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Add HRA capillary NTR template (32 new capillary terms) #3714

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e1f11ca
Add HRA capillary NTR template (32 new capillary terms)
zhengj2007 May 25, 2026
3752b9b
Merge remote-tracking branch 'origin/master' into add-hra-capillary-ntr
zhengj2007 Jun 26, 2026
0684f9f
Update capillary template labels, merges, and IDs
zhengj2007 Jun 27, 2026
0cf42ab
Remove empty hra-capillary-groups template
zhengj2007 Jun 27, 2026
3179c04
Register hra-capillary template with ODK
zhengj2007 Jul 5, 2026
3ff4697
Fix uberon-odk.yaml YAML formatting
zhengj2007 Jul 5, 2026
5a873b1
Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/
dosumis Jul 6, 2026
24fbb93
Complete ODK wiring for hra_capillary component
dosumis Jul 9, 2026
a9a57dd
Regenerate ODK Makefile to wire hra_capillary component (make update_…
dosumis Jul 9, 2026
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36 changes: 36 additions & 0 deletions bulk_ntr_workflow/source_data/capillary.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_alveolar-capillary,alveolar capillary,,pre-alveolar capillary,https://purl.org/ccf/ASCTB-TEMP_pre-alveolar-capillary,pre-alveolar capillary,https://doi.org/10.1152/japplphysiol.01177.2009
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_alveolar-mucosa-capillary,alveolar mucosa capillary,,alveolar mucosa arteriole,https://purl.org/ccf/ASCTB-TEMP_alveolar-mucosa-arteriole,alveolar mucosa arteriole,https://en.wikipedia.org/wiki/Posterior_superior_alveolar_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_anterior-lingual-gland-capillary,anterior lingual gland capillary,,anterior lingual gland arteriole,https://purl.org/ccf/ASCTB-TEMP_anterior-lingual-gland-arteriole,anterior lingual gland arteriole,https://en.wikipedia.org/wiki/Lingual_artery
spleen,https://purl.org/ccf/ASCTB-TEMP_arterial-capillary,Arterial Capillary,,red pulp of spleen,UBERON:0001250,red pulp of spleen,"https://doi.org/ 10.1182/ bloodadvances.2017015073, https://doi.org/10.1007/s00418-007-0320-8"
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_branch-of-superficial-white-pulp-capillary-of-spleen,branch of superficial white pulp capillary of spleen,,superficial white pulp capillary of spleen,https://purl.org/ccf/ASCTB-TEMP_superficial-white-pulp-capillary-of-spleen,superficial white pulp capillary of spleen,
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_bronchial-capillary,bronchial capillary,,bronchial arteriole,https://purl.org/ccf/ASCTB-TEMP_bronchial-arteriole,bronchial arteriole,https://en.wikipedia.org/wiki/Bronchial_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_buccal-mucosa-capillary,buccal mucosa capillary,,buccal mucosa arteriole,https://purl.org/ccf/ASCTB-TEMP_buccal-mucosa-arteriole,buccal mucosa arteriole,https://en.wikipedia.org/wiki/Buccal_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_capillary-plexus-of-posterior-pituitary-gland,capillary plexus of posterior pituitary gland,,inferior hypophysial artery,UBERON:0035492,inferior hypophysial artery,https://basicmedicalkey.com/endocrine-system-3/
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_deep-parotid-gland-capillary,deep parotid gland capillary,,deep parotid gland arteriole,https://purl.org/ccf/ASCTB-TEMP_deep-parotid-gland-arteriole,deep parotid gland arteriole,https://en.wikipedia.org/wiki/Maxillary_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_external-primary-capillary-plexus-of-median-eminence,external primary capillary plexus of median eminence,,superior hypophysial artery,UBERON:0035404,superior hypophysial artery,https://basicmedicalkey.com/endocrine-system-3/
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_inferior-labial-gland-capillary,inferior labial gland capillary,,inferior labial gland arteriole,https://purl.org/ccf/ASCTB-TEMP_inferior-labial-gland-arteriole,inferior labial gland arteriole,https://en.wikipedia.org/wiki/Inferior_labial_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_internal-primary-capillary-plexus-of-median-eminence,internal primary capillary plexus of median eminence,,external primary capillary plexus of median eminence,https://purl.org/ccf/ASCTB-TEMP_external-primary-capillary-plexus-of-median-eminence,external primary capillary plexus of median eminence,https://basicmedicalkey.com/endocrine-system-3/
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_lobular-capillary-of-pancreas,lobular capillary of pancreas,,intralobular arteriole of pancreas,https://purl.org/ccf/ASCTB-TEMP_intralobular-arteriole-of-pancreas,intralobular arteriole of pancreas,https://www.flandershealth.us/chronic-pancreatitis/microcirculation-of-the-pancreas.html
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_mandibular-pulp-capillary,mandibular pulp capillary,,mandibular pulp arteriole,https://purl.org/ccf/ASCTB-TEMP_mandibular-pulp-arteriole,mandibular pulp arteriole,https://en.wikipedia.org/wiki/Inferior_alveolar_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_maxillary-pulp-capillary,maxillary pulp capillary,,maxillary pulp arteriole,https://purl.org/ccf/ASCTB-TEMP_maxillary-pulp-arteriole,maxillary pulp arteriole,https://en.wikipedia.org/wiki/Posterior_superior_alveolar_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_palatine-gland-capillary,palatine gland capillary,,palatine gland arteriole,https://purl.org/ccf/ASCTB-TEMP_palatine-gland-arteriole,palatine gland arteriole,https://en.wikipedia.org/wiki/Greater_palatine_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_palatine-tonsil-capillary,palatine tonsil capillary,,palatine tonsil arteriole,https://purl.org/ccf/ASCTB-TEMP_palatine-tonsil-arteriole,palatine tonsil arteriole,https://en.wikipedia.org/wiki/Ascending_palatine_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-accessory-pancreatic-duct,periductal capillary of accessory pancreatic duct,,periductal arteriole of accessory pancreatic duct,https://purl.org/ccf/ASCTB-TEMP_periductal-arteriole-of-accessory-pancreatic-duct,periductal arteriole of accessory pancreatic duct,https://www.flandershealth.us/chronic-pancreatitis/microcirculation-of-the-pancreas.html
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-intercalated-duct-of-pancreas,periductal capillary of intercalated duct of pancreas,,intralobular arteriole of pancreas,https://purl.org/ccf/ASCTB-TEMP_intralobular-arteriole-of-pancreas,intralobular arteriole of pancreas,https://www.flandershealth.us/chronic-pancreatitis/microcirculation-of-the-pancreas.html
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-interlobular-duct-of-pancreas,periductal capillary of interlobular duct of pancreas,,periductal arteriole of interlobular duct of pancreas,https://purl.org/ccf/ASCTB-TEMP_periductal-arteriole-of-interlobular-duct-of-pancreas,periductal arteriole of interlobular duct of pancreas,https://www.flandershealth.us/chronic-pancreatitis/microcirculation-of-the-pancreas.html
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-intralobular-duct-of-panceas,periductal capillary of intralobular duct of panceas,,intralobular arteriole of pancreas,https://purl.org/ccf/ASCTB-TEMP_intralobular-arteriole-of-pancreas,intralobular arteriole of pancreas,https://www.flandershealth.us/chronic-pancreatitis/microcirculation-of-the-pancreas.html
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-main-pancreatic-duct,periductal capillary of main pancreatic duct,,periductal arteriole of main pancreatic duct,https://purl.org/ccf/ASCTB-TEMP_periductal-arteriole-of-main-pancreatic-duct,periductal arteriole of main pancreatic duct,https://www.flandershealth.us/chronic-pancreatitis/microcirculation-of-the-pancreas.html
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_post-alveolar-capillary,post-alveolar capillary,,intra-acinar venule,UBERON:8600061,intra-acinar venule,https://doi.org/10.1152/japplphysiol.01177.2009
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_post-sheath-open-capillary-of-spleen,post-sheath open capillary of spleen,,"sheathed capillary of spleen, Sheathed capillary of spleen",https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen,"sheathed capillary of spleen, Sheathed capillary of spleen",
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_pre-alveolar-capillary,pre-alveolar capillary,,intra-acinar arteriole,UBERON:8600094,intra-acinar arteriole,https://doi.org/10.1152/japplphysiol.01177.2009
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_secondary-capillary-plexus-of-anterior-pituitary-gland,secondary capillary plexus of anterior pituitary gland,,Hypophysial long portal vein,http://purl.org/sig/ont/fma/fma0327575,Hypophysial long portal vein,https://basicmedicalkey.com/endocrine-system-3/
spleen,https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen,sheathed capillary of spleen,,"red pulp of spleen, spleen perifollicular zone, non-penicillar arteriole of spleen","UBERON:0001250, UBERON:0005353, https://purl.org/ccf/ASCTB-TEMP_non-penicillar-arteriole-of-spleen","red pulp of spleen, spleen perifollicular zone, non-penicillar arteriole of spleen","https://doi.org/10.1007/s00418-013-1172-z, https://doi.org/10.1111/j.1365-2559.1985.tb02841.x, https://doi.org/10.1111/j.1365-2559.1986.tb02482.x, https://doi.org/10.1111/imm.12469, https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1017/CBO9780511545979, https://doi.org/10.1182/bloodadvances.2017015073, https://doi.org/10.1007/s00418-020-01924-3, https://doi.org/10.1371/journal.pone.0191019"
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_sublingual-gland-capillary,sublingual gland capillary,,sublingual gland arteriole,https://purl.org/ccf/ASCTB-TEMP_sublingual-gland-arteriole,sublingual gland arteriole,https://en.wikipedia.org/wiki/Lingual_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_submandibular-gland-capillary,submandibular gland capillary,,submandibular gland arteriole,https://purl.org/ccf/ASCTB-TEMP_submandibular-gland-arteriole,submandibular gland arteriole,https://en.wikipedia.org/wiki/Glandular_branches_of_facial_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_superficial-white-pulp-capillary-of-spleen,superficial white pulp capillary of spleen,,"sheathed capillary of spleen, Sheathed capillary of spleen",https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen,"sheathed capillary of spleen, Sheathed capillary of spleen",
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_superior-labial-gland-capillary,superior labial gland capillary,,superior labial gland arteriole,https://purl.org/ccf/ASCTB-TEMP_superior-labial-gland-arteriole,superior labial gland arteriole,https://en.wikipedia.org/wiki/Superior_labial_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_superior-parotid-gland-capillary,superior parotid gland capillary,,superior parotid gland arteriole,https://purl.org/ccf/ASCTB-TEMP_superior-parotid-gland-arteriole,superior parotid gland arteriole,https://en.wikipedia.org/wiki/Superficial_temporal_artery
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_tongue-capillary,tongue capillary,,tongue arteriole,https://purl.org/ccf/ASCTB-TEMP_tongue-arteriole,tongue arteriole,https://en.wikipedia.org/wiki/Lingual_artery
placenta,https://purl.org/ccf/ASCTB-TEMP_villous-capillary,villous capillary,,,UBERON:8600030,chorionic terminal villus,
blood-vasculature,https://purl.org/ccf/ASCTB-TEMP_weber-s-gland-capillary,Weber's gland capillary,,Weber's gland arteriole,https://purl.org/ccf/ASCTB-TEMP_weber-s-gland-arteriole,Weber's gland arteriole,PMID:32119400
2 changes: 2 additions & 0 deletions src/templates/hra-capillary-groups.template.tsv
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ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref
ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=|
2 changes: 2 additions & 0 deletions src/templates/hra-capillary-reports/candidates.tsv
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label as_iri uberon_id note
villous capillary UBERON:8600041 confirmed_match (confidence: high)
30 changes: 30 additions & 0 deletions src/templates/hra-capillary-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
alveolar capillary https://purl.org/ccf/ASCTB-TEMP_alveolar-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_pre-alveolar-capillary pre-alveolar capillary Parent not yet in UBERON; subagent should search OLS4 for correct parent
alveolar mucosa capillary https://purl.org/ccf/ASCTB-TEMP_alveolar-mucosa-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_alveolar-mucosa-arteriole alveolar mucosa arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
anterior lingual gland capillary https://purl.org/ccf/ASCTB-TEMP_anterior-lingual-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_anterior-lingual-gland-arteriole anterior lingual gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
branch of superficial white pulp capillary of spleen https://purl.org/ccf/ASCTB-TEMP_branch-of-superficial-white-pulp-capillary-of-spleen asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superficial-white-pulp-capillary-of-spleen superficial white pulp capillary of spleen Parent not yet in UBERON; subagent should search OLS4 for correct parent
bronchial capillary https://purl.org/ccf/ASCTB-TEMP_bronchial-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_bronchial-arteriole bronchial arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
buccal mucosa capillary https://purl.org/ccf/ASCTB-TEMP_buccal-mucosa-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_buccal-mucosa-arteriole buccal mucosa arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
deep parotid gland capillary https://purl.org/ccf/ASCTB-TEMP_deep-parotid-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_deep-parotid-gland-arteriole deep parotid gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
inferior labial gland capillary https://purl.org/ccf/ASCTB-TEMP_inferior-labial-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_inferior-labial-gland-arteriole inferior labial gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
internal primary capillary plexus of median eminence https://purl.org/ccf/ASCTB-TEMP_internal-primary-capillary-plexus-of-median-eminence asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_external-primary-capillary-plexus-of-median-eminence external primary capillary plexus of median eminence Parent not yet in UBERON; subagent should search OLS4 for correct parent
lobular capillary of pancreas https://purl.org/ccf/ASCTB-TEMP_lobular-capillary-of-pancreas asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_intralobular-arteriole-of-pancreas intralobular arteriole of pancreas Parent not yet in UBERON; subagent should search OLS4 for correct parent
mandibular pulp capillary https://purl.org/ccf/ASCTB-TEMP_mandibular-pulp-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_mandibular-pulp-arteriole mandibular pulp arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
maxillary pulp capillary https://purl.org/ccf/ASCTB-TEMP_maxillary-pulp-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_maxillary-pulp-arteriole maxillary pulp arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
palatine gland capillary https://purl.org/ccf/ASCTB-TEMP_palatine-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_palatine-gland-arteriole palatine gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
palatine tonsil capillary https://purl.org/ccf/ASCTB-TEMP_palatine-tonsil-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_palatine-tonsil-arteriole palatine tonsil arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
periductal capillary of accessory pancreatic duct https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-accessory-pancreatic-duct asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_periductal-arteriole-of-accessory-pancreatic-duct periductal arteriole of accessory pancreatic duct Parent not yet in UBERON; subagent should search OLS4 for correct parent
periductal capillary of intercalated duct of pancreas https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-intercalated-duct-of-pancreas asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_intralobular-arteriole-of-pancreas intralobular arteriole of pancreas Parent not yet in UBERON; subagent should search OLS4 for correct parent
periductal capillary of interlobular duct of pancreas https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-interlobular-duct-of-pancreas asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_periductal-arteriole-of-interlobular-duct-of-pancreas periductal arteriole of interlobular duct of pancreas Parent not yet in UBERON; subagent should search OLS4 for correct parent
periductal capillary of intralobular duct of panceas https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-intralobular-duct-of-panceas asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_intralobular-arteriole-of-pancreas intralobular arteriole of pancreas Parent not yet in UBERON; subagent should search OLS4 for correct parent
periductal capillary of main pancreatic duct https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-main-pancreatic-duct asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_periductal-arteriole-of-main-pancreatic-duct periductal arteriole of main pancreatic duct Parent not yet in UBERON; subagent should search OLS4 for correct parent
post-sheath open capillary of spleen https://purl.org/ccf/ASCTB-TEMP_post-sheath-open-capillary-of-spleen asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen sheathed capillary of spleen, Sheathed capillary of spleen Parent not yet in UBERON; subagent should search OLS4 for correct parent
secondary capillary plexus of anterior pituitary gland https://purl.org/ccf/ASCTB-TEMP_secondary-capillary-plexus-of-anterior-pituitary-gland fma_parent FMA:0327575 Hypophysial long portal vein Subagent should resolve FMA→UBERON via OLS4
sheathed capillary of spleen https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen asctb_temp_parent UBERON:0001250, UBERON:0005353, https://purl.org/ccf/ASCTB-TEMP_non-penicillar-arteriole-of-spleen red pulp of spleen, spleen perifollicular zone, non-penicillar arteriole of spleen Parent not yet in UBERON; subagent should search OLS4 for correct parent
sublingual gland capillary https://purl.org/ccf/ASCTB-TEMP_sublingual-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_sublingual-gland-arteriole sublingual gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
submandibular gland capillary https://purl.org/ccf/ASCTB-TEMP_submandibular-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_submandibular-gland-arteriole submandibular gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
superficial white pulp capillary of spleen https://purl.org/ccf/ASCTB-TEMP_superficial-white-pulp-capillary-of-spleen asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen sheathed capillary of spleen, Sheathed capillary of spleen Parent not yet in UBERON; subagent should search OLS4 for correct parent
superior labial gland capillary https://purl.org/ccf/ASCTB-TEMP_superior-labial-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superior-labial-gland-arteriole superior labial gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
superior parotid gland capillary https://purl.org/ccf/ASCTB-TEMP_superior-parotid-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superior-parotid-gland-arteriole superior parotid gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
tongue capillary https://purl.org/ccf/ASCTB-TEMP_tongue-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_tongue-arteriole tongue arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
Weber's gland capillary https://purl.org/ccf/ASCTB-TEMP_weber-s-gland-capillary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_weber-s-gland-arteriole Weber's gland arteriole Parent not yet in UBERON; subagent should search OLS4 for correct parent
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