Fixes #2671 - Clean up squamous epithelial cell and subclasses (#2962)

* Fixes #2671 - Squamous epithelial cell and subclasses Fixes #2671 - Squamous epithelial cell and subclasses * Update cl-edit.owl * updated periderm cells logical def
obophenotype · Feb 25, 2025 · 5928062 · 5928062
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diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
@@ -3202,6 +3202,7 @@ Declaration(Class(obo:PATO_0000405))
 Declaration(Class(obo:PATO_0001377))
 Declaration(Class(obo:PATO_0001408))
 Declaration(Class(obo:PATO_0001870))
+Declaration(Class(obo:PATO_0001872))
 Declaration(Class(obo:PATO_0001979))
 Declaration(Class(obo:PATO_0002064))
 Declaration(Class(obo:PATO_0010007))
@@ -4356,7 +4357,7 @@ SubClassOf(obo:CL_0000075 obo:CL_0000066)
 
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000076 "CALOHA:TS-1249")
 AnnotationAssertion(rdfs:label obo:CL_0000076 "squamous epithelial cell")
-EquivalentClasses(obo:CL_0000076 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006914)))
+SubClassOf(obo:CL_0000076 obo:CL_0000066)
 
 # Class: obo:CL_0000077 (mesothelial cell)
 
@@ -4373,7 +4374,7 @@ SubClassOf(obo:CL_0000077 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000222))
 # Class: obo:CL_0000078 (peridermal cell)
 
 AnnotationAssertion(rdfs:label obo:CL_0000078 "peridermal cell")
-SubClassOf(obo:CL_0000078 obo:CL_0000076)
+EquivalentClasses(obo:CL_0000078 ObjectIntersectionOf(obo:CL_0000076 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003055)))
 
 # Class: obo:CL_0000079 (stratified epithelial cell)
 
@@ -5913,6 +5914,7 @@ SubClassOf(obo:CL_0000239 obo:CL_0000075)
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30422572") Annotation(oboInOwl:hasDbXref "Wikipedia:Epithelium") Annotation(oboInOwl:hasDbXref "Wikipedia:Stratified_squamous_epithelium") obo:IAO_0000115 obo:CL_0000240 "A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus.")
 AnnotationAssertion(rdfs:label obo:CL_0000240 "stratified squamous epithelial cell")
 EquivalentClasses(obo:CL_0000240 ObjectIntersectionOf(obo:CL_0000079 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006915)))
+SubClassOf(obo:CL_0000240 obo:CL_0000076)
 
 # Class: obo:CL_0000241 (stratified cuboidal epithelial cell)
 
@@ -7135,7 +7137,7 @@ AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000411 "roundworm hypoderma
 AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000411 "WBbt:0007846")
 AnnotationAssertion(rdfs:comment obo:CL_0000411 "This term was originally added to CL for parity with the Worm anatomy ontology, which is dedicated to C elegans. It is not clear if it makes sense to try and generalize the concept and include in CL, and this term may be obsoleted in future. Note there is no similarity to the hypodermis in vertebrates.")
 AnnotationAssertion(rdfs:label obo:CL_0000411 "Caenorhabditis hypodermal cell")
-SubClassOf(obo:CL_0000411 obo:CL_0000076)
+SubClassOf(obo:CL_0000411 obo:CL_0000066)
 SubClassOf(obo:CL_0000411 obo:CL_0000228)
 SubClassOf(obo:CL_0000411 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_6237))
 
@@ -14427,6 +14429,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29463737") Annotation(ob
 AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0002062 "ATI")
 AnnotationAssertion(rdfs:label obo:CL_0002062 "pulmonary alveolar type 1 cell")
 EquivalentClasses(obo:CL_0002062 ObjectIntersectionOf(obo:CL_0000322 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0007585)))
+SubClassOf(obo:CL_0002062 obo:CL_0000076)
 
 # Class: obo:CL_0002063 (pulmonary alveolar type 2 cell)
 
@@ -14452,7 +14455,7 @@ AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0002063 "TII")
 AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0002063 "lung type II cell")
 AnnotationAssertion(rdfs:label obo:CL_0002063 "pulmonary alveolar type 2 cell")
 EquivalentClasses(obo:CL_0002063 ObjectIntersectionOf(obo:CL_0000322 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032940) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0043129)))
-SubClassOf(obo:CL_0002063 obo:CL_0000076)
+SubClassOf(obo:CL_0002063 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001872))
 SubClassOf(obo:CL_0002063 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4040003))
 
 # Class: obo:CL_0002064 (pancreatic acinar cell)
@@ -20211,7 +20214,7 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002620 obo:CL_0000057
 AnnotationAssertion(terms:contributor obo:CL_0002621 <https://orcid.org/0000-0003-1980-3228>)
 AnnotationAssertion(oboInOwl:creation_date obo:CL_0002621 "2011-03-14T12:46:28Z"^^xsd:dateTime)
 AnnotationAssertion(rdfs:label obo:CL_0002621 "gingival epithelial cell")
-EquivalentClasses(obo:CL_0002621 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001949)))
+EquivalentClasses(obo:CL_0002621 ObjectIntersectionOf(obo:CL_0000240 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001949)))
 
 # Class: obo:CL_0002622 (prostate stromal cell)
 
@@ -31030,6 +31033,7 @@ AnnotationAssertion(terms:date obo:CL_4030012 "2022-05-13T11:00:29Z"^^xsd:dateTi
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030012 "epithelial cell of the descending thin limb of the short loop of Henle")
 AnnotationAssertion(rdfs:label obo:CL_4030012 "kidney loop of Henle short descending thin limb epithelial cell")
 EquivalentClasses(obo:CL_4030012 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005099)))
+SubClassOf(obo:CL_4030012 obo:CL_0000076)
 SubClassOf(obo:CL_4030012 obo:CL_1001111)
 
 # Class: obo:CL_4030013 (kidney loop of Henle long descending thin limb outer medulla epithelial cell)

diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
@@ -8517,6 +8517,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000404>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000405>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000407>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000411>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000413>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000460>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000461>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000586>))
@@ -8584,13 +8585,15 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001796>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001857>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001870>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001871>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001872>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001873>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001874>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001908>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001910>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001925>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001979>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001987>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001988>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001992>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001993>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001995>))
@@ -8621,6 +8624,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002301>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002303>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002305>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002309>))
+Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002317>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002318>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002353>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002354>))
@@ -133835,6 +133839,16 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0000411> "circular")
 SubClassOf(<http://purl.obolibrary.org/obo/PATO_0000411> <http://purl.obolibrary.org/obo/PATO_0000947>)
 
+# Class: <http://purl.obolibrary.org/obo/PATO_0000413> (square)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "answers.com:answers.com") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0000413> "A shape quality inhering in a bearer by virtue of the bearer's having an equal-sided rectangular form.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/PATO_0000413> "quality")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/PATO_0000413> "PATO:0000413")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0000413> <http://purl.obolibrary.org/obo/pato#cell_quality>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0000413> <http://purl.obolibrary.org/obo/pato#value_slim>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0000413> "square")
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0000413> <http://purl.obolibrary.org/obo/PATO_0002317>)
+
 # Class: <http://purl.obolibrary.org/obo/PATO_0000460> (abnormal)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PATOC:GVG") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0000460> "A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.")
@@ -134583,6 +134597,19 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0001871> "reniform")
 SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001871> <http://purl.obolibrary.org/obo/PATO_0002008>)
 
+# Class: <http://purl.obolibrary.org/obo/PATO_0001872> (cuboid)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PATOC:MAH") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0001872> "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resemblance to a cube (a 3-D shape with a square cross section).")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PATO_0001872> "cuboidal")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/PATO_0001872> "quality")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/PATO_0001872> "block-like")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/PATO_0001872> "PATO:0001872")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0001872> <http://purl.obolibrary.org/obo/pato#cell_quality>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0001872> <http://purl.obolibrary.org/obo/pato#value_slim>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0001872> "cuboid")
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001872> <http://purl.obolibrary.org/obo/PATO_0002007>)
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001872> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0015011> <http://purl.obolibrary.org/obo/PATO_0000413>))
+
 # Class: <http://purl.obolibrary.org/obo/PATO_0001873> (cylindrical)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PATOC:MAH") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0001873> "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.")
@@ -134658,6 +134685,15 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0001987> "saccular")
 SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001987> <http://purl.obolibrary.org/obo/PATO_0002014>)
 
+# Class: <http://purl.obolibrary.org/obo/PATO_0001988> (quadrangular)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "url:http://www.oed.com/") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0001988> "A shape quality inhering in a bearer by virtue of the bearer's having four angles and four sides.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/PATO_0001988> "quality")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/PATO_0001988> "PATO:0001988")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0001988> <http://purl.obolibrary.org/obo/pato#value_slim>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0001988> "quadrangular")
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001988> <http://purl.obolibrary.org/obo/PATO_0002006>)
+
 # Class: <http://purl.obolibrary.org/obo/PATO_0001992> (cellularity)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PATOC:GVG") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0001992> "An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.")
@@ -135002,6 +135038,25 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/PATO_0002309> "
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0002309> "fiber shaped")
 SubClassOf(<http://purl.obolibrary.org/obo/PATO_0002309> <http://purl.obolibrary.org/obo/PATO_0002226>)
 
+# Class: <http://purl.obolibrary.org/obo/PATO_0002317> (parallelogram)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "wikipedia:Parallelogram") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0002317> "A convex quadrilateral is a parallelogram if and only if any one of the following statements are true:
+1. Each diagonal divides the quadrilateral into two congruent triangles with the same orientation.
+2. The opposite sides are congruent in pairs.
+3. The diagonals bisect each other.
+4. The opposite angles are congruent in pairs.
+5. The sum of the squares of the sides equals the sum of the squares of the diagonals. (This is the parallelogram law)
+6.It possesses rotational symmetry.
+7.One pair of opposite sides are parallel and congruent.
+8.Two pairs of adjacent angles are supplementary.")
+AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/PATO_0002317> <https://orcid.org/0000-0002-2061-091X>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/PATO_0002317> "2011-10-12T12:33:07Z")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/PATO_0002317> "quality")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/PATO_0002317> "PATO:0002317")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/PATO_0002317> <http://purl.obolibrary.org/obo/pato#value_slim>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0002317> "parallelogram")
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0002317> <http://purl.obolibrary.org/obo/PATO_0001988>)
+
 # Class: <http://purl.obolibrary.org/obo/PATO_0002318> (superelliptic)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "wiktionary:superellipse") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0002318> "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt")

diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt
@@ -35,4 +35,5 @@ PATO:0070047
 PATO:0070061
 PATO:0040072
 PATO:0002354
-PATO:0010007
+PATO:0010007
+PATO:0001872