disease" EXACT [NCIT:C2990]
@@ -93808,6 +93816,7 @@ relationship: disease_has_location UBERON:0001133 ! cardiac muscle tissue
 id: MONDO:0004995
 name: cardiovascular disorder
 def: "A disease involving the cardiovascular system." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "cardiovascular disease" EXACT [NCIT:C2931]
@@ -95251,6 +95260,7 @@ replaced_by: MONDO:0003847
 id: MONDO:0005039
 name: reproductive system disorder
 def: "A disease involving the reproductive system." [https://orcid.org/0000-0002-6601-2165]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of reproductive system" EXACT [MONDO:patterns/location_top]
@@ -95469,6 +95479,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
 id: MONDO:0005046
 name: immune system disorder
 def: "A disorder resulting from an abnormality in the immune system." [NCIT:C3507]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of immune system" EXACT [MONDO:patterns/location_top]
@@ -96251,6 +96262,7 @@ id: MONDO:0005071
 name: nervous system disorder
 def: "A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves." [NCIT:C26835]
 comment: 'psychiatric disorder' is not classified as a 'nervous system disorder' in Mondo (though it is often as such): the hallmarks of psychiatric disorders are based in behavior and emotional state, and the relation with nervous system malfunction or damage is not always clearly determined.
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of nervous system" EXACT [MONDO:patterns/location_top]
@@ -96770,6 +96782,7 @@ property_value: IAO:0000589 "renal cell carcinoma (disease)" xsd:string
 id: MONDO:0005087
 name: respiratory system disorder
 def: "A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma." [NCIT:C26871]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of respiratory system" EXACT [MONDO:patterns/location_top]
@@ -107635,6 +107648,7 @@ id: MONDO:0005550
 name: infectious disease
 def: "A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent in humans. It can be transmitted by direct or indirect contact." [NCIT:C26726]
 comment: Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself. {source="EFO:0005741"}
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "clinical infection" NARROW []
@@ -108127,6 +108141,7 @@ name: hematologic disorder
 def: "A disease involving the hematopoietic system." [https://orcid.org/0000-0002-6601-2165]
 comment: placeholder for lymphoid disease {source="EFO:0005803"}
 subset: disease_grouping
+subset: harrisons_view
 subset: ordo_group_of_disorders {source="Orphanet:97992"}
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
@@ -430582,6 +430597,7 @@ id: MONDO:0019040
 name: chromosomal disorder
 def: "Clinical conditions caused by an abnormal chromosome constitution in which there is extra or missing chromosome material (either a whole chromosome or a chromosome segment). (from Thompson et al., Genetics in Medicine, 5th ed, p429)" [MESH:D025063]
 subset: disease_grouping
+subset: harrisons_view
 subset: ordo_group_of_disorders {source="Orphanet:68335"}
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
@@ -436747,6 +436763,7 @@ name: premature aging syndrome
 def: "Changes in the organism associated with senescence, occurring at an accelerated rate." [MESH:D019588]
 subset: disease_grouping
 subset: gard_rare {source="GARD:19017", source="MONDO:GARD"}
+subset: harrisons_view
 subset: ordo_group_of_disorders {source="Orphanet:79389"}
 subset: otar {source="MONDO:OTAR"}
 subset: rare
@@ -490618,6 +490635,7 @@ property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/2751/hunter-
 id: MONDO:0024458
 name: disorder of visual system
 def: "A disease that involves the visual system." [MONDO:patterns/location]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 synonym: "disease of visual system" EXACT [MONDO:patterns/location_top]
@@ -493332,6 +493350,7 @@ id: MONDO:0024623
 name: otorhinolaryngologic disease
 def: "Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases." [MESH:D010038]
 comment: Editor note: consider uberon class
+subset: harrisons_view
 subset: rare_grouping
 synonym: "disease, ENT" RELATED [MESH:D010038]
 synonym: "disease, otolaryngologic" RELATED [MESH:D010038]
@@ -529989,6 +530008,7 @@ is_obsolete: true
 id: MONDO:0044970
 name: mitochondrial disease
 subset: clingen {source="MONDO:CLINGEN"}
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 subset: rare_grouping
 xref: MEDGEN:155901 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
@@ -530237,6 +530257,7 @@ is_obsolete: true
 id: MONDO:0044991
 name: upper digestive tract disorder
 def: "A disease or disorder that involves the upper digestive tract." [MONDO:patterns/location]
+subset: harrisons_view
 subset: otar {source="MONDO:OTAR"}
 synonym: "disease of upper digestive tract" EXACT [MONDO:patterns/location_top]
 synonym: "disease or disorder of upper digestive tract" EXACT []

diff --git a/src/sparql/reports/harrison-view.sparql b/src/sparql/reports/harrison-view.sparql
@@ -0,0 +1,15 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX MONDO: <http://purl.obolibrary.org/obo/MONDO_>
+
+SELECT DISTINCT ?mondo_id ?label ?harrison WHERE {
+  ?mondo_id rdfs:subClassOf+ <http://purl.obolibrary.org/obo/MONDO_0700096> ;
+            rdfs:label ?label .
+
+  	OPTIONAL {
+    	?mondo_id rdfs:subClassOf+ ?ancestor .
+  		 ?ancestor oboInOwl:inSubset <http://purl.obolibrary.org/obo/mondo#harrisons_view> .
+    	BIND("YES" as ?harrison)
+	}
+}