From 134ba4624e5d9271066736151ba527460c00846b Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 27 Mar 2026 12:10:18 +0000 Subject: [PATCH 1/4] Add "optical anisotropy". Add "optical anisotropy" as a "source of contrast". Reclassify the following three terms: * "intrinsic birefringence" * "stress-induced birefringence" * form birefringence" as subclasses of "optical anisotropy" and define them accordingly. --- src/ontology/fbbi-edit.owl | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/src/ontology/fbbi-edit.owl b/src/ontology/fbbi-edit.owl index 4fffbc7..d9837e5 100644 --- a/src/ontology/fbbi-edit.owl +++ b/src/ontology/fbbi-edit.owl @@ -671,6 +671,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) @@ -6076,30 +6077,37 @@ SubClassOf( (form birefringence) +AnnotationAssertion(Annotation( "PMID:2775834") "An optical anisotropy that is caused by the arrangement of structures with different refractive indexes, on a scale smaller than a wavelength.") +AnnotationAssertion( ) AnnotationAssertion( "jm") AnnotationAssertion( "2010-09-03T09:55:12Z") +AnnotationAssertion( "structural birefringence") AnnotationAssertion( "image") AnnotationAssertion( "FBbi:00000593") AnnotationAssertion(rdfs:label "form birefringence") -SubClassOf( ) +SubClassOf( ) # Class: (intrinsic birefringence) +AnnotationAssertion( "An optical anisotropy that is a constant, intrinsic property of the material.") +AnnotationAssertion( ) AnnotationAssertion( "jm") AnnotationAssertion( "2010-09-03T09:55:12Z") AnnotationAssertion( "image") AnnotationAssertion( "FBbi:00000594") AnnotationAssertion(rdfs:label "intrinsic birefringence") -SubClassOf( ) +SubClassOf( ) # Class: (stress-induced birefringence) +AnnotationAssertion( "An optical anisotropy that is the result of mechanical stress in an otherwise isotropic material.") +AnnotationAssertion( ) AnnotationAssertion( "jm") AnnotationAssertion( "2010-09-03T09:55:12Z") AnnotationAssertion( "image") AnnotationAssertion( "FBbi:00000595") AnnotationAssertion(rdfs:label "stress-induced birefringence") -SubClassOf( ) +SubClassOf( ) # Class: (distribution of a specific nucleic acid sequence) @@ -6634,6 +6642,15 @@ AnnotationAssertion( "cryogenic serial block face scanning electron microscopy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (optical anisotropy) + +AnnotationAssertion(Annotation( "ISBN:978-1-108-47743-7") "The property of a material whose refractive index depends on the polarization and propagation direction of light.") +AnnotationAssertion( ) +AnnotationAssertion( "2026-03-27T11:31:52Z"^^xsd:dateTime) +AnnotationAssertion( "birefringence") +AnnotationAssertion(rdfs:label "optical anisotropy") +SubClassOf( ) + # Class: (method involved in biological imaging) AnnotationAssertion( "image") From b2c1be4c72c37cb44913aca76afb8c2b131fed56 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 27 Mar 2026 12:34:52 +0000 Subject: [PATCH 2/4] Add definition for "polarization microscopy". Add a definition for FBbi:00000248 "polarization microscopy", as well as for FBbi:00000350 ("polarized light illumination") and FBbi:00000352 ("polarization-sensitive detection") on which the first term depends. --- src/ontology/fbbi-edit.owl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/ontology/fbbi-edit.owl b/src/ontology/fbbi-edit.owl index d9837e5..d428158 100644 --- a/src/ontology/fbbi-edit.owl +++ b/src/ontology/fbbi-edit.owl @@ -2653,11 +2653,13 @@ SubClassOf( (polarization microscopy) +AnnotationAssertion(Annotation( "PMID:23901032") "A form of light microscopy that uses polarized light. Such form can be used to image samples that exibit optical anisotropy.") +AnnotationAssertion( "anisotropy/polarization microscopy") +AnnotationAssertion( "polarized light microscopy") AnnotationAssertion( "image") AnnotationAssertion( "FBbi:00000248") AnnotationAssertion(rdfs:label "polarization microscopy") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (time lapse microscopy) @@ -3593,6 +3595,8 @@ SubClassOf( (polarized light illumination) +AnnotationAssertion( "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( ) AnnotationAssertion( "jm") AnnotationAssertion( "2010-03-09T10:23:41Z") AnnotationAssertion( "image") @@ -3611,6 +3615,8 @@ SubClassOf( (polarization-sensitive detection) +AnnotationAssertion( ) +AnnotationAssertion( "A detection method that only detects light that has a specific polarization.") AnnotationAssertion( "jm") AnnotationAssertion( "2010-03-09T10:27:11Z") AnnotationAssertion( "image") From b94af4deed94becb734b961b0e985247c4624d94 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 27 Mar 2026 13:00:21 +0000 Subject: [PATCH 3/4] Complete FBbi:00000603. Add a definition to FBbi:00000603 ("fluorescence polarization microscopy"). Add "fluorescence anisotropy imaging" and "FAIM" as exact synonyms. Make it a subclass of "polarization microscopy". --- src/ontology/fbbi-edit.owl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/ontology/fbbi-edit.owl b/src/ontology/fbbi-edit.owl index d428158..1cd96a2 100644 --- a/src/ontology/fbbi-edit.owl +++ b/src/ontology/fbbi-edit.owl @@ -6180,12 +6180,18 @@ SubClassOf( (fluorescence polarization microscopy) +AnnotationAssertion(Annotation( "PMID:2317548") "A mode of microscopy that detects the rotational motion of fluorophores.") +AnnotationAssertion( ) AnnotationAssertion( "jm") AnnotationAssertion( "2010-09-04T01:28:20Z") +AnnotationAssertion( "FAIM") +AnnotationAssertion( "fluorescence anisotropy imaging") AnnotationAssertion( "image") +AnnotationAssertion( ) AnnotationAssertion( "FBbi:00000603") AnnotationAssertion(rdfs:label "fluorescence polarization microscopy") SubClassOf( ) +SubClassOf( ) # Class: (compartmentalization of stain or label) From e4cfb44408ea0f8e940896ee5bf2ff5133abbbc3 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Fri, 27 Mar 2026 13:15:38 +0000 Subject: [PATCH 4/4] Misc fixes. Fix: * improper use of `dcterms:contributor` where IAO:0000115 was intended; * oboInOwl:hasSynonymType applied to a term rather to a synonym annotation. --- src/ontology/fbbi-edit.owl | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/ontology/fbbi-edit.owl b/src/ontology/fbbi-edit.owl index 1cd96a2..b70785e 100644 --- a/src/ontology/fbbi-edit.owl +++ b/src/ontology/fbbi-edit.owl @@ -3615,8 +3615,8 @@ SubClassOf( (polarization-sensitive detection) +AnnotationAssertion( "A detection method that only detects light that has a specific polarization.") AnnotationAssertion( ) -AnnotationAssertion( "A detection method that only detects light that has a specific polarization.") AnnotationAssertion( "jm") AnnotationAssertion( "2010-03-09T10:27:11Z") AnnotationAssertion( "image") @@ -6184,10 +6184,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "jm") AnnotationAssertion( "2010-09-04T01:28:20Z") -AnnotationAssertion( "FAIM") +AnnotationAssertion(Annotation( ) "FAIM") AnnotationAssertion( "fluorescence anisotropy imaging") AnnotationAssertion( "image") -AnnotationAssertion( ) AnnotationAssertion( "FBbi:00000603") AnnotationAssertion(rdfs:label "fluorescence polarization microscopy") SubClassOf( )