Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
zhengj2007 wants to merge 9 commits into
base: master
Choose a base branch
from
Open

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

Show file tree
Hide file tree
Changes from 7 commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions bulk_ntr_workflow/outputs/hra-capillary-reports/candidates.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
label as_iri uberon_id note
villous capillary UBERON:8600041 confirmed_match (confidence: high)
30 changes: 30 additions & 0 deletions bulk_ntr_workflow/outputs/hra-capillary-reports/errors.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
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
36 changes: 36 additions & 0 deletions bulk_ntr_workflow/outputs/hra-capillary-reports/input.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
table as_iri label uberon_id parent_id parent_label references term_type
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_alveolar-capillary alveolar capillary https://purl.org/ccf/ASCTB-TEMP_pre-alveolar-capillary pre-alveolar capillary https://doi.org/10.1152/japplphysiol.01177.2009 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_alveolar-mucosa-capillary alveolar mucosa capillary https://purl.org/ccf/ASCTB-TEMP_alveolar-mucosa-arteriole alveolar mucosa arteriole https://en.wikipedia.org/wiki/Posterior_superior_alveolar_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_anterior-lingual-gland-capillary anterior lingual gland capillary https://purl.org/ccf/ASCTB-TEMP_anterior-lingual-gland-arteriole anterior lingual gland arteriole https://en.wikipedia.org/wiki/Lingual_artery leaf
spleen https://purl.org/ccf/ASCTB-TEMP_arterial-capillary Arterial Capillary UBERON:0001250 red pulp of spleen https://doi.org/ 10.1182/ bloodadvances.2017015073, https://doi.org/10.1007/s00418-007-0320-8 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_branch-of-superficial-white-pulp-capillary-of-spleen branch of superficial white pulp capillary of spleen https://purl.org/ccf/ASCTB-TEMP_superficial-white-pulp-capillary-of-spleen superficial white pulp capillary of spleen leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_bronchial-capillary bronchial capillary https://purl.org/ccf/ASCTB-TEMP_bronchial-arteriole bronchial arteriole https://en.wikipedia.org/wiki/Bronchial_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_buccal-mucosa-capillary buccal mucosa capillary https://purl.org/ccf/ASCTB-TEMP_buccal-mucosa-arteriole buccal mucosa arteriole https://en.wikipedia.org/wiki/Buccal_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_capillary-plexus-of-posterior-pituitary-gland capillary plexus of posterior pituitary gland UBERON:0035492 inferior hypophysial artery https://basicmedicalkey.com/endocrine-system-3/ leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_deep-parotid-gland-capillary deep parotid gland capillary https://purl.org/ccf/ASCTB-TEMP_deep-parotid-gland-arteriole deep parotid gland arteriole https://en.wikipedia.org/wiki/Maxillary_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_external-primary-capillary-plexus-of-median-eminence external primary capillary plexus of median eminence UBERON:0035404 superior hypophysial artery https://basicmedicalkey.com/endocrine-system-3/ leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_inferior-labial-gland-capillary inferior labial gland capillary https://purl.org/ccf/ASCTB-TEMP_inferior-labial-gland-arteriole inferior labial gland arteriole https://en.wikipedia.org/wiki/Inferior_labial_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_internal-primary-capillary-plexus-of-median-eminence internal 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/ leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_lobular-capillary-of-pancreas lobular capillary 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_mandibular-pulp-capillary mandibular pulp capillary https://purl.org/ccf/ASCTB-TEMP_mandibular-pulp-arteriole mandibular pulp arteriole https://en.wikipedia.org/wiki/Inferior_alveolar_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_maxillary-pulp-capillary maxillary pulp capillary https://purl.org/ccf/ASCTB-TEMP_maxillary-pulp-arteriole maxillary pulp arteriole https://en.wikipedia.org/wiki/Posterior_superior_alveolar_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_palatine-gland-capillary palatine gland capillary https://purl.org/ccf/ASCTB-TEMP_palatine-gland-arteriole palatine gland arteriole https://en.wikipedia.org/wiki/Greater_palatine_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_palatine-tonsil-capillary palatine tonsil capillary https://purl.org/ccf/ASCTB-TEMP_palatine-tonsil-arteriole palatine tonsil arteriole https://en.wikipedia.org/wiki/Ascending_palatine_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-accessory-pancreatic-duct periductal capillary 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-intercalated-duct-of-pancreas periductal capillary of intercalated duct 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-interlobular-duct-of-pancreas periductal capillary 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-intralobular-duct-of-panceas periductal capillary of intralobular duct of panceas 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_periductal-capillary-of-main-pancreatic-duct periductal capillary 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_post-alveolar-capillary post-alveolar capillary UBERON:8600061 intra-acinar venule https://doi.org/10.1152/japplphysiol.01177.2009 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_post-sheath-open-capillary-of-spleen post-sheath open capillary of spleen https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen sheathed capillary of spleen, Sheathed capillary of spleen leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_pre-alveolar-capillary pre-alveolar capillary UBERON:8600094 intra-acinar arteriole https://doi.org/10.1152/japplphysiol.01177.2009 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_secondary-capillary-plexus-of-anterior-pituitary-gland secondary capillary plexus of anterior pituitary gland http://purl.org/sig/ont/fma/fma0327575 Hypophysial long portal vein https://basicmedicalkey.com/endocrine-system-3/ leaf
spleen https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen sheathed capillary 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 leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_sublingual-gland-capillary sublingual gland capillary https://purl.org/ccf/ASCTB-TEMP_sublingual-gland-arteriole sublingual gland arteriole https://en.wikipedia.org/wiki/Lingual_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_submandibular-gland-capillary submandibular gland capillary https://purl.org/ccf/ASCTB-TEMP_submandibular-gland-arteriole submandibular gland arteriole https://en.wikipedia.org/wiki/Glandular_branches_of_facial_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_superficial-white-pulp-capillary-of-spleen superficial white pulp capillary of spleen https://purl.org/ccf/ASCTB-TEMP_sheathed-capillary-of-spleen sheathed capillary of spleen, Sheathed capillary of spleen leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_superior-labial-gland-capillary superior labial gland capillary https://purl.org/ccf/ASCTB-TEMP_superior-labial-gland-arteriole superior labial gland arteriole https://en.wikipedia.org/wiki/Superior_labial_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_superior-parotid-gland-capillary superior parotid gland capillary https://purl.org/ccf/ASCTB-TEMP_superior-parotid-gland-arteriole superior parotid gland arteriole https://en.wikipedia.org/wiki/Superficial_temporal_artery leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_tongue-capillary tongue capillary https://purl.org/ccf/ASCTB-TEMP_tongue-arteriole tongue arteriole https://en.wikipedia.org/wiki/Lingual_artery leaf
placenta https://purl.org/ccf/ASCTB-TEMP_villous-capillary villous capillary UBERON:8600030 chorionic terminal villus leaf
blood-vasculature https://purl.org/ccf/ASCTB-TEMP_weber-s-gland-capillary Weber's gland capillary https://purl.org/ccf/ASCTB-TEMP_weber-s-gland-arteriole Weber's gland arteriole PMID:32119400 leaf
Loading
Loading