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Add HRA lymph NTR template (41 new terms) #3718

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47 changes: 47 additions & 0 deletions bulk_ntr_workflow/source_data/lymph.csv
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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,
2 changes: 2 additions & 0 deletions src/templates/hra-lymph-groups.template.tsv
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ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref
ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=|
9 changes: 9 additions & 0 deletions src/templates/hra-lymph-reports/candidates.tsv
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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.)
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