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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Add structures in LMHA and not in uberon #1940

Open cmungall opened 3 years ago

cmungall commented 3 years ago

See https://github.com/mapping-commons/lmha-obo-mappings/issues/1

subject_id subject_label subject_category
LMHA:00645 visceral afferent sensory nerve terminal AnatomicalSystem
LMHA:00378 subendothelial connective tissue cell AnatomicalSystem
LMHA:00516 left anterior bronchus AnatomicalStructure
LMHA:00546 respiratory autonomic nervous system AnatomicalSystem
LMHA:00525 left lateral basal bronchus AnatomicalStructure
LMHA:00523 inferior lingular bronchus AnatomicalStructure
LMHA:00518 left apical bronchus AnatomicalStructure
LMHA:00486 pulmonary muscular arteriole tunica adventitia AnatomicalSystem
LMHA:00517 left anterior basal bronchus AnatomicalStructure
LMHA:00473 bronchial artery tunica adventitia AnatomicalStructure
LMHA:00539 right anterior basal segmental bronchus AnatomicalStructure
LMHA:00472 bronchial arteriole tunica adventitia AnatomicalStructure
LMHA:00526 right lateral bronchus AnatomicalStructure
LMHA:00545 left posterior bronchus AnatomicalStructure
LMHA:00544 left posterior basal bronchus AnatomicalStructure
LMHA:00542 medial bronchus AnatomicalStructure
LMHA:00292 pulmonary artery tunica adventitia AnatomicalSystem
LMHA:00541 medial basal bronchus AnatomicalStructure
LMHA:00616 right apical bronchus AnatomicalStructure
LMHA:00554 right upper lobe anterior bronchus AnatomicalStructure
LMHA:00553 superior lingular bronchus AnatomicalStructure
LMHA:00552 left lower lobe superior bronchus AnatomicalStructure
LMHA:00315 pulmonary blood vessel AnatomicalSystem
LMHA:00620 right posterior bronchus AnatomicalStructure
LMHA:00619 right lower lobe superior bronchus AnatomicalStructure
LMHA:00618 right posterior basal bronchus AnatomicalStructure
LMHA:00617 right lateral basal bronchus AnatomicalStructure
LMHA:00297 pulmonary distal arteriole AnatomicalSystem
LMHA:00635 left pulmonary nerve plexus AnatomicalStructure
LMHA:00107 bronchial vein tunica intima AnatomicalStructure
LMHA:00106 bronchial vein tunica adventitia AnatomicalStructure
LMHA:00537 left upper lobe visceral pleura AnatomicalStructure
LMHA:00636 left anterior pulmonary nerve plexus AnatomicalStructure
LMHA:00108 bronchial vein tunica media AnatomicalStructure
LMHA:00257 non-adrenergic and non-cholinergic nerve AnatomicalSystem
LMHA:00632 intra-parenchymal blood vessel AnatomicalSystem
LMHA:00110 bronchial venule tunica adventitia AnatomicalStructure
LMHA:00109 bronchial venule AnatomicalStructure
LMHA:00111 bronchial venule tunica intima AnatomicalStructure
LMHA:00640 right posterior pulmonary nerve plexus AnatomicalSystem
LMHA:00139 respiratory bronchiolar wall AnatomicalStructure
LMHA:00114 bronchiolar adventitia AnatomicalStructure
LMHA:00112 bronchial venule tunica media AnatomicalStructure
LMHA:00641 pulmonary autonomic nerve AnatomicalSystem
LMHA:00637 left posterior pulmonary nerve plexus AnatomicalStructure
LMHA:00580 membranous bronchiolar wall AnatomicalStructure
LMHA:00358 terminal bronchiolar wall AnatomicalStructure
LMHA:00638 right pulmonary nerve plexus AnatomicalSystem
LMHA:00639 right anterior pulmonary nerve plexus AnatomicalStructure
LMHA:00031 right middle lobe hilum AnatomicalStructure
LMHA:00312 pulmonary muscular venule tunica media AnatomicalSystem
LMHA:00037 right middle lobe visceral pleura AnatomicalStructure
LMHA:00038 right upper lobe alveolar parenchyma AnatomicalStructure
LMHA:00818 alveolar sac lumen AnatomicalStructure
LMHA:00535 left upper lobe hilum AnatomicalStructure
LMHA:00040 right upper lobe hilum AnatomicalStructure
LMHA:00550 right lung segmental bronchus AnatomicalStructure
LMHA:00046 right upper lobe visceral pleura AnatomicalStructure
LMHA:00146 collecting duct cell AnatomicalStructure
LMHA:00094 bronchial adventitia AnatomicalStructure
LMHA:00300 pulmonary distal arteriole tunica media AnatomicalSystem
LMHA:00530 left lung segmental bronchus AnatomicalStructure
LMHA:00298 pulmonary distal arteriole tunica adventitia AnatomicalSystem
LMHA:00303 pulmonary distal venule tunica intima AnatomicalSystem
LMHA:00304 pulmonary muscular arteriole AnatomicalSystem
LMHA:00316 pulmonary venule AnatomicalSystem
LMHA:00301 pulmonary distal venule AnatomicalSystem
LMHA:00133 tracheal cartilaginous ring AnatomicalStructure
LMHA:00302 pulmonary distal venule tunica adventitia AnatomicalSystem
LMHA:00306 pulmonary vein tunica adventitia AnatomicalSystem
LMHA:00560 left upper lobe interlobular septum AnatomicalStructure
LMHA:00020 right lower lobe alveolar parenchyma AnatomicalStructure
LMHA:00559 left lower lobe interlobular septum AnatomicalStructure
LMHA:00440 vascular connective tissue AnatomicalSystem
LMHA:00589 bronchiolar lamina propria AnatomicalStructure
LMHA:00309 pulmonary muscular venule AnatomicalSystem
LMHA:00566 right upper lobe interlobular septum AnatomicalStructure
LMHA:00565 right middle lobe interlobular septum AnatomicalStructure
LMHA:00310 pulmonary muscular venule tunica adventitia AnatomicalSystem
LMHA:00564 right lower lobe interlobular septum AnatomicalStructure
LMHA:00022 right lower lobe hilum AnatomicalStructure
LMHA:00308 pulmonary vein tunica media AnatomicalSystem
LMHA:00138 respiratory bronchiolar lumen AnatomicalStructure
LMHA:00028 right lower lobe visceral pleura AnatomicalStructure
LMHA:00029 right middle lobe alveolar parenchyma AnatomicalStructure
LMHA:00547 respiratory immune system AnatomicalSystem
LMHA:00357 terminal bronchiolar lumen AnatomicalStructure
LMHA:00068 alveolar lumen AnatomicalStructure
LMHA:00307 pulmonary vein tunica intima AnatomicalSystem
LMHA:00311 pulmonary muscular venule tunica intima AnatomicalSystem
LMHA:00529 left lung lower lobe AnatomicalStructure
LMHA:00290 pulmonary arteriole AnatomicalSystem
LMHA:00096 bronchial arteriole tunica intima AnatomicalStructure
LMHA:00202 left lower lobe hilum AnatomicalStructure
LMHA:00299 pulmonary distal arteriole tunica intima AnatomicalSystem
LMHA:00207 left lower lobe visceral pleura AnatomicalStructure
LMHA:00488 pulmonary muscular arteriole tunica intima AnatomicalSystem
LMHA:00367 tracheal adventitia AnatomicalStructure
LMHA:00060 alveolar capillary bed AnatomicalSystem
LMHA:00064 alveolar duct wall AnatomicalStructure
LMHA:00071 alveolar septal crest AnatomicalStructure
LMHA:00489 pulmonary muscular arteriole tunica media AnatomicalSystem
LMHA:00563 respiratory bronchiolar alveolus AnatomicalStructure
LMHA:00634 pulmonary autonomic ganglion AnatomicalSystem
LMHA:00294 pulmonary artery tunica media AnatomicalSystem
LMHA:00061 alveolar capillary endothelium AnatomicalSystem
LMHA:00533 left upper lobe alveolar parenchyma AnatomicalStructure
LMHA:00200 left lower lobe alveolar parenchyma AnatomicalStructure
LMHA:00063 alveolar duct lumen AnatomicalStructure
LMHA:00351 submucosal gland epithelium AnatomicalStructure
LMHA:00067 alveolar interstitial tissue AnatomicalStructure
LMHA:00124 bronchus wall AnatomicalStructure
LMHA:00104 bronchial blood vessel AnatomicalSystem
LMHA:00095 bronchial arteriole AnatomicalSystem
LMHA:00097 bronchial arteriole tunica media AnatomicalStructure
LMHA:00100 bronchial artery tunica media AnatomicalStructure
LMHA:00694 submucosal gland epithelial cell AnatomicalStructure
LMHA:00595 bronchial cartilaginous ring AnatomicalStructure
LMHA:00099 bronchial artery tunica intima AnatomicalStructure
LMHA:00293 pulmonary artery tunica intima AnatomicalSystem
LMHA:00579 membranous bronchiolar lumen AnatomicalStructure
LMHA:00578 membranous bronchiole AnatomicalStructure
LMHA:00366 trachea wall AnatomicalStructure
LMHA:00693 submucosal gland duct epithelial cell AnatomicalStructure
LMHA:00286 respiratory bronchiolar epithelium AnatomicalStructure
LMHA:00222 lymphatic vessel tunica media AnatomicalSystem
LMHA:00221 lymphatic vessel tunica intima AnatomicalSystem
LMHA:00220 lymphatic vessel tunica adventitia AnatomicalSystem
LMHA:00581 membranous bronchiolar epithelium AnatomicalStructure
dosumis commented 3 years ago
  1. [ ] Review to see if some are actually in Uberon & add xrefs to LHMA.
  2. [ ] Map to FMA where possible
  3. [ ] Mark cases that could be added via patterns
  4. [ ] Cell terms -> CL repo. (Note there is a parallel ticket to this on the CL repo).

TBD - should we add L/R terms to Uberon on this case?

dosumis commented 2 years ago

Looks like this needs to be broken down before we can start to make progress on this. @JoshuaFortriede - are you happy to make a start or would you like to discuss further.

github-actions[bot] commented 1 year ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

dosumis commented 1 year ago

@aleixpuigb & @JoshuaFortriede - would you be able to work together on this?

aleixpuigb commented 1 year ago

Yes, of course. @JoshuaFortriede, I would like to have a look to the related issue to see what has been done and we could have a chat then if you are available, to discuss how to approach it

github-actions[bot] commented 9 months ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

dosumis commented 6 months ago

@aleixpuigb to discuss with @JoshuaFortriede - can we come up with a set of design patterns as a way to get this in? Could more work be done to map some of these to existing terms?