Merge pull request #608 from monarch-initiative/INCLUDE

Close #329 

Added new surgery by site pattern.
Updated
MAXO:0000479	orthopedic surgery
MAXO:0000024	surgical procedure on the eye
MAXO:0000946     nervous system surgical procedure
MAXO:0000012      surgery by site
MAXO:0025005      nasolacrimal duct surgery

added
MAXO:0001513	skin surgery
MAXO:0001503	digestive system surgery
MAXO:0001504	alimentary part of gastrointestinal system surgery
MAXO:0025001	cardiovascular system surgery
MAXO:0001506	circulatory system surgery
MAXO:0001507	musculoskeletal system
MAXO:0001508	genitourinary system surgery	
MAXO:0001510	pancreatic system surgery
MAXO:0001511	renal collecting system surgery
MAXO:0001512	reproductive system surgery
MAXO:0001514	vascular system surgery
MAXO:0001515	skeletal system surgery

src/ontology/reports/maxo-base.owl-obo-report.tsv

@@ -539,6 +539,17 @@ WARN	missing_superclass	MAXO:0001498	rdfs:subClassOf
 WARN	missing_superclass	MAXO:0001499	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0001500	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0001501	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001503	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001504	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001506	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001507	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001508	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001510	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001511	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001512	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001513	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001514	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001515	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0010004	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0010005	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0010006	rdfs:subClassOf	

src/ontology/reports/maxo-edit.owl-obo-report.tsv

@@ -539,6 +539,17 @@ WARN	missing_superclass	MAXO:0001498	rdfs:subClassOf
 WARN	missing_superclass	MAXO:0001499	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0001500	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0001501	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001503	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001504	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001506	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001507	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001508	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001510	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001511	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001512	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001513	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001514	rdfs:subClassOf	
+WARN	missing_superclass	MAXO:0001515	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0010004	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0010005	rdfs:subClassOf	
 WARN	missing_superclass	MAXO:0010006	rdfs:subClassOf	

src/ontology/reports/owldef-self-reference-violation.csv

@@ -1,2 +1,2 @@
 term
-http://purl.obolibrary.org/obo/MAXO_0001269
+http://purl.obolibrary.org/obo/MAXO_0000012

src/patterns/data/manual/surgery_by_location.tsv

@@ -0,0 +1,17 @@
+defined_class	defined_class_name	location	location_label	created_by	date	defined_class_definition	comment	xref	syns
+MAXO:0001513	skin surgery	UBERON:0000014	zone of skin	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001503		UBERON:0001007	digestive system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001504		UBERON:0005409	alimentary part of gastrointestinal system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0025001		UBERON:0004535	cardiovascular system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				cardiac surgery|heart surgery
+MAXO:0001506		UBERON:0001009	circulatory system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001507		UBERON:0004122	genitourinary system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001508		UBERON:0002204	musculoskeletal system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0000946		UBERON:0001016	nervous system	http://orcid.org/0000-0001-7941-2961	2021-08-12T19:44:10Z				neurosurgical procedure
+MAXO:0001510		UBERON:2001371	pancreatic system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001511		UBERON:0004100	renal collecting system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001512		UBERON:0000990	reproductive system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001514		UBERON:0001004	respiratory system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0001515		UBERON:0007798	vascular system	http://orcid.org/0000-0001-7941-2961	2023-10-19T20:39:14Z				
+MAXO:0000479	orthopedic surgery	UBERON:0001434	skeletal system		2020-01-20T17:51:02Z				orthopedics surgery
+MAXO:0000024	surgical procedure on the eye	UBERON:0000019	carmera-type eye		2023-02-24T15:25:58Z				eye surgery|eye procedure|surgery of the eye
+MAXO:0025005		UBERON:0002392	nasolacrimal duct						dacryocystorhinostomy|tear duct surgery

src/patterns/data/todo/MAXO_availableIDs.txt

@@ -1,18 +1,6 @@
 
-MAXO:0001502
-MAXO:0001503
-MAXO:0001504
-MAXO:0001505
-MAXO:0001506
-MAXO:0001507
-MAXO:0001508
+
 MAXO:0001509
-MAXO:0001510
-MAXO:0001511
-MAXO:0001512
-MAXO:0001513
-MAXO:0001514
-MAXO:0001515
 MAXO:0001516
 MAXO:0001517
 MAXO:0001518

src/patterns/dosdp-patterns/surgery_by_location.yaml

@@ -0,0 +1,76 @@
+pattern_name: surgery_by_location
+pattern_iri: http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml
+description: "Surgical procedure of a particular organ."
+
+contributors:
+  - https://orcid.org/0000-0001-7941-2961
+
+classes:
+  surgerybysite: MAXO:0000012
+  location: UBERON:0001062
+
+relations:
+  has_input: RO:0002233
+  part_of: BFO:0000050
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym 
+  created_by: dcterms:creator
+  date: dc:date
+  comment: rdfs:comment
+  xref: oio:hasDbXref
+
+vars:
+  location: "'location'"
+
+data_vars:
+  date: "'date'"
+  created_by: "'created_by'"
+  comment: "'comment'"
+  xref: "database cross reference"
+data_list_vars:
+  syns: xsd:string
+name:
+  text: "surgical procedure on %s"
+  vars:
+   - location
+
+annotations:
+  - annotationProperty: exact_synonym
+    text: "%s surgical procedure"
+    vars:
+     - location
+
+  - annotationProperty: date
+    text: "%s"
+    vars:
+     - date
+
+  - annotationProperty: created_by
+    text: "%s"
+    vars:
+     - created_by
+
+  - annotationProperty: comment
+    text: "%s"
+    vars:
+     - comment
+
+  - annotationProperty: xref
+    text: "%s"
+    vars:
+     - xref
+
+exact_synonym:
+  value: syns
+
+def:
+  text: "Any surgical procedure conducted on the %s."
+  vars:
+    - location
+
+equivalentTo:
+  text: "'surgerybysite' and 'has_input' some ('part_of' some %s)"
+  vars:
+    - location
+

src/patterns/pattern.owl

@@ -15,6 +15,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_52210>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/HP_0000118>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000001>))
+Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000012>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000033>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000034>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000056>))
@@ -81,6 +82,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/removal_by_locat
 Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/removal_by_phenotype.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/repair_by_location.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml>))
+Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/surgical_repair_by_location.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/swab_by_location.yaml>))
 Declaration(Class(<http://purl.obolibrary.org/obo/maxo/patterns/therapeuticprocedure_by_location.yaml>))
@@ -544,6 +546,19 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/maxo/patterns/s
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml> "'location' specimen collection"^^xsd:string)
 EquivalentClasses(<http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000547> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>))))
 
+# Class: <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> (surgical procedure on 'location')
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "Any surgical procedure conducted on the 'location'."^^xsd:string)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/dcterms_creator> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'created_by'"^^xsd:string)
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'date'"^^xsd:string)
+AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "surgery_by_location"^^xsd:string)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "database cross reference"^^xsd:string)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'location' surgical procedure"^^xsd:string)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "xsd:string"^^xsd:string)
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "'comment'"^^xsd:string)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> "surgical procedure on 'location'"^^xsd:string)
+EquivalentClasses(<http://purl.obolibrary.org/obo/maxo/patterns/surgery_by_location.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MAXO_0000012> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002233> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>))))
+
 # Class: <http://purl.obolibrary.org/obo/maxo/patterns/surgical_repair_by_location.yaml> ('location' repair)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/maxo/patterns/surgical_repair_by_location.yaml> "Surgical procedure to repair a 'location'."^^xsd:string)