diff --git a/bulk_ntr_workflow/source_data/lymph.csv b/bulk_ntr_workflow/source_data/lymph.csv new file mode 100644 index 000000000..f91226b0f --- /dev/null +++ b/bulk_ntr_workflow/source_data/lymph.csv @@ -0,0 +1,47 @@ +tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel,anterior interosseous lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node,superior ulnar lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_anterior-lymph-trunk-of-accompanying-suprarenal-vein,anterior lymph trunk of accompanying suprarenal vein,,,FMA:323951,Pre-aortic thoracic lymph node group, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_circumflex-lymphatic-channel,circumflex lymphatic channel,,,FMA:14187,Subscapular lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_collecting-lymph-trunk-of-lymphatics-of-soft-parts-covering-posterior-thoracic-wall,collecting lymph trunk of lymphatics of soft parts covering posterior thoracic wall,,,FMA:276805,Axillary lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_cubital-fossa-lymph-node,cubital fossa lymph node,,,FMA:234924,Brachial lymphatic vessel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_deep-lymph-node-of-neck,deep lymph node of neck,,,https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node,posterior extrathoracic lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_deep-radial-lymphatic-channel,deep radial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_cubital-fossa-lymph-node,cubital fossa lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_deep-ulnar-lymphatic-channel,deep ulnar lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node,superior ulnar lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_efferent-lymphatics-from-fifth-or-sixth-lowermost-intercostal-spaces,efferent lymphatics from fifth or sixth lowermost intercostal spaces,,,UBERON:0001631,thoracic duct, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_efferent-lymphatics-from-third-fourth-and-fifth-intercostal-spaces,"efferent lymphatics from third, fourth, and fifth intercostal spaces",,,UBERON:0001631,thoracic duct, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node,epitrochlear lymph node,,,FMA:234924,Brachial lymphatic vessel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_index-finger-lateral-lymphatic-channel,index finger lateral lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel,radial lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_index-finger-medial-lymphatic-channel,index finger medial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel,radial lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_lateral-lymphatic-pathway-of-upper-arm,lateral lymphatic pathway of upper arm,,,UBERON:0035279,supraclavicular lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node,left anterior mediastinal lymph node,,,UBERON:0001631,thoracic duct, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_left-collecting-lymph-trunk-of-lymphatics-of-ovary,left collecting lymph trunk of lymphatics of ovary,,,FMA:323951,Pre-aortic thoracic lymph node group, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_left-lateral-aortic-lymph-node,left lateral aortic lymph node,,,FMA:5841,Left lumbar lymphatic trunk, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_left-suprabronchial-lymph-node-of-superior-lymph-collecting-vessel-of-superior-inferior-lobe-of-left-lung,left suprabronchial lymph node of superior lymph collecting vessel of superior inferior lobe of left lung,,,https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node,left anterior mediastinal lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_little-finger-lateral-lymphatic-channel,little finger lateral lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel,superficial ulnar lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_little-finger-medial-lymphatic-channel,little finger medial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel,superficial ulnar lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_lymphatics-of-great-omentum,lymphatics of great omentum,,,UBERON:0005435,upper part of cisterna chyli, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_lymphatics-of-pleura-pericardium-heart-thymus-and-left-lung,"lymphatics of pleura, pericardium, heart, thymus, and left lung",,,https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node,left anterior mediastinal lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_medial-lymph-node-of-common-illiac-lymph-nodes,medial lymph node of common illiac lymph nodes,,,FMA:323951,Pre-aortic thoracic lymph node group, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_medial-lymph-trunk-of-principal-axillary-lymph-vessel,medial lymph trunk of principal axillary lymph vessel,,,FMA:276805,Axillary lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_medial-lymphatic-pathway-of-upper-arm,medial lymphatic pathway of upper arm,,,FMA:71749,Central axillary lymph node group, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_middle-finger-lateral-lymphatic-channel,middle finger lateral lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel,radial lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_middle-finger-medial-lymphatic-channel,middle finger medial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel,superficial ulnar lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_palmar-arch-lymphatic-channel,palmar arch lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel,anterior interosseous lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node,posterior extrathoracic lymph node,,,FMA:276805,Axillary lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_posterior-interosseous-lymphatic-channel,posterior interosseous lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node,superior ulnar lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel,radial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_lateral-lymphatic-pathway-of-upper-arm,lateral lymphatic pathway of upper arm, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_retropectoral-lymph-vessel,retropectoral lymph vessel,,,FMA:12252,Subclavian lymphatic trunk, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_right-anterior-mediastinal-lymph-node,right anterior mediastinal lymph node,,,FMA:5832,Right lymphatic duct, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_right-collecting-lymph-trunk-of-lymphatics-of-testicle,right collecting lymph trunk of lymphatics of testicle,,,FMA:323951,Pre-aortic thoracic lymph node group, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_right-lateral-aortic-lymph-node,right lateral aortic lymph node,,,FMA:5841,Left lumbar lymphatic trunk, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_ring-finger-lateral-lymphatic-channel,ring finger lateral lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel,superficial ulnar lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_ring-finger-medial-lymphatic-channel,ring finger medial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel,superficial ulnar lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_subclavicular-lymph-node,subclavicular lymph node,,,FMA:12252,Subclavian lymphatic trunk, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel,superficial ulnar lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node,epitrochlear lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node,superior ulnar lymph node,,,FMA:234924,Brachial lymphatic vessel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_supraescapular-lymphatic-channel,supraescapular lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_supraspinatus-fossa-lymph-node,supraspinatus fossa lymph node, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_supraspinatus-fossa-lymph-node,supraspinatus fossa lymph node,,,https://purl.org/ccf/ASCTB-TEMP_deep-lymph-node-of-neck,deep lymph node of neck, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_thumb-lateral-lymphatic-channel,thumb lateral lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel,radial lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_thumb-medial-lymphatic-channel,thumb medial lymphatic channel,,,https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel,radial lymphatic channel, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_transpectoral-lymph-vessel,transpectoral lymph vessel,,,FMA:12252,Subclavian lymphatic trunk, +lymph-vasculature,https://purl.org/ccf/ASCTB-TEMP_transverse-cervical-lymph-node,transverse cervical lymph node,,,UBERON:0001631,thoracic duct, \ No newline at end of file diff --git a/src/templates/hra-lymph-groups.template.tsv b/src/templates/hra-lymph-groups.template.tsv new file mode 100644 index 000000000..dff359c07 --- /dev/null +++ b/src/templates/hra-lymph-groups.template.tsv @@ -0,0 +1,2 @@ +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=| diff --git a/src/templates/hra-lymph-reports/candidates.tsv b/src/templates/hra-lymph-reports/candidates.tsv new file mode 100644 index 000000000..a2d2939c3 --- /dev/null +++ b/src/templates/hra-lymph-reports/candidates.tsv @@ -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.) diff --git a/src/templates/hra-lymph-reports/errors.tsv b/src/templates/hra-lymph-reports/errors.tsv new file mode 100644 index 000000000..16498303a --- /dev/null +++ b/src/templates/hra-lymph-reports/errors.tsv @@ -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 diff --git a/src/templates/hra-lymph-reports/input.tsv b/src/templates/hra-lymph-reports/input.tsv new file mode 100644 index 000000000..b9adc8fa8 --- /dev/null +++ b/src/templates/hra-lymph-reports/input.tsv @@ -0,0 +1,47 @@ +table as_iri label uberon_id parent_id parent_label references term_type + https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel anterior interosseous lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_anterior-lymph-trunk-of-accompanying-suprarenal-vein anterior lymph trunk of accompanying suprarenal vein FMA:323951 Pre-aortic thoracic lymph node group leaf + https://purl.org/ccf/ASCTB-TEMP_circumflex-lymphatic-channel circumflex lymphatic channel FMA:14187 Subscapular lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_collecting-lymph-trunk-of-lymphatics-of-soft-parts-covering-posterior-thoracic-wall collecting lymph trunk of lymphatics of soft parts covering posterior thoracic wall FMA:276805 Axillary lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_cubital-fossa-lymph-node cubital fossa lymph node FMA:234924 Brachial lymphatic vessel leaf + https://purl.org/ccf/ASCTB-TEMP_deep-lymph-node-of-neck deep lymph node of neck https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node posterior extrathoracic lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_deep-radial-lymphatic-channel deep radial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_cubital-fossa-lymph-node cubital fossa lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_deep-ulnar-lymphatic-channel deep ulnar lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_efferent-lymphatics-from-fifth-or-sixth-lowermost-intercostal-spaces efferent lymphatics from fifth or sixth lowermost intercostal spaces UBERON:0001631 thoracic duct leaf + https://purl.org/ccf/ASCTB-TEMP_efferent-lymphatics-from-third-fourth-and-fifth-intercostal-spaces efferent lymphatics from third, fourth, and fifth intercostal spaces UBERON:0001631 thoracic duct leaf + https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node epitrochlear lymph node FMA:234924 Brachial lymphatic vessel leaf + https://purl.org/ccf/ASCTB-TEMP_index-finger-lateral-lymphatic-channel index finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_index-finger-medial-lymphatic-channel index finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_lateral-lymphatic-pathway-of-upper-arm lateral lymphatic pathway of upper arm UBERON:0035279 supraclavicular lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node left anterior mediastinal lymph node UBERON:0001631 thoracic duct leaf + https://purl.org/ccf/ASCTB-TEMP_left-collecting-lymph-trunk-of-lymphatics-of-ovary left collecting lymph trunk of lymphatics of ovary FMA:323951 Pre-aortic thoracic lymph node group leaf + https://purl.org/ccf/ASCTB-TEMP_left-lateral-aortic-lymph-node left lateral aortic lymph node FMA:5841 Left lumbar lymphatic trunk leaf + https://purl.org/ccf/ASCTB-TEMP_left-suprabronchial-lymph-node-of-superior-lymph-collecting-vessel-of-superior-inferior-lobe-of-left-lung left suprabronchial lymph node of superior lymph collecting vessel of superior inferior lobe of left lung https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node left anterior mediastinal lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_little-finger-lateral-lymphatic-channel little finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_little-finger-medial-lymphatic-channel little finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_lymphatics-of-great-omentum lymphatics of great omentum UBERON:0005435 upper part of cisterna chyli leaf + https://purl.org/ccf/ASCTB-TEMP_lymphatics-of-pleura-pericardium-heart-thymus-and-left-lung lymphatics of pleura, pericardium, heart, thymus, and left lung https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node left anterior mediastinal lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_medial-lymph-node-of-common-illiac-lymph-nodes medial lymph node of common illiac lymph nodes FMA:323951 Pre-aortic thoracic lymph node group leaf + https://purl.org/ccf/ASCTB-TEMP_medial-lymph-trunk-of-principal-axillary-lymph-vessel medial lymph trunk of principal axillary lymph vessel FMA:276805 Axillary lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_medial-lymphatic-pathway-of-upper-arm medial lymphatic pathway of upper arm FMA:71749 Central axillary lymph node group leaf + https://purl.org/ccf/ASCTB-TEMP_middle-finger-lateral-lymphatic-channel middle finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_middle-finger-medial-lymphatic-channel middle finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_palmar-arch-lymphatic-channel palmar arch lymphatic channel https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel anterior interosseous lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node posterior extrathoracic lymph node FMA:276805 Axillary lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_posterior-interosseous-lymphatic-channel posterior interosseous lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_lateral-lymphatic-pathway-of-upper-arm lateral lymphatic pathway of upper arm leaf + https://purl.org/ccf/ASCTB-TEMP_retropectoral-lymph-vessel retropectoral lymph vessel FMA:12252 Subclavian lymphatic trunk leaf + https://purl.org/ccf/ASCTB-TEMP_right-anterior-mediastinal-lymph-node right anterior mediastinal lymph node FMA:5832 Right lymphatic duct leaf + https://purl.org/ccf/ASCTB-TEMP_right-collecting-lymph-trunk-of-lymphatics-of-testicle right collecting lymph trunk of lymphatics of testicle FMA:323951 Pre-aortic thoracic lymph node group leaf + https://purl.org/ccf/ASCTB-TEMP_right-lateral-aortic-lymph-node right lateral aortic lymph node FMA:5841 Left lumbar lymphatic trunk leaf + https://purl.org/ccf/ASCTB-TEMP_ring-finger-lateral-lymphatic-channel ring finger lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_ring-finger-medial-lymphatic-channel ring finger medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_subclavicular-lymph-node subclavicular lymph node FMA:12252 Subclavian lymphatic trunk leaf + https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel superficial ulnar lymphatic channel https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node epitrochlear lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node superior ulnar lymph node FMA:234924 Brachial lymphatic vessel leaf + https://purl.org/ccf/ASCTB-TEMP_supraescapular-lymphatic-channel supraescapular lymphatic channel https://purl.org/ccf/ASCTB-TEMP_supraspinatus-fossa-lymph-node supraspinatus fossa lymph node leaf + https://purl.org/ccf/ASCTB-TEMP_supraspinatus-fossa-lymph-node supraspinatus fossa lymph node https://purl.org/ccf/ASCTB-TEMP_deep-lymph-node-of-neck deep lymph node of neck leaf + https://purl.org/ccf/ASCTB-TEMP_thumb-lateral-lymphatic-channel thumb lateral lymphatic channel https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_thumb-medial-lymphatic-channel thumb medial lymphatic channel https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel radial lymphatic channel leaf + https://purl.org/ccf/ASCTB-TEMP_transpectoral-lymph-vessel transpectoral lymph vessel FMA:12252 Subclavian lymphatic trunk leaf + https://purl.org/ccf/ASCTB-TEMP_transverse-cervical-lymph-node transverse cervical lymph node UBERON:0001631 thoracic duct leaf diff --git a/src/templates/hra-lymph-reports/manual_curation.tsv b/src/templates/hra-lymph-reports/manual_curation.tsv new file mode 100644 index 000000000..19807301c --- /dev/null +++ b/src/templates/hra-lymph-reports/manual_curation.tsv @@ -0,0 +1,2 @@ +label definition reason similar_terms suggestion +supraspinatus fossa lymph node A lymph node that is located in the supraclavicular fossa, above the clavicle in the lower neck region, receiving lymphatic drainage from deep cervical structures. Term name contains anatomical inconsistency that requires curator review. The 'supraspinatus fossa' is part of the scapula, not the neck. If intended as 'supraclavicular', UBERON:0035279 already exists. Cannot proceed with NTR without source data verification. UBERON:0035279=supraclavicular lymph node; UBERON:0004722=deep cervical lymph node; UBERON:0001097=axillary lymph node Verify source data for naming error. If 'supraclavicular' was intended, use existing UBERON:0035279. If truly a lymph node near the scapula's supraspinatus fossa, reclassify under axillary lymph nodes, not cervical. diff --git a/src/templates/hra-lymph-reports/name_corrections.tsv b/src/templates/hra-lymph-reports/name_corrections.tsv new file mode 100644 index 000000000..7d68c0e73 --- /dev/null +++ b/src/templates/hra-lymph-reports/name_corrections.tsv @@ -0,0 +1,8 @@ +source_label corrected_label reason +medial lymph node of common illiac lymph nodes medial lymph node of common iliac lymph nodes Corrected spelling from 'illiac' to 'iliac' (standard anatomical term). Source name should be kept as synonym. +retropectoral lymph vessel retropectoral lymph node Term describes a lymph node based on definition and location (retropectoral space), not a vessel. The source may have mislabeled this structure. Updated definition and relationships to reflect lymph node type. +palmar arch lymphatic channel lymphatic capillary of palmar arch The term 'channel' is non-standard in anatomical nomenclature for lymphatic vessels. UBERON and standard anatomical terminology use 'lymphatic capillary', 'lymphatic vessel', or specific named structures. The pattern 'lymphatic capillary of [region]' is consistent with existing UBERON terms like 'lymphatic capillary of small intestine' (lacteal). +supraspinatus fossa lymph node supraclavicular lymph node Anatomical error: 'supraspinatus fossa' is part of the scapula (shoulder blade, UBERON:1200261), not the neck. The source likely intended 'supraclavicular' (above the clavicle), which refers to well-known deep cervical lymph nodes. UBERON:0035279 already covers supraclavicular lymph nodes. +radial lymphatic channel radial lymphatic vessel UBERON standard terminology uses 'lymphatic vessel' rather than 'channel'. The term 'channel' is non-standard in UBERON nomenclature. Regional lymphatic vessels in UBERON use the pattern '{region} lymphatic vessel' (e.g., facial lymphatic vessel, pectoral lymphatic vessel). Consider using 'radial lymphatic vessel' as primary label and keeping 'radial lymphatic channel' as a synonym to match source data. +left suprabronchial lymph node of superior lymph collecting vessel of superior inferior lobe of left lung lymph node of superior lymphatic collecting vessel of left lung The original term contains the grammatically nonsensical phrase 'superior inferior lobe' (a lobe cannot be both superior and inferior). The term 'suprabronchial' is non-standard in anatomical nomenclature. The term appears to describe a mediastinal lymph node receiving drainage from superior lymphatic vessels of the left lung. Consider simplifying to standard anatomical terminology. +supraescapular lymphatic channel suprascapular lymphatic channel Standard anatomical terminology uses 'suprascapular' (relating to structures above the scapular spine or passing through the suprascapular foramen), not 'supraescapular'. The source name appears to be a variant or error. Standard term should be used as primary label with source name retained as synonym. diff --git a/src/templates/hra-lymph-reports/out_of_scope.tsv b/src/templates/hra-lymph-reports/out_of_scope.tsv new file mode 100644 index 000000000..c0bbe2dfb --- /dev/null +++ b/src/templates/hra-lymph-reports/out_of_scope.tsv @@ -0,0 +1,2 @@ +label reason suggestion +lymphatics of pleura, pericardium, heart, thymus, and left lung This term describes a collective network of lymphatic vessels spanning five different anatomical structures (pleura, pericardium, heart, thymus, and left lung), not a single discrete anatomical entity. UBERON typically models individual lymphatic vessels of specific organs (e.g., 'lymphatic vessel of pleura', 'lymphatic vessel of heart') rather than collective drainage pathways spanning multiple organs. This term may be better represented as: (1) separate terms for each structure's lymphatic vessels, (2) a grouping class with has_part relationships to individual vessel terms, or (3) a pathway/network term outside UBERON's typical scope of discrete anatomical structures. Consider splitting into individual terms: 'lymphatic vessel of pleura', 'lymphatic vessel of pericardium', 'lymphatic vessel of heart', 'lymphatic vessel of thymus', 'lymphatic vessel of left lung'. Or, if this represents a functional drainage pathway, consider whether it belongs in a different ontology focused on physiological pathways rather than anatomical structures. diff --git a/src/templates/hra-lymph.template.tsv b/src/templates/hra-lymph.template.tsv new file mode 100644 index 000000000..7318d139b --- /dev/null +++ b/src/templates/hra-lymph.template.tsv @@ -0,0 +1,43 @@ +ID LABEL Definition def_xref is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| SC % SC BFO:0000050 some % SC RO:0002202 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| +http://purl.obolibrary.org/obo/UBERON_8930107 anterior interosseous lymphatic channel A lymphatic vessel that drains lymph from the anterior compartment of the forearm and courses alongside the anterior interosseous artery and nerve between the radius and ulna. https://purl.org/ccf/ASCTB-TEMP_anterior-interosseous-lymphatic-channel|PMID:31636930 UBERON:0001473 UBERON:0002386 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930108 anterior lymph trunk of accompanying suprarenal vein A lymphatic collecting trunk that drains lymph from structures adjacent to the suprarenal vein and conveys it toward regional lymph nodes. https://purl.org/ccf/ASCTB-TEMP_anterior-lymph-trunk-of-accompanying-suprarenal-vein UBERON:0001473 UNRESOLVABLE:suprarenal vein region http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930109 circumflex lymphatic channel A lymphatic vessel that follows a curved or circular course around an anatomical structure, facilitating lymph drainage from surrounding tissues. https://purl.org/ccf/ASCTB-TEMP_circumflex-lymphatic-channel UBERON:0001473 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930110 collecting lymph trunk of lymphatics of soft parts covering posterior thoracic wall A lymphatic collecting trunk that receives lymph from the superficial and deep soft tissues overlying the posterior thoracic wall, including skin, subcutaneous tissue, and muscles. https://purl.org/ccf/ASCTB-TEMP_collecting-lymph-trunk-of-lymphatics-of-soft-parts-covering-posterior-thoracic-wall UBERON:0001473 UNRESOLVABLE:posterior thoracic wall http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930113 deep radial lymphatic channel A lymphatic vessel that courses deep along the radial artery in the forearm, draining lymph from the radial aspect of the forearm and hand toward regional lymph nodes in the upper limb. https://purl.org/ccf/ASCTB-TEMP_deep-radial-lymphatic-channel|PMID:40665199 UBERON:0001473 UBERON:0007302 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930114 deep ulnar lymphatic channel A lymphatic vessel that accompanies the deep ulnar artery and drains lymph from structures in the ulnar aspect of the forearm. https://purl.org/ccf/ASCTB-TEMP_deep-ulnar-lymphatic-channel|PMID:31636930 UBERON:0001473 UBERON:0002386 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930115 efferent lymphatics from fifth or sixth lowermost intercostal spaces A lymphatic vessel that drains lymph from the fifth or sixth lowermost intercostal spaces, typically conveying it toward the thoracic duct for systemic circulation. https://purl.org/ccf/ASCTB-TEMP_efferent-lymphatics-from-fifth-or-sixth-lowermost-intercostal-spaces UBERON:0001473 UBERON:0001631 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930116 efferent lymphatics from third, fourth, and fifth intercostal spaces A lymphatic vessel that drains lymph from the third, fourth, and fifth intercostal spaces, typically conveying it toward the thoracic duct or associated lymph nodes. https://purl.org/ccf/ASCTB-TEMP_efferent-lymphatics-from-third-fourth-and-fifth-intercostal-spaces UBERON:0001473 UBERON:0001631 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930117 epitrochlear lymph node A lymph node located in the epitrochlear region, situated in the superficial fascia above the medial epicondyle of the humerus, approximately 3-4 cm proximal to the elbow joint. It receives lymph from the ulnar side of the forearm and hand and drains to the axillary lymph nodes. https://purl.org/ccf/ASCTB-TEMP_epitrochlear-lymph-node|PMID:23397026 UBERON:0000029 UBERON:0001461 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930118 index finger lateral lymphatic channel A lymphatic vessel that is located on the lateral aspect of the index finger and drains lymph from the lateral side of the digit toward the dorsal lymphatic network of the hand. https://purl.org/ccf/ASCTB-TEMP_index-finger-lateral-lymphatic-channel|PMID:28844822|PMID:31636930 UBERON:0001473 UBERON:0003622 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930119 index finger medial lymphatic channel A lymphatic vessel that is located on the medial aspect of the index finger and drains lymph from the medial side of the digit toward the dorsal lymphatic network of the hand. https://purl.org/ccf/ASCTB-TEMP_index-finger-medial-lymphatic-channel|PMID:28844822|PMID:31636930 UBERON:0001473 UBERON:0003622 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930120 lateral lymphatic pathway of upper arm A lymphatic vessel that is located along the lateral aspect of the upper arm which provides superficial lymphatic drainage, bypassing the axilla to drain to the deltopectoral, clavicular, and cervical lymph nodes. https://purl.org/ccf/ASCTB-TEMP_lateral-lymphatic-pathway-of-upper-arm|PMID:40665199|PMID:40563073|PMID:7223234 UBERON:0001473 UBERON:0003822 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Lymphatic_vessel +http://purl.obolibrary.org/obo/UBERON_8930121 left anterior mediastinal lymph node A lymph node located in the superior mediastinum on the left side, collecting lymph from mediastinal structures including portions of the pericardium and left side of the heart. https://purl.org/ccf/ASCTB-TEMP_left-anterior-mediastinal-lymph-node UBERON:0002524 UBERON:0003728 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 FMA:12775 +http://purl.obolibrary.org/obo/UBERON_8930122 left collecting lymph trunk of lymphatics of ovary A lymphatic collecting trunk that drains lymph from the left ovary, typically ascending along the ovarian vessels toward the left lateral aortic lymph nodes. https://purl.org/ccf/ASCTB-TEMP_left-collecting-lymph-trunk-of-lymphatics-of-ovary|PMID:17321572 UBERON:0001473 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930123 left lateral aortic lymph node A lymph node of the paraaortic group positioned on the left lateral aspect of the abdominal aorta, typically between the renal vessels and the aortic bifurcation. These nodes receive lymph from pelvic organs, kidneys, gonads, and inferior mesenteric drainage areas. https://purl.org/ccf/ASCTB-TEMP_left-lateral-aortic-lymph-node|PMID:29523410 UBERON:0016386 UNRESOLVABLE:left lateral aortic region http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930124 lymph node of superior lymphatic collecting vessel of left lung A lymph node located in the mediastinum near the bronchi of the left lung that receives lymph from the superior lymphatic collecting vessels of the left lung and drains to the anterior mediastinal lymph nodes. https://purl.org/ccf/ASCTB-TEMP_left-suprabronchial-lymph-node-of-superior-lymph-collecting-vessel-of-superior-inferior-lobe-of-left-lung|PMID:28844822|PMID:31636930 UBERON:0000029 UBERON:0035520 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 FMA:12775 +http://purl.obolibrary.org/obo/UBERON_8930125 little finger lateral lymphatic channel A lymphatic vessel that drains the lateral (radial) border of the little finger, which collects interstitial fluid from the lateral digital skin and subcutaneous tissue and conveys it to the dorsal lymphatic plexus of the hand. https://purl.org/ccf/ASCTB-TEMP_little-finger-lateral-lymphatic-channel UBERON:0001473 UBERON:0003625 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930126 little finger medial lymphatic channel A lymphatic vessel that drains the medial (ulnar) border of the little finger, which collects interstitial fluid from the medial digital skin and subcutaneous tissue and conveys it to the palmar or dorsal lymphatic plexus of the hand. https://purl.org/ccf/ASCTB-TEMP_little-finger-medial-lymphatic-channel UBERON:0001473 UBERON:0003625 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930127 lymphatics of great omentum A lymphatic vessel that is part of the greater omentum and drains lymph from the omental tissue to regional lymph nodes. https://purl.org/ccf/ASCTB-TEMP_lymphatics-of-great-omentum|PMID:33606979|ISBN:9780323393225 UBERON:0001473 UBERON:0005448 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Greater_omentum +http://purl.obolibrary.org/obo/UBERON_8930130 medial lymph trunk of principal axillary lymph vessel A lymphatic collecting trunk that represents the medial pathway within the principal axillary lymphatic drainage system, conveying lymph from the upper limb and thoracic wall toward the central axillary lymph nodes. https://purl.org/ccf/ASCTB-TEMP_medial-lymph-trunk-of-principal-axillary-lymph-vessel UBERON:0001473 UBERON:0009472 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930131 medial lymphatic pathway of upper arm A lymphatic drainage route following the medial aspect of the upper arm, typically accompanying the basilic vein and conveying lymph from the medial forearm and hand toward the axillary lymph nodes. https://purl.org/ccf/ASCTB-TEMP_medial-lymphatic-pathway-of-upper-arm UBERON:0001473 UBERON:0003822 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930132 middle finger lateral lymphatic channel A lymphatic vessel that is located on the lateral aspect of the middle finger and drains lymph from the lateral side of the digit toward the dorsal lymphatic network of the hand. https://purl.org/ccf/ASCTB-TEMP_middle-finger-lateral-lymphatic-channel|PMID:28844822|PMID:31636930 UBERON:0001473 UBERON:0003623 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930133 middle finger medial lymphatic channel A lymphatic vessel that drains the medial (ulnar) border of the middle finger, which collects interstitial fluid from the medial digital skin and subcutaneous tissue and conveys it to the palmar or dorsal lymphatic plexus of the hand. https://purl.org/ccf/ASCTB-TEMP_middle-finger-medial-lymphatic-channel UBERON:0001473 UBERON:0003623 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930134 lymphatic capillary of palmar arch A lymphatic capillary that drains lymph from the palmar region of the hand, running in association with the superficial palmar arterial arch. https://purl.org/ccf/ASCTB-TEMP_palmar-arch-lymphatic-channel|PMID:31181226 UBERON:0006842 UBERON:0008878 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Lymphatic_system +http://purl.obolibrary.org/obo/UBERON_8930135 posterior extrathoracic lymph node A lymph node positioned in the posterior extrathoracic region, likely receiving lymph from posterior thoracic wall structures and draining toward mediastinal or axillary lymph node groups. https://purl.org/ccf/ASCTB-TEMP_posterior-extrathoracic-lymph-node UBERON:0000029 UNRESOLVABLE:posterior extrathoracic region http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930136 posterior interosseous lymphatic channel A lymphatic vessel that drains lymph from the posterior compartment of the forearm and courses alongside the posterior interosseous artery between the radius and ulna. https://purl.org/ccf/ASCTB-TEMP_posterior-interosseous-lymphatic-channel|PMID:31636930 UBERON:0001473 UBERON:0002386 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930137 radial lymphatic vessel A lymphatic vessel that drains lymph from the radial (lateral) aspect of the forearm and upper limb, running along the superficial lymphatic pathways on the radial side of the upper extremity. https://purl.org/ccf/ASCTB-TEMP_radial-lymphatic-channel|PMID:41406423|PMID:42010368 UBERON:0001473 UBERON:0002102 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930138 retropectoral lymph node A lymph node located in the retropectoral space, deep to the pectoralis major muscle and receiving lymph from the breast and anterior thoracic wall structures. https://purl.org/ccf/ASCTB-TEMP_retropectoral-lymph-vessel UBERON:0000029 UBERON:0002381 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930139 right anterior mediastinal lymph node A lymph node located in the anterior mediastinum on the right side, positioned anterior to the heart and great vessels. These nodes receive lymph from thymus, pericardium, and anterior thoracic structures. https://purl.org/ccf/ASCTB-TEMP_right-anterior-mediastinal-lymph-node|PMID:37648781 UBERON:0000029 UBERON:0008820 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930140 right collecting lymph trunk of lymphatics of testicle A lymphatic collecting trunk that drains lymph from the right testis, ascending along the testicular vessels toward the right lateral aortic and pre-aortic lymph nodes at the level of the renal vessels. https://purl.org/ccf/ASCTB-TEMP_right-collecting-lymph-trunk-of-lymphatics-of-testicle|PMID:37648781 UBERON:0001473 UBERON:0000473 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930141 right lateral aortic lymph node A lymph node of the paraaortic group positioned on the right lateral aspect of the abdominal aorta, typically between the renal vessels and the aortic bifurcation. These nodes receive lymph from pelvic organs, kidneys, gonads, and drainage from the inferior vena cava region. https://purl.org/ccf/ASCTB-TEMP_right-lateral-aortic-lymph-node|PMID:29523410 UBERON:0016386 UNRESOLVABLE:right lateral aortic region http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930142 ring finger lateral lymphatic channel A lymphatic vessel that drains the lateral (radial) border of the ring finger, which collects interstitial fluid from the lateral digital skin and subcutaneous tissue and conveys it to the dorsal lymphatic plexus of the hand. https://purl.org/ccf/ASCTB-TEMP_ring-finger-lateral-lymphatic-channel UBERON:0001473 UBERON:0003624 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930143 ring finger medial lymphatic channel A lymphatic vessel that drains the medial (ulnar) border of the ring finger, which collects interstitial fluid from the medial digital skin and subcutaneous tissue and conveys it to the palmar or dorsal lymphatic plexus of the hand. https://purl.org/ccf/ASCTB-TEMP_ring-finger-medial-lymphatic-channel UBERON:0001473 UBERON:0003624 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930144 subclavicular lymph node A lymph node located in the subclavicular region, beneath or adjacent to the clavicle, representing either a deep infraclavicular node or a component of the apical axillary group. These nodes receive lymph from upper limb and thoracic wall structures. https://purl.org/ccf/ASCTB-TEMP_subclavicular-lymph-node UBERON:0000029 UNRESOLVABLE:subclavicular region http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930145 superficial ulnar lymphatic channel A lymphatic vessel that courses superficially along the ulnar (medial) aspect of the forearm, collecting lymph from the medial forearm and ulnar side of the hand, and draining toward the epitrochlear or cubital lymph nodes at the elbow. https://purl.org/ccf/ASCTB-TEMP_superficial-ulnar-lymphatic-channel|PMID:17578977|PMID:15054407 UBERON:0001473 UBERON:0002386 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930146 superior ulnar lymph node A lymph node positioned along the superior aspect of the ulnar vessels in the forearm or proximal arm, receiving lymph from the ulnar side of the hand and forearm. https://purl.org/ccf/ASCTB-TEMP_superior-ulnar-lymph-node UBERON:0000029 UBERON:0003822 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930147 suprascapular lymphatic channel A lymphatic vessel that drains lymph from the suprascapular region, passing near or through the suprascapular foramen and contributing to lymphatic drainage of the shoulder and upper posterior thorax. https://purl.org/ccf/ASCTB-TEMP_supraescapular-lymphatic-channel|PMID:28844822|PMID:31636930 UBERON:0001473 UBERON:0001467 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930149 thumb lateral lymphatic channel A lymphatic vessel that is located on the lateral aspect of the thumb and drains lymph from the lateral side of the digit toward the dorsal lymphatic network of the hand. https://purl.org/ccf/ASCTB-TEMP_thumb-lateral-lymphatic-channel|PMID:28844822|PMID:31636930 UBERON:0001473 UBERON:0001463 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930150 thumb medial lymphatic channel A lymphatic vessel that is located on the medial aspect of the thumb and drains lymph from the medial side of the digit toward the dorsal lymphatic network of the hand. https://purl.org/ccf/ASCTB-TEMP_thumb-medial-lymphatic-channel|PMID:28844822|PMID:31636930 UBERON:0001473 UBERON:0001463 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930151 transpectoral lymph vessel A lymphatic vessel that traverses through the pectoralis major muscle, facilitating lymph drainage from the breast parenchyma and anterior thoracic wall toward the axillary lymph nodes. https://purl.org/ccf/ASCTB-TEMP_transpectoral-lymph-vessel UBERON:0001473 UBERON:0002381 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_8930152 transverse cervical lymph node A cervical lymph node located along or near the transverse cervical artery in the lateral neck region, receiving lymphatic drainage from adjacent cervical structures. https://purl.org/ccf/ASCTB-TEMP_transverse-cervical-lymph-node UBERON:0002429 UBERON:0000974 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-26T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Cervical_lymph_nodes