New term: conducting airway epithelium

[dosumis]

Added new term for conducting airway epithelium + attempts at related refactoring. DRAFT!
#3491

[dosumis]

#gogoeditdiff

[github-actions]

Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

[dosumis]

Hi @cmungall - still very much draft. Disentangling this stuff is hard!

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -base file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2025-03-17/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-main.owl/uberon-base.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2025-03-17/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

conducting airway epithelium http://purl.obolibrary.org/obo/UBERON_1100003

Added

• conducting airway epithelium label "conducting airway epithelium"

• conducting airway epithelium hasOBONamespace "uberon"

• conducting airway epithelium id "UBERON:1100003"

• conducting airway epithelium contributor 0000-0002-7073-9172

• conducting airway epithelium hasDbXref "CALOHA:TS-0023"

• conducting airway epithelium IAO_0000115 "The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi."

  • hasDbXref "MGI:anna"

  • hasDbXref "ISBN:0-683-40008-8"

  • hasDbXref "MP:0010942"

• conducting airway epithelium hasDbXref "MA:0001480"

• conducting airway epithelium date "2025-03-17T12:43:44Z"^^dateTime

• conducting airway epithelium hasDbXref "EMAPA:32827"

• conducting airway epithelium hasRelatedSynonym "airway epithelium"

  • hasDbXref "BTO:0000419"

• conducting airway epithelium hasDbXref "SCTID:321764001"

• Class: conducting airway epithelium

• conducting airway epithelium EquivalentTo pseudostratified ciliated columnar epithelium and (BFO_0000050 some respiratory tract)

• conducting airway epithelium SubClassOf respiratory tract epithelium

• conducting airway epithelium SubClassOf pseudostratified ciliated columnar epithelium

endothelium of main bronchus http://purl.obolibrary.org/obo/UBERON_0003280

Removed

• endothelium of main bronchus SubClassOf epithelium of main bronchus

Added

• endothelium of main bronchus SubClassOf BFO_0000050 some main bronchus

• endothelium of main bronchus SubClassOf tracheobronchial epithelium

endothelium of trachea http://purl.obolibrary.org/obo/UBERON_0003279

Removed

• endothelium of trachea SubClassOf mixed endoderm/mesoderm-derived structure

• endothelium of trachea SubClassOf epithelium of trachea

Added

• endothelium of trachea SubClassOf tracheobronchial epithelium

• endothelium of trachea SubClassOf BFO_0000050 some trachea

epithelium of bronchiole http://purl.obolibrary.org/obo/UBERON_0002051

Added

• epithelium of bronchiole SubClassOf ciliated columnar epithelium

epithelium of bronchus http://purl.obolibrary.org/obo/UBERON_0002031

Removed

• epithelium of bronchus EquivalentTo epithelium and (BFO_0000050 some bronchus)

Added

• epithelium of bronchus EquivalentTo conducting airway epithelium and (BFO_0000050 some bronchus)

• epithelium of bronchus SubClassOf conducting airway epithelium

epithelium of lobar bronchus http://purl.obolibrary.org/obo/UBERON_0002339

Removed

• epithelium of lobar bronchus EquivalentTo epithelium and (BFO_0000050 some lobar bronchus)

Added

• epithelium of lobar bronchus EquivalentTo conducting airway epithelium and (BFO_0000050 some lobar bronchus)

epithelium of lobular bronchiole http://purl.obolibrary.org/obo/UBERON_8600001

Removed

• epithelium of lobular bronchiole EquivalentTo epithelium and (BFO_0000050 some lobular bronchiole)

Added

• epithelium of lobular bronchiole EquivalentTo conducting airway epithelium and (BFO_0000050 some lobular bronchiole)

• epithelium of lobular bronchiole SubClassOf conducting airway epithelium

epithelium of main bronchus http://purl.obolibrary.org/obo/UBERON_0002340

Removed

• epithelium of main bronchus EquivalentTo epithelium and (BFO_0000050 some main bronchus)

Added

• epithelium of main bronchus EquivalentTo conducting airway epithelium and (BFO_0000050 some main bronchus)

epithelium of nasopharynx http://purl.obolibrary.org/obo/UBERON_0001951

Added

• epithelium of nasopharynx SubClassOf simple columnar epithelium

epithelium of segmental bronchus http://purl.obolibrary.org/obo/UBERON_0002341

Removed

• epithelium of segmental bronchus EquivalentTo epithelium and (BFO_0000050 some segmental bronchus)

Added

• epithelium of segmental bronchus EquivalentTo conducting airway epithelium and (BFO_0000050 some segmental bronchus)

epithelium of trachea http://purl.obolibrary.org/obo/UBERON_0001901

Removed

• epithelium of trachea EquivalentTo epithelium and (BFO_0000050 some trachea)

Added

• epithelium of trachea EquivalentTo conducting airway epithelium and (BFO_0000050 some trachea)

• epithelium of trachea SubClassOf conducting airway epithelium

left lung lobar bronchus epithelium http://purl.obolibrary.org/obo/UBERON_0015794

Removed

• left lung lobar bronchus epithelium EquivalentTo epithelium and (BFO_0000050 some lobar bronchus of left lung)

Added

• left lung lobar bronchus epithelium EquivalentTo conducting airway epithelium and (BFO_0000050 some lobar bronchus of left lung)

nasal cavity respiratory epithelium http://purl.obolibrary.org/obo/UBERON_0005385

Added

• nasal cavity respiratory epithelium SubClassOf conducting airway epithelium

olfactory epithelium http://purl.obolibrary.org/obo/UBERON_0001997

Added

• olfactory epithelium SubClassOf conducting airway epithelium

pseudostratified ciliated epithelium of larynx http://purl.obolibrary.org/obo/UBERON_1100004

Added

• pseudostratified ciliated epithelium of larynx contributor 0000-0002-7073-9172

• pseudostratified ciliated epithelium of larynx date "2025-03-17T12:59:29Z"^^dateTime

• pseudostratified ciliated epithelium of larynx id "UBERON:1100004"

• pseudostratified ciliated epithelium of larynx label "pseudostratified ciliated epithelium of larynx"

• pseudostratified ciliated epithelium of larynx hasOBONamespace "uberon"

• Class: pseudostratified ciliated epithelium of larynx

• pseudostratified ciliated epithelium of larynx EquivalentTo pseudostratified ciliated columnar epithelium and (BFO_0000050 some larynx)

• pseudostratified ciliated epithelium of larynx SubClassOf larynx epithelium

• pseudostratified ciliated epithelium of larynx SubClassOf conducting airway epithelium

respiratory tract epithelium http://purl.obolibrary.org/obo/UBERON_0004802

Removed

• respiratory tract epithelium IAO_0000115 "The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi."

  • hasDbXref "MGI:anna"

  • hasDbXref "ISBN:0-683-40008-8"

  • hasDbXref "MP:0010942"

• respiratory tract epithelium inSubset pheno_slim

• respiratory tract epithelium hasDbXref "MA:0001480"

• respiratory tract epithelium hasDbXref "EMAPA:32827"

• respiratory tract epithelium SubClassOf pseudostratified ciliated columnar epithelium

Added

• respiratory tract epithelium IAO_0000115 "An epithelium that is part of the respiratory tract."
  • hasDbXref "ISBN:0-683-40008-8"

right lung lobar bronchus epitheium http://purl.obolibrary.org/obo/UBERON_0015795

Removed

• right lung lobar bronchus epitheium EquivalentTo epithelium and (BFO_0000050 some lobar bronchus of right lung)

Added

• right lung lobar bronchus epitheium EquivalentTo conducting airway epithelium and (BFO_0000050 some lobar bronchus of right lung)

terminal bronchus epithelium http://purl.obolibrary.org/obo/UBERON_0004818

Removed

• terminal bronchus epithelium SubClassOf epithelium of bronchus

Added

• terminal bronchus epithelium SubClassOf tracheobronchial epithelium

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/__w/uberon/uberon/master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/__w/uberon/uberon/branch/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

conducting airway epithelium http://purl.obolibrary.org/obo/UBERON_1100003

Added

• conducting airway epithelium label "conducting airway epithelium"^^string

• conducting airway epithelium has_obo_namespace "uberon"^^string

• conducting airway epithelium database_cross_reference "EMAPA:32827"^^string

• conducting airway epithelium id "UBERON:1100003"^^string

• conducting airway epithelium contributor David Osumi-Sutherland

• conducting airway epithelium database_cross_reference "CALOHA:TS-0023"^^string

• conducting airway epithelium definition "The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi."^^string

  • database_cross_reference "MGI:anna"^^string

  • database_cross_reference "ISBN:0-683-40008-8"^^string

  • database_cross_reference "MP:0010942"^^string

• conducting airway epithelium database_cross_reference "MA:0001480"^^string

• conducting airway epithelium date "2025-03-17T12:43:44Z"^^dateTime

• conducting airway epithelium has_related_synonym "airway epithelium"^^string

  • database_cross_reference "BTO:0000419"^^string

• conducting airway epithelium database_cross_reference "SCTID:321764001"^^string

• Class: conducting airway epithelium

• conducting airway epithelium EquivalentTo pseudostratified ciliated columnar epithelium and (part of some respiratory tract)

epithelium of bronchus http://purl.obolibrary.org/obo/UBERON_0002031

Removed

• epithelium of bronchus EquivalentTo epithelium and (part of some bronchus)

• epithelium of bronchus SubClassOf simple columnar epithelium

Added

• epithelium of bronchus EquivalentTo conducting airway epithelium and (part of some bronchus)

epithelium of lobar bronchus http://purl.obolibrary.org/obo/UBERON_0002339

Removed

• epithelium of lobar bronchus EquivalentTo epithelium and (part of some lobar bronchus)

Added

• epithelium of lobar bronchus EquivalentTo conducting airway epithelium and (part of some lobar bronchus)

epithelium of lobular bronchiole http://purl.obolibrary.org/obo/UBERON_8600001

Removed

• epithelium of lobular bronchiole EquivalentTo epithelium and (part of some lobular bronchiole)

Added

• epithelium of lobular bronchiole EquivalentTo conducting airway epithelium and (part of some lobular bronchiole)

epithelium of main bronchus http://purl.obolibrary.org/obo/UBERON_0002340

Removed

• epithelium of main bronchus EquivalentTo epithelium and (part of some main bronchus)

Added

• epithelium of main bronchus EquivalentTo conducting airway epithelium and (part of some main bronchus)

epithelium of segmental bronchus http://purl.obolibrary.org/obo/UBERON_0002341

Removed

• epithelium of segmental bronchus EquivalentTo epithelium and (part of some segmental bronchus)

Added

• epithelium of segmental bronchus EquivalentTo conducting airway epithelium and (part of some segmental bronchus)

epithelium of trachea http://purl.obolibrary.org/obo/UBERON_0001901

Removed

• epithelium of trachea EquivalentTo epithelium and (part of some trachea)

• epithelium of trachea SubClassOf simple columnar epithelium

Added

• epithelium of trachea EquivalentTo conducting airway epithelium and (part of some trachea)

left lung lobar bronchus epithelium http://purl.obolibrary.org/obo/UBERON_0015794

Removed

• left lung lobar bronchus epithelium EquivalentTo epithelium and (part of some lobar bronchus of left lung)

Added

• left lung lobar bronchus epithelium EquivalentTo conducting airway epithelium and (part of some lobar bronchus of left lung)

pseudostratified ciliated epithelium of larynx http://purl.obolibrary.org/obo/UBERON_1100004

Added

• pseudostratified ciliated epithelium of larynx contributor David Osumi-Sutherland

• pseudostratified ciliated epithelium of larynx date "2025-03-17T12:59:29Z"^^dateTime

• pseudostratified ciliated epithelium of larynx id "UBERON:1100004"^^string

• pseudostratified ciliated epithelium of larynx has_obo_namespace "uberon"^^string

• pseudostratified ciliated epithelium of larynx label "pseudostratified ciliated epithelium of larynx"^^string

• Class: pseudostratified ciliated epithelium of larynx

• pseudostratified ciliated epithelium of larynx EquivalentTo pseudostratified ciliated columnar epithelium and (part of some larynx)

respiratory tract epithelium http://purl.obolibrary.org/obo/UBERON_0004802

Removed

• respiratory tract epithelium definition "The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi."^^string

  • database_cross_reference "MGI:anna"^^string

  • database_cross_reference "ISBN:0-683-40008-8"^^string

  • database_cross_reference "MP:0010942"^^string

• respiratory tract epithelium in_subset pheno_slim

• respiratory tract epithelium database_cross_reference "MA:0001480"^^string

• respiratory tract epithelium database_cross_reference "EMAPA:32827"^^string

• respiratory tract epithelium SubClassOf pseudostratified ciliated columnar epithelium

Added

• respiratory tract epithelium definition "An epithelium that is part of the respiratory tract."^^string
  • database_cross_reference "ISBN:0-683-40008-8"^^string

right lung lobar bronchus epitheium http://purl.obolibrary.org/obo/UBERON_0015795

Removed

• right lung lobar bronchus epitheium EquivalentTo epithelium and (part of some lobar bronchus of right lung)

Added

• right lung lobar bronchus epitheium EquivalentTo conducting airway epithelium and (part of some lobar bronchus of right lung)

[cmungall]

LGTM