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Add HRA palatine-tonsil NTR template (7 new terms) #3719

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Add HRA palatine-tonsil NTR template (7 new terms) #3719

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8 changes: 8 additions & 0 deletions bulk_ntr_workflow/source_data/palatine-tonsil.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_peritonsillar-plexus-of-veins,peritonsillar plexus of veins,,,UBERON:0001981,blood vessel,
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_tonsil-follicle,tonsil follicle,,,UBERON:0002373,palatine tonsil,
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-dark-zone,tonsil germinal center dark zone,,,UBERON:0013688,tonsil germinal center,
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-light-zone,tonsil germinal center light zone,,,UBERON:0013688,tonsil germinal center,
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-mantle-zone,tonsil germinal center mantle zone,,,https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle,tonsil secondary follicle,
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle,tonsil secondary follicle,,,https://purl.org/ccf/ASCTB-TEMP_tonsil-follicle,tonsil follicle,"https://doi.org/10.1101/2022.06.24.497299, https://doi.org/10.1126/sciimmunol.abh3768"
palatine-tonsil,https://purl.org/ccf/ASCTB-TEMP_tonsil-t-cell-zone,tonsil T cell zone,,,http://purl.org/sig/ont/fma/fma55221,Diffuse lymphoid tissue,
2 changes: 2 additions & 0 deletions src/templates/hra-palatine-tonsil-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=|
1 change: 1 addition & 0 deletions src/templates/hra-palatine-tonsil-reports/candidates.tsv
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label as_iri uberon_id note
4 changes: 4 additions & 0 deletions src/templates/hra-palatine-tonsil-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
tonsil germinal center mantle zone https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-mantle-zone asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle tonsil secondary follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
tonsil secondary follicle https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_tonsil-follicle tonsil follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
tonsil T cell zone https://purl.org/ccf/ASCTB-TEMP_tonsil-t-cell-zone fma_parent FMA:55221 Diffuse lymphoid tissue Subagent should resolve FMA→UBERON via OLS4
8 changes: 8 additions & 0 deletions src/templates/hra-palatine-tonsil-reports/input.tsv
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table as_iri label uberon_id parent_id parent_label references term_type
https://purl.org/ccf/ASCTB-TEMP_peritonsillar-plexus-of-veins peritonsillar plexus of veins UBERON:0001981 blood vessel leaf
https://purl.org/ccf/ASCTB-TEMP_tonsil-follicle tonsil follicle UBERON:0002373 palatine tonsil leaf
https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-dark-zone tonsil germinal center dark zone UBERON:0013688 tonsil germinal center leaf
https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-light-zone tonsil germinal center light zone UBERON:0013688 tonsil germinal center leaf
https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-mantle-zone tonsil germinal center mantle zone https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle tonsil secondary follicle leaf
https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle tonsil secondary follicle https://purl.org/ccf/ASCTB-TEMP_tonsil-follicle tonsil follicle https://doi.org/10.1101/2022.06.24.497299, https://doi.org/10.1126/sciimmunol.abh3768 leaf
https://purl.org/ccf/ASCTB-TEMP_tonsil-t-cell-zone tonsil T cell zone http://purl.org/sig/ont/fma/fma55221 Diffuse lymphoid tissue leaf
9 changes: 9 additions & 0 deletions src/templates/hra-palatine-tonsil.template.tsv
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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_8930153 peritonsillar plexus of veins A venous plexus located in the peritonsillar region surrounding the palatine tonsil, which drains blood from the tonsillar region and communicates with the pharyngeal veins and lingual vein, ultimately draining into the internal jugular vein. https://purl.org/ccf/ASCTB-TEMP_peritonsillar-plexus-of-veins|PMID:34430822 UBERON:0001593 UBERON:0035228 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:Palatine_tonsil|Wikipedia:Tonsillar_fossa
http://purl.obolibrary.org/obo/UBERON_8930154 tonsil follicle A lymphoid follicle that is part of a palatine tonsil. https://purl.org/ccf/ASCTB-TEMP_tonsil-follicle|PMID:417886|PMID:11789984 UBERON:0000444 UBERON:0002373 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:Palatine_tonsil
http://purl.obolibrary.org/obo/UBERON_8930155 tonsil germinal center dark zone Tonsil germinal centers contain two distinct microenvironments: the light zone and the dark zone. The dark zone is densely populated with B cell blasts (centroblasts) and reticular cells, where somatic hypermutation and clonal expansion occur. https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-dark-zone|PMID:25656706|PMID:8011279 UBERON:0001744 UBERON:0013688 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:Germinal_center
http://purl.obolibrary.org/obo/UBERON_8930156 tonsil germinal center light zone Tonsil germinal centers contain two distinct microenvironments: the light zone and the dark zone. The light zone is sparsely populated with B cells (centrocytes) and includes additional cell types such as follicular dendritic cells, tingible macrophages, and T follicular helper cells, where B cell selection takes place. https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-light-zone|PMID:25656706|PMID:8011279 UBERON:0001744 UBERON:0013688 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:Germinal_center
http://purl.obolibrary.org/obo/UBERON_8930157 tonsil germinal center mantle zone A part of the secondary follicle of the tonsil in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these cells are displaced by the expanding germinal center and form a 'mantle' around it. https://purl.org/ccf/ASCTB-TEMP_tonsil-germinal-center-mantle-zone|PMID:25656706 UBERON:0010755 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:Palatine_tonsil
http://purl.obolibrary.org/obo/UBERON_8930158 tonsil secondary follicle A secondary follicle that is located in a tonsil. https://doi.org/10.1101/2022.06.24.497299|https://doi.org/10.1126/sciimmunol.abh3768|https://purl.org/ccf/ASCTB-TEMP_tonsil-secondary-follicle|PMID:28844822 UBERON:0001745 UBERON:0002372 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 https://upload.wikimedia.org/wikipedia/commons/thumb/4/44/Centrocyte%2C_centroblast_and_follicular_dendritic_cell_in_a_follicular_lymphoma.jpg/250px-Centrocyte%2C_centroblast_and_follicular_dendritic_cell_in_a_follicular_lymphoma.jpg Wikipedia:Germinal_center
http://purl.obolibrary.org/obo/UBERON_8930159 tonsil T cell zone A T cell domain that is part of a tonsil, comprising the extrafollicular and paracortical regions where T lymphocytes interact with dendritic cells to initiate and regulate adaptive immune responses. https://purl.org/ccf/ASCTB-TEMP_tonsil-t-cell-zone|PMID:30801022 UBERON:0010393 UBERON:0002372 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:55221
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