Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
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
9 changes: 9 additions & 0 deletions bulk_ntr_workflow/outputs/hra-lymph-reports/candidates.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
label as_iri uberon_id note
cubital fossa lymph node UBERON:0038870 confirmed_match (confidence: high)
medial lymph node of common iliac lymph nodes UBERON:0037532 confirmed_match (confidence: high)
deep lymph node of neck UBERON:0004722 confirmed_match (confidence: high)
left anterior mediastinal lymph node UBERON:0035520 possible_match (UBERON:0035520 is 'anterior mediastinal lymph node' but its definition specifies 'right side of the heart', suggesting this left-lateralized term may be distinct. The existing term has FMA:12775 which may or may not cover bilateral structures. Further investigation needed to confirm if this is truly a new term or if the existing definition should be updated to remove laterality bias.)
left lateral aortic lymph node UBERON:0016386 possible_match (UBERON has 'paraaortic lymph node' with exact synonym 'lateral aortic lymph node' (FMA:16604). However, this term is left-specific, while UBERON term is not lateralized. May need new term or clarify if UBERON term encompasses bilateral structures.)
right lateral aortic lymph node UBERON:0016386 possible_match (UBERON has 'paraaortic lymph node' with exact synonym 'lateral aortic lymph node' (FMA:16604). However, this term is right-specific, while UBERON term is not lateralized. May need new term or clarify if UBERON term encompasses bilateral structures.)
supraspinatus fossa lymph node UBERON:0035279 possible_match (If the intended term is 'supraclavicular lymph node', then UBERON:0035279 is the match. However, the source name 'supraspinatus fossa' suggests a different (anatomically incorrect) location.)
epitrochlear lymph node UBERON:0038870 possible_match (The parent term 'epitrochlear lymph node' was not found in UBERON, but 'cubital lymph node' (UBERON:0038870) exists and may represent the same or a closely related structure. Cubital refers to the elbow region, and epitrochlear specifically refers to the area near the medial epicondyle (trochlea) of the humerus. These terms may be synonymous in some anatomical literature. Recommend manual verification of whether epitrochlear should be added as a synonym to cubital lymph node, or if it represents a distinct structure that requires a new term.)
41 changes: 41 additions & 0 deletions bulk_ntr_workflow/outputs/hra-lymph-reports/errors.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
label as_iri issue_type parent_id parent_label detail
anterior interosseous lymphatic channel https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
anterior lymph trunk of accompanying suprarenal vein https://purl.org/ccf/ASCTB-TEMP_anterior-lymph-trunk-of-accompanying-suprarenal-vein unknown_parent FMA:323951 Pre-aortic thoracic lymph node group Unrecognised parent ID format
circumflex lymphatic channel https://purl.org/ccf/ASCTB-TEMP_circumflex-lymphatic-channel unknown_parent FMA:14187 Subscapular lymph node Unrecognised parent ID format
collecting lymph trunk of lymphatics of soft parts covering posterior thoracic wall https://purl.org/ccf/ASCTB-TEMP_collecting-lymph-trunk-of-lymphatics-of-soft-parts-covering-posterior-thoracic-wall unknown_parent FMA:276805 Axillary lymph node Unrecognised parent ID format
cubital fossa lymph node https://purl.org/ccf/ASCTB-TEMP_cubital-fossa-lymph-node unknown_parent FMA:234924 Brachial lymphatic vessel Unrecognised parent ID format
deep lymph node of neck https://purl.org/ccf/ASCTB-TEMP_deep-lymph-node-of-neck asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node posterior extrathoracic lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
deep radial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_deep-radial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_cubital-fossa-lymph-node cubital fossa lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
deep ulnar lymphatic channel https://purl.org/ccf/ASCTB-TEMP_deep-ulnar-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
epitrochlear lymph node https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node unknown_parent FMA:234924 Brachial lymphatic vessel Unrecognised parent ID format
index finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_index-finger-lateral-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
index finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_index-finger-medial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
left collecting lymph trunk of lymphatics of ovary https://purl.org/ccf/ASCTB-TEMP_left-collecting-lymph-trunk-of-lymphatics-of-ovary unknown_parent FMA:323951 Pre-aortic thoracic lymph node group Unrecognised parent ID format
left lateral aortic lymph node https://purl.org/ccf/ASCTB-TEMP_left-lateral-aortic-lymph-node unknown_parent FMA:5841 Left lumbar lymphatic trunk Unrecognised parent ID format
left suprabronchial lymph node of superior lymph collecting vessel of superior inferior lobe of left lung https://purl.org/ccf/ASCTB-TEMP_left-suprabronchial-lymph-node-of-superior-lymph-collecting-vessel-of-superior-inferior-lobe-of-left-lung asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node left anterior mediastinal lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
little finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_little-finger-lateral-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
little finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_little-finger-medial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
lymphatics of pleura, pericardium, heart, thymus, and left lung https://purl.org/ccf/ASCTB-TEMP_lymphatics-of-pleura-pericardium-heart-thymus-and-left-lung asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node left anterior mediastinal lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial lymph node of common illiac lymph nodes https://purl.org/ccf/ASCTB-TEMP_medial-lymph-node-of-common-illiac-lymph-nodes unknown_parent FMA:323951 Pre-aortic thoracic lymph node group Unrecognised parent ID format
medial lymph trunk of principal axillary lymph vessel https://purl.org/ccf/ASCTB-TEMP_medial-lymph-trunk-of-principal-axillary-lymph-vessel unknown_parent FMA:276805 Axillary lymph node Unrecognised parent ID format
medial lymphatic pathway of upper arm https://purl.org/ccf/ASCTB-TEMP_medial-lymphatic-pathway-of-upper-arm unknown_parent FMA:71749 Central axillary lymph node group Unrecognised parent ID format
middle finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_middle-finger-lateral-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
middle finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_middle-finger-medial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
palmar arch lymphatic channel https://purl.org/ccf/ASCTB-TEMP_palmar-arch-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel anterior interosseous lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
posterior extrathoracic lymph node https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node unknown_parent FMA:276805 Axillary lymph node Unrecognised parent ID format
posterior interosseous lymphatic channel https://purl.org/ccf/ASCTB-TEMP_posterior-interosseous-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
radial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-lymphatic-pathway-of-upper-arm lateral lymphatic pathway of upper arm Parent not yet in UBERON; subagent should search OLS4 for correct parent
retropectoral lymph vessel https://purl.org/ccf/ASCTB-TEMP_retropectoral-lymph-vessel unknown_parent FMA:12252 Subclavian lymphatic trunk Unrecognised parent ID format
right anterior mediastinal lymph node https://purl.org/ccf/ASCTB-TEMP_right-anterior-mediastinal-lymph-node unknown_parent FMA:5832 Right lymphatic duct Unrecognised parent ID format
right collecting lymph trunk of lymphatics of testicle https://purl.org/ccf/ASCTB-TEMP_right-collecting-lymph-trunk-of-lymphatics-of-testicle unknown_parent FMA:323951 Pre-aortic thoracic lymph node group Unrecognised parent ID format
right lateral aortic lymph node https://purl.org/ccf/ASCTB-TEMP_right-lateral-aortic-lymph-node unknown_parent FMA:5841 Left lumbar lymphatic trunk Unrecognised parent ID format
ring finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_ring-finger-lateral-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
ring finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_ring-finger-medial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
subclavicular lymph node https://purl.org/ccf/ASCTB-TEMP_subclavicular-lymph-node unknown_parent FMA:12252 Subclavian lymphatic trunk Unrecognised parent ID format
superficial ulnar lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node epitrochlear lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
superior ulnar lymph node https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node unknown_parent FMA:234924 Brachial lymphatic vessel Unrecognised parent ID format
supraescapular lymphatic channel https://purl.org/ccf/ASCTB-TEMP_supraescapular-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_supraspinatus-fossa-lymph-node supraspinatus fossa lymph node Parent not yet in UBERON; subagent should search OLS4 for correct parent
supraspinatus fossa lymph node https://purl.org/ccf/ASCTB-TEMP_supraspinatus-fossa-lymph-node asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_deep-lymph-node-of-neck deep lymph node of neck Parent not yet in UBERON; subagent should search OLS4 for correct parent
thumb lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_thumb-lateral-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
thumb medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_thumb-medial-lymphatic-channel asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel Parent not yet in UBERON; subagent should search OLS4 for correct parent
transpectoral lymph vessel https://purl.org/ccf/ASCTB-TEMP_transpectoral-lymph-vessel unknown_parent FMA:12252 Subclavian lymphatic trunk Unrecognised parent ID format
Loading
Loading