Add new term: sinus of lymph node (UBERON:9900001)

[dragon-ai-agent]

Summary

This PR adds a new term UBERON:9900001 'sinus of lymph node' as requested in issue #3586.

Changes

• Term ID: UBERON:9900001
• Name: sinus of lymph node
• Synonyms:
  • lymphatic sinus (EXACT)
  • lymph node sinus (EXACT)
• Definition: A sinus located in a lymph node. Lymph nodes have subcapsular, cortical (trabecular) and medullary sinuses.
• Logical definition:
  • intersection_of: UBERON:0000464 (anatomical space)
  • intersection_of: part_of UBERON:0000029 (lymph node)
• Reference: Wikipedia:Lymph_node
• Attribution: John Fostel (ORCID: 0000-0001-5858-4393)

Context

This term was requested by @jmfostel who works with pathologists at NIEHS. They have many pathology findings in the lymphatic sinus and need an anatomy term in UBERON to map these to. The term serves as a grouping class for the existing specific sinus terms:

• UBERON:0005463 - subcapsular sinus of lymph node
• UBERON:8410032 - trabecular sinus of lymph node
• UBERON:8410074 - lymph node paracortical sinus
• UBERON:0009744 - lymph node medullary sinus

Test plan

• Term created with proper OBO format
• Logical definition follows genus-differentia pattern
• Attribution metadata included (dc-contributor, dcterms-date, term_tracker_item)
• Synonyms added as requested
• Reference to Wikipedia included

Closes #3586

🤖 Generated with Claude Code

Signed-off-by: @dragon-ai-agent

[github-actions]

This PR modifies some logical definitions. See details below:

Number of classes with modified logical definitions: 1

sinus of lymph node

Added subclasses: 2

• trabecular sinus of lymph node
• subcapsular sinus of lymph node

[dosumis]

#gogoeditdiff

[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/2025-11-03/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/2025-11-03/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

hepatic sinusoid of left lobe of liver http://purl.obolibrary.org/obo/UBERON_0009548

Removed

• hepatic sinusoid of left lobe of liver label "hepatic sinusoid of left lobe of liver"

Added

• hepatic sinusoid of left lobe of liver label "hepatic sinusoid of left of lobe of liver"

hepatic sinusoid of right lobe of liver http://purl.obolibrary.org/obo/UBERON_0009549

Removed

• hepatic sinusoid of right lobe of liver label "hepatic sinusoid of right lobe of liver"

Added

• hepatic sinusoid of right lobe of liver label "hepatic sinusoid of right of lobe of liver"

sinus of lymph node http://purl.obolibrary.org/obo/UBERON_9900001

Added

• Class: sinus of lymph node

• sinus of lymph node IAO_0000233 "https://github.com/obophenotype/uberon/issues/3586"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• sinus of lymph node contributor 0000-0001-5858-4393

• sinus of lymph node date "2025-11-03T00:00:00Z"^^dateTime

• sinus of lymph node created_by "dragon-ai-agent"

• sinus of lymph node hasExactSynonym "lymph node sinus"

• sinus of lymph node hasExactSynonym "lymphatic sinus"

• sinus of lymph node id "UBERON:9900001"

• sinus of lymph node IAO_0000115 "A sinus located in a lymph node. Lymph nodes have subcapsular, cortical (trabecular) and medullary sinuses."

  • hasDbXref "Wikipedia:Lymph_node"

• sinus of lymph node label "sinus of lymph node"

• sinus of lymph node EquivalentTo anatomical space and (BFO_0000050 some lymph node)

• sinus of lymph node SubClassOf anatomical space

• sinus of lymph node SubClassOf BFO_0000050 some lymph node

subcapsular sinus of lymph node http://purl.obolibrary.org/obo/UBERON_0005463

Removed

• subcapsular sinus of lymph node SubClassOf anatomical space

• subcapsular sinus of lymph node SubClassOf BFO_0000050 some lymph node

Added

• subcapsular sinus of lymph node SubClassOf sinus of lymph node

trabecular sinus of lymph node http://purl.obolibrary.org/obo/UBERON_8410032

Removed

• trabecular sinus of lymph node SubClassOf anatomical space

• trabecular sinus of lymph node SubClassOf BFO_0000050 some lymph node

Added

• trabecular sinus of lymph node SubClassOf sinus of lymph node

[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

hepatic sinusoid of left of lobe of liver http://purl.obolibrary.org/obo/UBERON_0009548

Removed

• hepatic sinusoid of left of lobe of liver label "hepatic sinusoid of left lobe of liver"^^string

Added

• hepatic sinusoid of left of lobe of liver label "hepatic sinusoid of left of lobe of liver"^^string

hepatic sinusoid of right of lobe of liver http://purl.obolibrary.org/obo/UBERON_0009549

Removed

• hepatic sinusoid of right of lobe of liver label "hepatic sinusoid of right lobe of liver"^^string

Added

• hepatic sinusoid of right of lobe of liver label "hepatic sinusoid of right of lobe of liver"^^string

sinus of lymph node http://purl.obolibrary.org/obo/UBERON_9900001

Added

• Class: sinus of lymph node

• sinus of lymph node term tracker item "https://github.com/obophenotype/uberon/issues/3586"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• sinus of lymph node contributor 0000-0001-5858-4393

• sinus of lymph node date "2025-11-03T00:00:00Z"^^dateTime

• sinus of lymph node created by "dragon-ai-agent"^^string

• sinus of lymph node has exact synonym "lymph node sinus"^^string

• sinus of lymph node has exact synonym "lymphatic sinus"^^string

• sinus of lymph node id "UBERON:9900001"^^string

• sinus of lymph node definition "A sinus located in a lymph node. Lymph nodes have subcapsular, cortical (trabecular) and medullary sinuses."^^string

  • database_cross_reference "Wikipedia:Lymph_node"^^string

• sinus of lymph node label "sinus of lymph node"^^string

• sinus of lymph node EquivalentTo anatomical space and (part of some lymph node)

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.