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Add laser-scanning confocal microscopy #56

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686c0e9
Add term for Laser Scanning Confocal Microscopy
lubianat May 7, 2026
a18eb3a
Fix ID, label and dc:date
lubianat May 8, 2026
e2366cd
Add reference to LSCM definition
lubianat May 8, 2026
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16 changes: 14 additions & 2 deletions src/ontology/fbbi-edit.owl
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Expand Up @@ -672,6 +672,7 @@ 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_d022f173_7141_4007_a8e0_486721e5d43d>))
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 @@ -2666,7 +2667,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000252> "FBbi:00000252")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000252> "single-spot confocal microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00000252> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000251> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000286>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000394>)))
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000252> <http://purl.obolibrary.org/obo/FBbi_00000251>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000252> <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000253> (spinning disk confocal microscopy)

Expand Down Expand Up @@ -4003,7 +4004,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/FBbi_00000393> "FBbi:00000393")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_00000393> "array-scan confocal microscopy")
EquivalentClasses(<http://purl.obolibrary.org/obo/FBbi_00000393> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbi_00000251> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000289>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/FBbi_00000346> <http://purl.obolibrary.org/obo/FBbi_00000294>)))
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000393> <http://purl.obolibrary.org/obo/FBbi_00000251>)
SubClassOf(<http://purl.obolibrary.org/obo/FBbi_00000393> <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d>)

# Class: <http://purl.obolibrary.org/obo/FBbi_00000394> (spot detector)

Expand Down Expand Up @@ -6638,6 +6639,17 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
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_d022f173_7141_4007_a8e0_486721e5d43d> (laser scanning confocal microscopy)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d> "A confocal microscopy method in which mirrors are used to scan the laser across the sample.")

@gouttegd gouttegd May 7, 2026

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Any chance of having a reference (PMID, DOI, etc.) for that definition?

If not, it’s not a big deal (many terms in FBbi don’t even have a definition, even less a definition with a reference), but just in case.

AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d> <https://orcid.org/0000-0002-1069-1816>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d> <https://orcid.org/0000-0002-8783-8599>)

@gouttegd gouttegd May 7, 2026

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There should also be a dcterms:date annotation with the date/time when the term was added. You can configure Protégé to add such an annotation automatically.

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_d022f173_7141_4007_a8e0_486721e5d43d> "CLSM")
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_d022f173_7141_4007_a8e0_486721e5d43d> "LSCM")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d> "confocal laser scanning microscopy")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d> "laser scanning confocal microscopy"@pt)

@gouttegd gouttegd May 7, 2026

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This @pt language tag should not be here.

We don’t normally use language tags in FBbi (nor, as far as I know, across all OBO ontologies). All labels, definitions, and synonyms are expected to be in English with no explicit language tag.

@lubianat lubianat May 7, 2026

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Thanks, Damien! I will fix the Protégé configs tomorrow; sorry for the mess

@gouttegd gouttegd May 7, 2026

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I can be available for a quick Zoom call in the first part of the morning (before 10am UK time) if that would help. :)

SubClassOf(<http://purl.obolibrary.org/obo/FBbi_d022f173_7141_4007_a8e0_486721e5d43d> <http://purl.obolibrary.org/obo/FBbi_00000251>)

# 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")
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