obophenotype / obophenotype/uberon

Add specific bronchopulmonary segments

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Description

Currently curating a dataset for HCA lung for CELLxGENE, and Gloria Pryhuber and her team have assigned their samples to the specific bronchopulmonary segment of the lung. We did not see the lung ontologized at this level of granularity and was hoping to have it added as below:

Preferred term label:

  • Right lobe:
    • upper lobe of right lung (UBERON:0002170):
      • right apical bronchopulmonary segment
      • right posterior bronchopulmonary segment
      • right anterior bronchopulmonary segment
    • middle lobe of right lung (UBERON:0002174):
      • right lateral bronchopulmonary segment
      • right medial bronchopulmonary segment
    • lower lobe of right lung (UBERON:0002171):
      • right superior bronchopulmonary segment
      • right medial basal bronchopulmonary segment
      • right anterior basal bronchopulmonary segment
      • right lateral basal bronchopulmonary segment
      • right posterior basal bronchopulmonary segment
  • Left lobe:
    • upper lobe of left lung (UBERON:0008952):
      • left apical-posterior bronchopulmonary segment
        • left apical bronchopulmonary segment
        • left posterior bronchopulmonary segment
      • left anterior bronchopulmonary segment
      • left superior lingular bronchopulmonary segment
      • left inferior lingular bronchopulmonary segment
    • lower lobe of left lung (UBERON:0008953):
      • left superior bronchopulmonary segment
      • left antero-medial basal bronchopulmonary segment
        • left medial basal bronchopulmonary segment
        • left anterior basal bronchopulmonary segment
      • left lateral basal bronchopulmonary segment
      • left posterior basal bronchopulmonary segment

Synonyms

Definition
The segment of the lung that is supplied by the tertiary bronchus of the same name.
There are a number of diagrams online, but here are a few publications/resources with images:

Screenshot 2024-12-11 at 4 06 05 PM

Parent term

  • "bronchopulmonary segment" (UBERON:8600017)
  • Also have lobe as parent, as listed above

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the existing UBERON:8600017 bronchopulmonary segment term and the listed lung-lobe terms to understand their current hierarchy. Add the requested right- and left-lung segment terms with the stated parent relationships and definition, then verify that all requested segments are represented consistently in the ontology.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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