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May 9, 2025
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Allow selecting punned entities in remove and filter command #1251

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08872be
Allow selecting punned entities in remove/filter.
gouttegd Mar 25, 2025
7c1bdf1
Document/test the new --allow-punning option.
gouttegd Mar 25, 2025
abe2acf
Add unit test for OntologyHelper#getEntities().
gouttegd Mar 25, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added
- Add `--clean-obo` option to [`convert`] [#995]
- Allow interpolation of ontology IRI and version IRI within annotation values [#1241]
- Allow selecting punned entities in [`remove`] and [`filter`]

### Fixed
- Update owl-diff dependency for stable ordering and to avoid large string creation [#1227]
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183 changes: 183 additions & 0 deletions docs/examples/uo_mole_subset.ofn
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@@ -0,0 +1,183 @@
Prefix(:=<http://purl.obolibrary.org/obo/uo.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/uo.owl>

Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000006>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000013>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000039>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000040>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000041>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000042>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000043>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000044>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000046>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000297>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000299>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000300>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000302>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000303>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_0000304>))
Declaration(Class(<http://purl.obolibrary.org/obo/UO_1000013>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/has_prefix>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000013>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000039>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000040>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000041>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000042>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000043>))
Declaration(NamedIndividual(<http://purl.obolibrary.org/obo/UO_0000044>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>))



############################
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/UO_0000000> (unit)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000000> "\"A unit of measurement is a standardized quantity of a physical quality.\" [Wikipedia:Wikipedia]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000000> "unit")

# Class: <http://purl.obolibrary.org/obo/UO_0000006> (substance unit)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000006> "\"A unit which is a standardised quantity of an element or compound with uniform composition.\" [Wikipedia:Wikipedia]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000006> "substance unit")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000006> <http://purl.obolibrary.org/obo/UO_0000000>)

# Class: <http://purl.obolibrary.org/obo/UO_0000013> (mole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000013> "mol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000013> "\"A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12.\" [BIPM:BIPM, NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000013> "mole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000013> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000013>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000013> <http://purl.obolibrary.org/obo/UO_0000000>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000013> <http://purl.obolibrary.org/obo/UO_1000013>)

# Class: <http://purl.obolibrary.org/obo/UO_0000039> (micromole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000039> "umol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000039> "\"A substance unit equal to a millionth of a mol or 10^[-6] mol.\" [NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000039> "micromole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000039> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UO_1000013> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000299>)))
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000039> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000039>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000039> <http://purl.obolibrary.org/obo/UO_1000013>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000039> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000299>))

# Class: <http://purl.obolibrary.org/obo/UO_0000040> (millimole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000040> "mmol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000040> "\"A substance unit equal to a thousandth of a mol or 10^[-3] mol.\" [NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000040> "millimole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000040> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UO_1000013> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000297>)))
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000040> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000040>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000040> <http://purl.obolibrary.org/obo/UO_1000013>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000040> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000297>))

# Class: <http://purl.obolibrary.org/obo/UO_0000041> (nanomole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000041> "nmol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000041> "\"A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.\" [NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000041> "nanomole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000041> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UO_1000013> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000300>)))
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000041> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000041>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000041> <http://purl.obolibrary.org/obo/UO_1000013>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000041> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000300>))

# Class: <http://purl.obolibrary.org/obo/UO_0000042> (picomole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000042> "pmol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000042> "\"A substance unit equal to 10^[-12] mol.\" [NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000042> "picomole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000042> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UO_1000013> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000302>)))
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000042> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000042>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000042> <http://purl.obolibrary.org/obo/UO_1000013>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000042> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000302>))

# Class: <http://purl.obolibrary.org/obo/UO_0000043> (femtomole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000043> "fmol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000043> "\"A substance unit equal to 10^[-15] mol.\" [NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000043> "femtomole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000043> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UO_1000013> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000303>)))
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000043> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000043>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000043> <http://purl.obolibrary.org/obo/UO_1000013>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000043> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000303>))

# Class: <http://purl.obolibrary.org/obo/UO_0000044> (attomole)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000044> "amol")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000044> "\"A substance unit equal to 10^[-18] mol.\" [NIST:NIST]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000044> "attomole")
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000044> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/UO_1000013> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000304>)))
EquivalentClasses(<http://purl.obolibrary.org/obo/UO_0000044> ObjectOneOf(<http://purl.obolibrary.org/obo/UO_0000044>))
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000044> <http://purl.obolibrary.org/obo/UO_1000013>)
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000044> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/has_prefix> <http://purl.obolibrary.org/obo/UO_0000304>))

# Class: <http://purl.obolibrary.org/obo/UO_0000046> (prefix)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000046> "prefix")

# Class: <http://purl.obolibrary.org/obo/UO_0000297> (milli)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000297> "10^[-3]")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000297> "m")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000297> "\"A prefix in the metric system denoting a factor of one thousand.\" [UO:GVG]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000297> "milli")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000297> <http://purl.obolibrary.org/obo/UO_0000046>)

# Class: <http://purl.obolibrary.org/obo/UO_0000299> (micro)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000299> "10^[-6]")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000299> "\"A prefix in the metric system denoting a factor of 10 to the power of -6.\" [UO:GVG]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000299> "micro")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000299> <http://purl.obolibrary.org/obo/UO_0000046>)

# Class: <http://purl.obolibrary.org/obo/UO_0000300> (nano)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000300> "10^[-9]")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000300> "n")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000300> "\"A prefix in the metric system denoting a factor of 10 to the power of -9.\" [UO:GVG]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000300> "nano")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000300> <http://purl.obolibrary.org/obo/UO_0000046>)

# Class: <http://purl.obolibrary.org/obo/UO_0000302> (pico)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000302> "10^[-12]")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000302> "n")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000302> "\"A prefix in the metric system denoting a factor of 10 to the power of -12.\" [GVG:UO]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000302> "pico")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000302> <http://purl.obolibrary.org/obo/UO_0000046>)

# Class: <http://purl.obolibrary.org/obo/UO_0000303> (femto)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000303> "10^[-15]")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000303> "f")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000303> "\"A prefix in the metric system denoting a factor of 10 to the power of -15.\" [UO:GVG]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000303> "femto")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000303> <http://purl.obolibrary.org/obo/UO_0000046>)

# Class: <http://purl.obolibrary.org/obo/UO_0000304> (atto)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000304> "a")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/UO_0000304> "10^[-18]")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/UO_0000304> "\"A prefix in the metric system denoting a factor of 10 to the power of -18.\" [UO:GVG]")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_0000304> "atto")
SubClassOf(<http://purl.obolibrary.org/obo/UO_0000304> <http://purl.obolibrary.org/obo/UO_0000046>)

# Class: <http://purl.obolibrary.org/obo/UO_1000013> (mole based unit)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/UO_1000013> "mole based unit")
SubClassOf(<http://purl.obolibrary.org/obo/UO_1000013> <http://purl.obolibrary.org/obo/UO_0000006>)



)
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