text:
import $ivy.`net.sourceforge.owlapi:owlapi-distribution:4.5.16`
import $ivy.`com.outr::scribe-slf4j:2.7.12`
import org.semanticweb.owlapi.apibinding.OWLManager
import org.semanticweb.owlapi.model._
import org.semanticweb.owlapi.vocab.OWLFacet
import java.io.File
import scala.collection
import scala.collection.mutable
import scala.jdk.CollectionConverters._
@main
def main(id_range_file: os.Path) = {
    val o = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(id_range_file.toIO))
    val allMyFacets = mutable.ListBuffer.empty[MyFacet]
    for (dt <- o.getDatatypesInSignature().asScala) {
        val defs = o.getAxioms(dt)
        for (ax <- defs.asScala) {
            val range = ax.getDataRange()
            val f = new MyFacet()
            f.id = dt.toString()
            range.accept(new OWLDataRangeVisitor() {
                override
                def visit(owlDatatype: OWLDatatype) = ()
                override
                def visit(owlDataOneOf: OWLDataOneOf) =  ()
                override
                def visit(owlDataComplementOf: OWLDataComplementOf) =  ()
                override
                def visit(owlDataIntersectionOf: OWLDataIntersectionOf) = ()
                override
                def visit(owlDataUnionOf: OWLDataUnionOf) = ()
                override
                def visit(owlDatatypeRestriction: OWLDatatypeRestriction) = {
                    for (fr <- owlDatatypeRestriction.getFacetRestrictions().asScala) {
                        var i = fr.getFacetValue().parseInteger()
                        if(fr.getFacet().equals(OWLFacet.MIN_INCLUSIVE)) {
                            f.min = i
                        } else if(fr.getFacet().equals(OWLFacet.MAX_INCLUSIVE)) {
                            f.max = i
                        } else if(fr.getFacet().equals(OWLFacet.MIN_EXCLUSIVE)) {
                            i += 1
                            f.min = i
                        } else if(fr.getFacet().equals(OWLFacet.MAX_EXCLUSIVE)) {
                            i -= 1
                            f.max = i
                        } else {
                            log("Unknown range restriction: "+fr)
                        }
                    }
                }
            })
            log("Testing range: "+f)
            testFacetViolation(f,allMyFacets)
            allMyFacets.append(f)
        }
    }
}
def testFacetViolation(f: MyFacet , allMyFacets: collection.Seq[MyFacet]) = {
    for (f_p <- allMyFacets) {
        if (((f.min <= f_p.max) && (f_p.min <= f.max))) {
            throw new IllegalStateException(f + " overlaps with " + f_p + "!")
        }
    }
}
def log(o: Object) = {
    println(o.toString())
}
class MyFacet {
    var min: Int = _
    var max: Int = _
    var id: String = _
    override
    def toString(): String = {
        return "Facet{" + id + "}[min:" + min + " max:" + max + "]"
    }
}

repo_name: obophenotype/upheno

repo_language: Makefile

mime_type: text/plain


_comment: Created with OWL2VOWL (version 0.3.7), http://vowl.visualdataweb.org

value: Decreased or reduced ability to move 'anatomical entity'.

type: label

identifier: title

undefined: decreased 'anatomical entity' mobility

value: An abnormally early start time of 'biological process'.

value: abnormallyPrematureBiologicalProcess

undefined: premature 'biological process'

value: Delayed 'biological process'.

value: abnormallyDelayedBiologicalProcess

undefined: delayed 'biological process'

value: decreased 'biological_process'.

undefined: decreased 'biological_process'

value: An abnormal level of 'chemical entity'.

value: abnormalLevelOfChemicalEntity

undefined: abnormal 'chemical entity' level

value: Complete wasting (loss) of 'anatomical entity' tissue that was once present.

identifier: hasExactSynonym

value: loss of 'anatomical entity' due to degeneration

undefined: missing 'anatomical entity' due to degeneration

value: distance decreased between 'anatomical entity1' and 'anatomical entity2'

value: Decreased distance between 'anatomical entity1' and 'anatomical entity2'.

undefined: decreased distance between 'anatomical entity1' and 'anatomical entity2'

value: anomaly in the ability to move 'anatomical entity'.

value: abnormalMobilityOfAnatomicalEntity

undefined: abnormal 'anatomical entity' mobility

value: An abnormal amount of role in the 'independent continuant'.

undefined: abnormal role 'independent continuant' level

value: distance abnormal between 'anatomical_entity1' and 'anatomical_entity2'

value: abnormal distance between 'anatomical_entity1' and 'anatomical_entity2'.

value: longer 'anatomical entity'

value: longer, increased length of, 'anatomical entity'

undefined: increased length of the 'anatomical entity'

value: The presence of a reduced number of 'cellular component'.

value: Reduced number of 'cellular component'

undefined: Decreased number of 'cellular component'

value: A morphological abnormality of the 'anatomical entity' in the 'independent continuant'.

value: Abnormal morphology of the 'anatomical entity' in the 'independent continuant'

undefined: abnormal 'anatomical entity' morphology in the 'independent continuant'

value: A deviation from the normal size of the 'anatomical entity'.

value: abnormal size of the 'anatomical entity'

value: abnormalSizeOfAnatomicalEntity

undefined: abnormal size of 'anatomical entity'

value: An abnormality in the cell differentiation of the 'cell type'.

value: abnormalCellDifferentiation

undefined: abnormal 'cell type' cell differentiation

value: A decrease in the level of 'chemical entity' in 'independent continuant'.

undefined: decreased level of 'chemical entity' in 'independent continuant'

value: Extra 'anatomical entity'

value: The presence of an increased number of 'anatomical entity'.

undefined: Increased number of 'anatomical entity'

value: Any abnormal duplication of the 'anatomical entity' in 'independent continuant'.

value: abnormally duplicated 'anatomical entity' in 'independent continuant'

undefined: abnormal duplication of 'anatomical entity' in 'independent continuant'

value: An increase in the size of the 'anatomical entity'.

value: enlarged 'anatomical entity'

undefined: increased size of the 'anatomical entity'

value: altered number of 'anatomical entity's in 'independent continuant'

value: abnormal number of 'anatomical entity's in 'independent continuant'

value: Any structural anomaly that causes there to be an abnormal number 'anatomical entity' in 'independent continuant'.

undefined: abnormal number of anatomical entities of type 'anatomical entity' in 'independent continuant'

value: An increase in the size of the 'anatomical entity' in the 'independent continuant'.

value: enlarged 'anatomical entity' in 'independent continuant'

undefined: increased size of the 'anatomical entity' in 'independent continuant'

value: abnormal increased 'anatomical entity' coiling

value: Abnormally increased coiling of the 'anatomical entity'.

undefined: abnormally increased coiling of 'anatomical entity'

value: Absent or undetectable level of 'molecular function'.

value: decreased sensitivity of organism to 'entity'

value: Increased resistance of organism to 'entity'.

undefined: increased resistance of organism to 'entity'

value: increased level of 'chemical entity' in 'independent continuant'

value: An increase in the level of 'chemical entity' in 'independent continuant'.

undefined: increased level of 'chemical entity' in 'independent continuant'

value: An increased occurrence of 'biological_process'.

undefined: increased occurrence of 'biological_process'

value: Any structural anomaly of the 'cellular component'.

undefined: abnormal morphology of 'cellular component'

value: Any unspecified morphological anomaly of part of the 'anatomical entity', such as, for example, abnormal shape or colour.

value: abnormal morphology of 'anatomical entity'

value: An abnormally blistered 'anatomical entity' in 'independent continuant'.

value: 'independent continuant' 'anatomical entity' with blister

undefined: abnormally blistered 'anatomical entity' in 'independent continuant'

value: An abnormal reduction in the size of the 'anatomical entity'.

undefined: decreased size of the 'anatomical entity'

value: An abnormally increased level of role in the 'independent continuant'.

undefined: increased 'independent continuant' role level

value: Absent or undetectable level of 'chemical entity'.

value: An abnormally localised 'anatomical entity'.

value: abnormal position of 'anatomical entity'

undefined: Abnormally localised 'anatomical entity'

value: An increase in the height of the 'anatomical entity' in the 'independent continuant'.

value: higher 'anatomical entity' in 'independent continuant'

undefined: increased height of 'anatomical entity' in 'independent continuant'

value: The presence of a reduced number of 'anatomical entity' in the 'independent continuant'.

value: Reduced number of 'anatomical entity' in the 'independent continuant'

undefined: Decreased number of 'anatomical entity' in the 'independent continuant'

value: The presence of an abscess of the 'anatomical entity'.

value: Enhanced or improved 'behavior process'.

value: Increased resistance of organism to 'chemical entity'.

value: decreased sensitivity of organism to 'chemical entity'

undefined: increased resistance of organism to 'chemical entity'

value: Partial or complete wasting (loss) of 'anatomical entity' tissue that was once present.

value: abnormally changed resistance of organism to 'entity'.

value: abnormally changed  sensitivity of organism to 'entity'

undefined: abnormally changed resistance of organism to 'entity'

value: Decreased length or shortening of the 'anatomical entity'.

value: Partial or complete degeneration of 'anatomical entity' tissue that was once present.

value: A developmental defect resulting in complete obliteration of the lumen of the 'anatomical entity'.

value: An abnormal decrease in weight or a decreased distribution of mass in the 'anatomical entity'.

value: Abnormal ability to move 'cellular component'.

value: extra 'anatomical entity's in 'independent continuant'

value: Any structural anomaly that causes there to be extra parts of type 'anatomical entity' in 'independent continuant'.

undefined: has extra parts of type 'anatomical entity' in 'independent continuant'

value: An abnormal development of the 'anatomical entity'.

undefined: abnormal development of 'anatomical entity'

value: Defective development of the 'anatomical entity'.

value: An abnormal location of 'anatomical entity'.

undefined: abnormal location of 'anatomical entity'

value: Abnormally reduced functionality of 'molecular function'.

value: Increased distance between 'entity1' and 'entity2'.

value: distance increased between 'entity1' and 'entity2'

undefined: increased distance between 'entity1' and 'entity2'

value: An abnormal increase in weight or an increased distribution of mass in the 'anatomical entity'.

value: Any functional anomaly of the 'anatomical entity'.

undefined: abnormality of 'anatomical entity' physiology

value: An abnormally decreased level of role in the 'independent continuant'.

undefined: decreased role 'independent continuant' level

value: The presence of excessive fibrous connective tissue in the 'anatomical entity'.

value: increased sensitivity of organism to 'entity'

value: Decreased resistance of organism to 'entity'.

undefined: decreased resistance of organism to 'entity'

value: Increased or enhanced ability to move 'anatomical entity'.

value: Impaired or decreased 'behavior process'.

value: Partial or complete degeneration of 'anatomical entity' tissue in the 'independent continuant' that was once present.

value: degeneration of the 'anatomical entity' in 'independent continuant'

undefined: 'anatomical entity' degeneration in 'independent continuant'

undefined: abnormal opening of the 'anatomical entity'

value: Missing 'anatomical entity' in the 'independent continuant'

value: Absence of the 'anatomical entity' in the 'independent continuant'.

undefined: Absent 'anatomical entity' in the 'independent continuant'

value: Any functional anomaly of the 'cellular component'.

undefined: abnormality of 'cellular component' function

value: An abnormally formed/malformed 'anatomical entity'.

value: Any abnormal bending of the 'anatomical entity'.

value: A decreased occurrence of 'biological_process'.

undefined: decreased occurrence of 'biological_process'

value: fewer 'anatomical entity's in 'anatomical entity'

value: Any structural anomaly of 'anatomical entity' that causes there to be fewer parts of type 'anatomical entity'.

undefined: 'anatomical entity' that has fewer parts of type 'anatomical entity'

value: abnormal pigmentation of the 'anatomical entity'

value: abnormal degree of pigmentation of the 'anatomical entity'.

undefined: abnormal degree of pigmentation of the 'anatomical entity'

value: Arrested 'biological_process' in 'independent continuant'.

undefined: arrested 'biological_process' in 'independent continuant'

value: Increased or increasing of pigmentation of 'anatomical entity'.

value: increasing of pigment in the 'anatomical entity'

undefined: increased pigmentation in the 'anatomical entity'

value: An abnormally blistered 'anatomical entity'.

undefined: abnormally blistered 'anatomical entity'

value: An increased amount in the level of 'chemical entity'.

value: An abnormal 'anatomical entity' with one or more lesions.

value: Any abnormal coiling of the 'anatomical entity'.

value: An abnormally formed/malformed 'anatomical entity' in 'independent continuant'.

value: malformed 'anatomical entity' in 'independent continuant'

undefined: abnormally formed 'anatomical entity' in 'independent continuant'

value: increased sensitivity of organism to 'chemical entity'

value: Decreased resistance of organism to 'chemical entity'.

undefined: decreased resistance of organism to 'chemical entity'

value: A decreased occurrence of 'biological process' in 'independent continuant'.

value: Any structural anomaly that causes there to be extra parts of type 'anatomical entity'.

undefined: has extra parts of type 'anatomical entity'

value: Any structural anomaly that causes there to be fewer parts of type 'anatomical entity' in the 'anatomical entity'.

value: fewer 'anatomical entity's in 'anatomical entity', located in 'independent continuant'

undefined: has fewer parts of type 'anatomical entity' in 'anatomical entity', which is located in 'independent continuant'

value: Absent or undetectable level of 'chemical entity' in 'independent continuant'.

undefined: absent 'chemical entity' in 'independent continuant'

value: abnormal fusion of 'anatomical entity' and 'anatomical entity'

value: Any abnormal fusion of the 'anatomical entity' and the 'anatomical entity'.

undefined: abnormally fused 'anatomical entity' and 'anatomical entity'

value: decreased 'biological_process' in 'independent continuant'.

undefined: decreased 'biological_process' in 'independent continuant'

value: Partial or complete degeneration of 'cellular component' tissue in the 'independent continuant' that was once present.

value: degeneration of the 'cellular component' in 'independent continuant'

undefined: 'cellular component' degeneration in 'independent continuant'

value: A partial or complete breakage of the 'anatomical entity'.

value: An increased occurrence of 'biological process' in 'independent continuant'.

value: An abnormal increase or decrease of weight or an abnormal distribution of mass in the 'anatomical entity'.

undefined: abnormality of 'anatomical entity' weight

value: An abnormal reduction in the volume of the 'anatomical entity'.

undefined: decreased volume of the 'anatomical entity'

value: Any anomaly that causes there to be an abnormal number 'cellular component'.

value: abnormal number of 'cellular component's

value: Abnormally decreased coiling of the 'anatomical entity'.

value: abnormal decreased 'anatomical entity' coiling

undefined: abnormally decreased coiling of 'anatomical entity'

value: Abnormal 'biological process' involving the active participant 'cellular component'.

undefined: abnormal 'biological process' involving 'cellular component'

value: Abnormal cell proliferation in 'anatomical_entity'.

undefined: abnormal cell proliferation in 'anatomical_entity'

value: The presence of a reduced number of 'anatomical entity'.

undefined: abnormal closing of the 'anatomical entity'

value: Abnormal proliferation of 'cell' in 'anatomical entity'.

undefined: abnormal 'cell' proliferation in 'anatomical entity'

value: abnormally incompletely closed 'anatomical entity'

value: Abnormally incompletely closed 'anatomical entity'.

undefined: abnormal incomplete closing of the 'anatomical entity'

value: Extra 'anatomical entity' in the 'independent continuant'

value: The presence of an increased number of 'anatomical entity' in the 'independent continuant'.

undefined: Increased number of 'anatomical entity' in the 'independent continuant'

value: A functional abnormality of the 'anatomical entity' in 'independent continuant'.

undefined: 'anatomical entity' dysfunction in 'independent continuant'

value: An abnormality of the 'biological process' in 'independent continuant'.

undefined: abnormal 'biological process' in 'independent continuant'

value: A decreased amount in the level of 'chemical entity'.

value: An abnormal position of the 'anatomical entity' in the 'independent continuant'.

undefined: abnormal 'anatomical entity' topology in 'independent continuant'

value: Absent or undetectable 'biological process' in 'independent continuant'.

undefined: absent 'biological process' in 'independent continuant'

value: skinny or decreased width of the 'anatomical entity'.

undefined: decreased width of the 'anatomical entity'

value: An abnormal increase in length in 'anatomical entity' in location 'independent continuant'.

undefined: increased 'anatomical entity' length in 'independent continuant'

value: An abnormally apoptotic 'anatomical entity'.

undefined: abnormally apoptotic 'anatomical entity'

value: An abnormal concentration of chemical in 'independent continuant'.

undefined: abnormal chemical concentration in 'independent continuant'

value: absence of pigment in the 'anatomical entity'

value: complete loss of pigmentation in the 'anatomical entity'

value: complete loss of pigmenation of the 'anatomical entity'.

value: skinny or decreased width of the 'anatomical entity' in 'independent continuant'.

value: skinny 'anatomical entity' in 'independent continuant'

undefined: decreased width of the 'anatomical entity' in 'independent continuant'

value: An increase in the height of the 'anatomical entity'.

undefined: increased height of the 'anatomical entity'

value: degeneration of the 'cellular component'

value: Partial or complete degeneration of 'cellular component'.

value: A hyperactivity of the 'anatomical entity' in the 'independent continuant'.

undefined: 'anatomical entity' hyperactivity in 'independent continuant'

value: An increase in the thickness of the 'anatomical entity' in the 'independent continuant'.

value: thickened 'anatomical entity' in 'independent continuant'

undefined: increased thickness of the 'anatomical entity' in 'independent continuant'

value: An abnormal level of 'chemical entity' in the 'independent continuant'.

undefined: abnormal 'independent continuant' 'chemical entity' level

value: short 'anatomical entity' in 'independent continuant'

value: Decreased length or shortening of the 'anatomical entity' in the 'independent continuant'.

undefined: decreased length of 'anatomical entity' in 'independent continuant'

value: An abnormally decreased functionality of the 'anatomical entity'.

undefined: abnormally decreased functionality of the 'anatomical entity'

value: Any abnormal duplication of the 'anatomical entity'.

value: abnormally duplicated 'anatomical entity'

value: abnormal duplication of 'anatomical entity'

undefined: abnormal duplication of 'anatomical entity'

value: Any structural anomaly that causes there to be an abnormal number 'anatomical entity'.

undefined: abnormal number of anatomical enitites of type 'anatomical entity'

value: protruding 'anatomical entity' in 'independent continuant'

value: hernial protrusion of the 'anatomical entity' through an opening or defect in the 'independent continuant'.

undefined: abnormal protrusion of 'anatomical entity' through 'independent continuant'

value: Decreased qualitatively 'biological process' in 'independent continuant'.

undefined: decreased qualitatively 'biological process' in 'independent continuant'

value: Any structural anomaly in the shape of the 'entity'.

value: Any abnormal 'anatomical entity' that is 'curved'ly.

value: Calcification of the 'anatomical entity'.

value: An increase in the thickness of the 'anatomical entity'.

undefined: increased thickness of the 'anatomical entity'

value: loss of pigment in the 'anatomical entity'

value: Decreased or loss of pigmentation of 'anatomical entity'.

undefined: decreased pigmentation in the 'anatomical entity'

value: The presence of an increased number of 'cellular component'.

undefined: Increased number of 'cellular component'

value: abnormally small 'anatomical entity' in 'independent continuant'

value: An abnormal reduction in the size of the 'anatomical entity' in the 'independent continuant'.

undefined: decreased size of the 'anatomical entity' in the 'independent continuant'

value: Any unspecified morphological anomaly of the 'anatomical entity', such as, for example, abnormal shape or colour.

value: Increased 'biological process' in 'independent continuant'.

undefined: increased 'biological process' in 'independent continuant'

value: An abnormally apoptotic 'anatomical entity' in 'independent continuant'.

value: 'independent continuant' 'anatomical entity' with apoptosis

undefined: abnormally apoptotic 'anatomical entity' in 'independent continuant'

value: Decreased qualitatively 'biological process'.

undefined: decreased qualitatively 'biological process'

value: abnormal 'shape' shape of 'anatomical entity'

value: Any structural anomaly that causes 'anatomical entity' to be 'shape' shaped.


text:
# Download VOWL from here http://vowl.visualdataweb.org/webvowl.html
java -jar owl2vowl.jar -file ../patterns/pattern-simple.owl


text:
@chris-grove Thank you for your amazing review. I structured it a bit and was able to fix some of the stuff you found already! Thanks!

Missing subsumption (problem with PATO):
- [ ] abnormalAbsenceOfChemicalEntity.yaml SubClassOf abnormallyDecreasedLevelOfChemicalEntity.yaml
- [ ] abnormalAbsenceOfBiologicalProcess.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcessInLocation.yaml (maybe?)
- [ ] abnormalAbsenceOfChemicalEntityInLocation.yaml SubClassOf abnormallyDecreasedLevelOfChemicalEntityInLocation.yaml
- [ ] abnormalAbsenceOfChemicalEntity.yaml SubClassOf abnormallyDecreasedLevelOfChemicalEntity.yaml
- [ ] abnormalAbsenceOfPigmentationOfAnatomicalEntity.yaml SubClassOf abnormallyDecreasedPigmentationOfAnatomicalEntity.yaml
- [ ] abnormalAbsenceOfAnatomicalEntity.yaml SubClassOf abnormalQuantityOfAnatomicalEntity.yaml
- [ ] abnormalQuantityOfAnatomicalEntity.yaml SubClassOf abnormalMorphologyOfAnatomicalEntity.yaml

Missing subsumptions that were missing because of imports (fixed now):
- [X] abnormalShapeOfAnatomicalEntityByShapeType.yaml SubClassOf abnormalAnatomicalEntity.yaml (related to #11)
- [X] abnormalMorphologyOfAnatomicalEntity.yaml SubClassOf abnormalAnatomicalEntity.yaml (related to #3)
- [X] abnormalWeightOfAnatomicalEntity.yaml SubClassOf abnormalAnatomicalEntity.yaml

Missing because of missing alignment between reference ontologies:
- [ ] abnormalBehavior.yaml SubClassOf abnormalBiologicalProcess.yaml

Missing for logical reasons:
- [X] abnormallyDecreasedRateOfBiologicalProcess.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcessInLocation.yaml: You are right in that decreased rate is a sub-quality of process quality. However, unless there is an axiom statig somewhere (which maybe should?) that EVERY biological process occurs somewhere, the second pattern is more specific in that regard!
- [X] abnormallyArrestedBiologicalProcess.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcessInLocation.yaml: Same as above. None of the two is a generalisation of the other.
- [X] abnormalFunctionalityOfAnatomicalEntity.yaml SubClassOf abnormalBiologicalProcess.yaml: This is not possible, as the former is a anatomical entity phenotype, while the latter is a biological process phenotype.

Missing because pattern was broken, now fixed:
- [X] abnormallyDecreasedDistanceBetweenAnatomicalEntities.yaml SubClassOf abnormalDistanceBetweenAnatomicalEntities.yaml
- [X] abnormallyIncreasedDistanceBetweenAnatomicalEntities.yaml SubClassOf abnormalDistanceBetweenAnatomicalEntities.yaml
- [X] abnormallyDecreasedQualityOfBiologicalProcess.yaml SubClassOf abnormalBiologicalProcess.yaml: decreased quality pattern used wrong PATO quality (process quality instead of decreased process quality)
- [X] abnormallyIncreasedRateOfBiologicalProcessInLocation.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcessInLocation.yaml
- [X] abnormalBiologicalProcessInLocation.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcess.yaml
- [X] abnormalDevelopmentOfAnatomicalEntity.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcess.yaml
- [X] abnormallyIncreasedRateOfBiologicalProcess.yaml SubClassOf abnormallyDecreasedQualityOfBiologicalProcess.yaml

Missing because pattern is broken, not (yet) fixed:
- [ ] abnormallyDecreasedNumberOfAnatomicalEntity.yaml SubClassOf abnormalQuantityOfAnatomicalEntity.yaml: abnormalQuantityPattern needs to be changed to abnormalNumberOfAnatomicalEntity. Right now makes no sense.
- [ ] abnormallyDecreasedNumberOfCellularComponent.yaml SubClassOf abnormallyAlteredNumberOfCellularComponent.yaml
- [ ] abnormallyIncreasedNumberOfAnatomicalEntity.yaml SubClassOf abnormalQuantityOfAnatomicalEntity.yaml
- [ ] abnormallyIncreasedNumberOfCellularComponent.yaml SubClassOf abnormallyAlteredNumberOfCellularComponent.yaml
- [ ] lesionInAnatomicalEntity SubClassOf abnormalAnatomicalEntity.yaml: Broken EQ.
- [ ] abnormalCellProliferationInAnatomicalEntity: Broken EQ.

> Existing subsumptions that seem wrong:

- [X] All fixed.

> I don't understand the difference between:

- [ ] 'abnormalPositionOfAnatomicalEntity.yaml' and 'mislocalisedAnatomicalEntity.yaml': Will discuss at next phenotype call
- [ ] 'abnormalQuantityOfAnatomicalEntity.yaml' and 'abnormallyAlteredNumberOfAnatomicalEntities.yaml': Will discuss at next phenotype call
- [X] 'abnormallyLackingAllPartsOfTypeAnatomicalEntity.yaml' and 'abnormalAbsenceOfAnatomicalEntity.yaml': Former is now deprecated.

Same label, different entities:
- [X] abnormallyIncreasedHeightOfAnatomicalEntity.yaml and abnormallyIncreasedHeightOfAnatomicalEntityInLocation.yaml both have the same label "increased height of the 'anatomical entity'": `fixed`