Add specific bronchopulmonary segment terms for HCA lung dataset #3623

dragon-ai-agent · 2025-11-03T17:55:56Z

Summary

This PR adds 18 new bronchopulmonary segment terms to support anatomical annotation of lung samples in the Human Cell Atlas (HCA) CELLxGENE dataset, as requested in #3444.

Terms Added

Right lung (10 segments):

Upper lobe of right lung (UBERON:0002170):
- UBERON:9900001 right apical bronchopulmonary segment
- UBERON:9900002 right posterior bronchopulmonary segment
- UBERON:9900003 right anterior bronchopulmonary segment
Middle lobe of right lung (UBERON:0002174):
- UBERON:9900004 right lateral bronchopulmonary segment
- UBERON:9900005 right medial bronchopulmonary segment
Lower lobe of right lung (UBERON:0002171):
- UBERON:9900006 right superior bronchopulmonary segment
- UBERON:9900007 right medial basal bronchopulmonary segment
- UBERON:9900008 right anterior basal bronchopulmonary segment
- UBERON:9900009 right lateral basal bronchopulmonary segment
- UBERON:9900010 right posterior basal bronchopulmonary segment

Left lung (8 segments):

Upper lobe of left lung (UBERON:0008952):
- UBERON:9900011 left apical-posterior bronchopulmonary segment
- UBERON:9900012 left anterior bronchopulmonary segment
- UBERON:9900013 left superior lingular bronchopulmonary segment
- UBERON:9900014 left inferior lingular bronchopulmonary segment
Lower lobe of left lung (UBERON:0008953):
- UBERON:9900015 left superior bronchopulmonary segment
- UBERON:9900016 left antero-medial basal bronchopulmonary segment
- UBERON:9900017 left lateral basal bronchopulmonary segment
- UBERON:9900018 left posterior basal bronchopulmonary segment

Term Structure

Each term includes:

Logical definitions: intersection_of axioms properly linking each segment to its parent lung lobe (UBERON:0002170, UBERON:0002174, UBERON:0002171, UBERON:0008952, UBERON:0008953) and the bronchopulmonary segment class (UBERON:8600017)
Definitions: Based on anatomical location and bronchial supply, referenced to PMID:18271171
Synonyms: Including standard clinical terminology and segment numbering (S1-S10)
Metadata: Proper contributor attribution (Gloria S. Pryhuber, ORCID:0000-0002-9185-3994), timestamps, and issue tracking

Openly Licensed Images

For illustration purposes, I identified several openly licensed resources:

Wikipedia/Wikimedia Commons: The Wikipedia article on bronchopulmonary segments contains images under Creative Commons Attribution-ShareAlike 4.0 License, including:
- Category:Bronchopulmonary segment on Wikimedia Commons: https://commons.wikimedia.org/wiki/Category:Bronchopulmonary_segment
PMC Open Access Article: "Application of 3D-printed pulmonary segment specimens in experimental teaching of sectional anatomy" (PMC10157950) is licensed under CC BY 4.0 and contains detailed anatomical images of bronchopulmonary segments.
Radiopaedia: While specific licensing details would need verification, Radiopaedia has annotated CT images showing bronchopulmonary segments: https://radiopaedia.org/cases/bronchopulmonary-segments-annotated-ct-2

Pulmonary Arterial Branches

As noted in the issue comments by @gpryhuber, each bronchopulmonary segment is supplied by its own bronchus and pulmonary arterial branch. This anatomical organization allows segments to be functionally and anatomically discrete, permitting surgical resection of individual segments. While I didn't add specific arterial branch relationships in this initial implementation (as detailed pulmonary arterial terminology would need to be verified/added to UBERON first), this could be a future enhancement.

Clinical Significance

As noted by @gpryhuber, bronchopulmonary segments are particularly important in:

Radiology interpretation
Thoracic surgery planning
Understanding infection patterns (segments are separated by connective tissue, which can restrict infection spread)
Functional independence allowing segmentectomy

Fixes #3444

🤖 Generated with Claude Code

@dragon-ai-agent

@dragon-ai-agent

…ung dataset Added comprehensive set of bronchopulmonary segment terms requested for CELLxGENE curation: Right lung (10 segments): - Upper lobe: apical, posterior, anterior - Middle lobe: lateral, medial - Lower lobe: superior, medial basal, anterior basal, lateral basal, posterior basal Left lung (8 segments): - Upper lobe: apical-posterior, anterior, superior lingular, inferior lingular - Lower lobe: superior, antero-medial basal, lateral basal, posterior basal Each term includes: - Logical definitions with intersection_of axioms linking segments to their parent lung lobes - References to PMID:18271171 for anatomical definitions - Proper metadata including contributor attribution (Gloria S. Pryhuber), timestamps, and issue tracking - Standard synonyms including segment numbers (S1-S10) These terms provide the anatomical granularity needed for lung sample annotation in HCA datasets. Fixes #3444 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com> @dragon-ai-agent

github-actions · 2025-11-03T17:58:11Z

This PR modifies some logical definitions. See details below:

Number of classes with modified logical definitions: 18