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Fix "polarisation microscopy" and related terms. #45

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Merged
gouttegd merged 4 commits into from
Mar 27, 2026
Merged

Fix "polarisation microscopy" and related terms. #45

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134ba46
Add "optical anisotropy".
gouttegd Mar 27, 2026
b2c1be4
Add definition for "polarization microscopy".
gouttegd Mar 27, 2026
b94af4d
Complete FBbi:00000603.
gouttegd Mar 27, 2026
e4cfb44
Misc fixes.
gouttegd Mar 27, 2026
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36 changes: 32 additions & 4 deletions src/ontology/fbbi-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -671,6 +671,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100014>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100015>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100016>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100017>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_00100018>))
Declaration(Class(<http://purl.obolibrary.org/obo/FBbi_root_00000000>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/FBbi_00000346>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Expand Down Expand Up @@ -2652,11 +2653,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000247> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/FBbi_00000248> (polarization microscopy)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:23901032") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000248> "A form of light microscopy that uses polarized light. Such form can be used to image samples that exibit optical anisotropy.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00000248> "anisotropy/polarization microscopy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00000248> "polarized light microscopy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000248> "image")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000248> "FBbi:00000248")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000248> "polarization microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00000248> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000345> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000313>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000350>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000352>)))
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000248> <http://purl.obolibrary.org/obo/FBbi_00000345>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000249> (time lapse microscopy)

Expand Down Expand Up @@ -3592,6 +3595,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000349> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/FBbi_00000350> (polarized light illumination)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000350> "An illumination method in which the sample is illuminated by light waves of only one polarization, instead of a mix of waves of various polarizations.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00000350> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/FBbi_00000350> "jm")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/FBbi_00000350> "2010-03-09T10:23:41Z")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000350> "image")
Expand All @@ -3610,6 +3615,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000351> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/FBbi_00000352> (polarization-sensitive detection)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000352> "A detection method that only detects light that has a specific polarization.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00000352> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/FBbi_00000352> "jm")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/FBbi_00000352> "2010-03-09T10:27:11Z")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000352> "image")
Expand Down Expand Up @@ -6076,30 +6083,37 @@ SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000592> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/FBbi_00000593> (form birefringence)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:2775834") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000593> "An optical anisotropy that is caused by the arrangement of structures with different refractive indexes, on a scale smaller than a wavelength.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00000593> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/FBbi_00000593> "jm")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/FBbi_00000593> "2010-09-03T09:55:12Z")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00000593> "structural birefringence")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000593> "image")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000593> "FBbi:00000593")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000593> "form birefringence")
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000593> <http://purl.obolibrary.org/obo/FBbi_00000590>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000593> <http://purl.obolibrary.org/obo/FBbi_00100018>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000594> (intrinsic birefringence)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000594> "An optical anisotropy that is a constant, intrinsic property of the material.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00000594> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/FBbi_00000594> "jm")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/FBbi_00000594> "2010-09-03T09:55:12Z")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000594> "image")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000594> "FBbi:00000594")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000594> "intrinsic birefringence")
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000594> <http://purl.obolibrary.org/obo/FBbi_00000590>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000594> <http://purl.obolibrary.org/obo/FBbi_00100018>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000595> (stress-induced birefringence)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000595> "An optical anisotropy that is the result of mechanical stress in an otherwise isotropic material.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00000595> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/FBbi_00000595> "jm")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/FBbi_00000595> "2010-09-03T09:55:12Z")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000595> "image")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000595> "FBbi:00000595")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000595> "stress-induced birefringence")
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000595> <http://purl.obolibrary.org/obo/FBbi_00000590>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000595> <http://purl.obolibrary.org/obo/FBbi_00100018>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000596> (distribution of a specific nucleic acid sequence)

Expand Down Expand Up @@ -6166,12 +6180,17 @@ SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000602> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/FBbi_00000603> (fluorescence polarization microscopy)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:2317548") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00000603> "A mode of microscopy that detects the rotational motion of fluorophores.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00000603> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/FBbi_00000603> "jm")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/FBbi_00000603> "2010-09-04T01:28:20Z")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/OMO_0003000>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00000603> "FAIM")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00000603> "fluorescence anisotropy imaging")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_00000603> "image")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000603> "FBbi:00000603")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000603> "fluorescence polarization microscopy")
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000603> <http://purl.obolibrary.org/obo/FBbi_00000246>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000603> <http://purl.obolibrary.org/obo/FBbi_00000248>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000604> (compartmentalization of stain or label)

Expand Down Expand Up @@ -6634,6 +6653,15 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00100017> "cryogenic serial block face scanning electron microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00100017> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000585> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000013>)))

# Class: <http://purl.obolibrary.org/obo/FBbi_00100018> (optical anisotropy)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ISBN:978-1-108-47743-7") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_00100018> "The property of a material whose refractive index depends on the polarization and propagation direction of light.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_00100018> <https://orcid.org/0000-0002-6095-8718>)
AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/FBbi_00100018> "2026-03-27T11:31:52Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_00100018> "birefringence")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00100018> "optical anisotropy")
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00100018> <http://purl.obolibrary.org/obo/FBbi_00000590>)

# Class: <http://purl.obolibrary.org/obo/FBbi_root_00000000> (method involved in biological imaging)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/FBbi_root_00000000> "image")
Expand Down
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