From df5b9d7757ab1e06ed55082c07c737467a25e313 Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Tue, 26 May 2026 10:11:32 -0400 Subject: [PATCH 1/5] Add HRA palatine-tonsil NTR template (7 new terms) Generated via bulk_ntr_workflow from source_data/palatine-tonsil.csv. Pipeline completed through Stage 4: - 7 new UBERON terms in leaf template - 0 group terms - 0 confirmed matches excluded - 0 out-of-scope exclusions - 0 manual-curation exclusions Parent mapping handled in Stage 3 for mixed source parents: - UBERON parents (4) - ASCTB-TEMP parents (2) - FMA parent mapping (1) Final template has no [PENDING], INFER, NEEDS_MAPPING, or UNRESOLVABLE markers. Signed-off-by: dragon-ai-agent --- bulk_ntr_workflow/source_data/palatine-tonsil.csv | 8 ++++++++ src/templates/hra-palatine-tonsil-groups.template.tsv | 2 ++ src/templates/hra-palatine-tonsil-reports/candidates.tsv | 1 + src/templates/hra-palatine-tonsil-reports/errors.tsv | 4 ++++ src/templates/hra-palatine-tonsil-reports/input.tsv | 8 ++++++++ src/templates/hra-palatine-tonsil.template.tsv | 9 +++++++++ 6 files changed, 32 insertions(+) create mode 100644 bulk_ntr_workflow/source_data/palatine-tonsil.csv create mode 100644 src/templates/hra-palatine-tonsil-groups.template.tsv create mode 100644 src/templates/hra-palatine-tonsil-reports/candidates.tsv create mode 100644 src/templates/hra-palatine-tonsil-reports/errors.tsv create mode 100644 src/templates/hra-palatine-tonsil-reports/input.tsv create mode 100644 src/templates/hra-palatine-tonsil.template.tsv diff --git a/bulk_ntr_workflow/source_data/palatine-tonsil.csv b/bulk_ntr_workflow/source_data/palatine-tonsil.csv new file mode 100644 index 000000000..49c352b04 --- /dev/null +++ b/bulk_ntr_workflow/source_data/palatine-tonsil.csv @@ -0,0 +1,8 @@ +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, \ No newline at end of file diff --git a/src/templates/hra-palatine-tonsil-groups.template.tsv b/src/templates/hra-palatine-tonsil-groups.template.tsv new file mode 100644 index 000000000..dff359c07 --- /dev/null +++ b/src/templates/hra-palatine-tonsil-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-palatine-tonsil-reports/candidates.tsv b/src/templates/hra-palatine-tonsil-reports/candidates.tsv new file mode 100644 index 000000000..6db5d8134 --- /dev/null +++ b/src/templates/hra-palatine-tonsil-reports/candidates.tsv @@ -0,0 +1 @@ +label as_iri uberon_id note diff --git a/src/templates/hra-palatine-tonsil-reports/errors.tsv b/src/templates/hra-palatine-tonsil-reports/errors.tsv new file mode 100644 index 000000000..5648fec10 --- /dev/null +++ b/src/templates/hra-palatine-tonsil-reports/errors.tsv @@ -0,0 +1,4 @@ +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 diff --git a/src/templates/hra-palatine-tonsil-reports/input.tsv b/src/templates/hra-palatine-tonsil-reports/input.tsv new file mode 100644 index 000000000..a8241bf1e --- /dev/null +++ b/src/templates/hra-palatine-tonsil-reports/input.tsv @@ -0,0 +1,8 @@ +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 diff --git a/src/templates/hra-palatine-tonsil.template.tsv b/src/templates/hra-palatine-tonsil.template.tsv new file mode 100644 index 000000000..fbb512237 --- /dev/null +++ b/src/templates/hra-palatine-tonsil.template.tsv @@ -0,0 +1,9 @@ +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 From c23861e96a6b6f60613daddff07745d1a400236a Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Wed, 8 Jul 2026 18:02:50 +0000 Subject: [PATCH 2/5] Apply review feedback to HRA palatine-tonsil template MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Remove empty groups template (hra-palatine-tonsil-groups.template.tsv) - UBERON:8930154: rename 'tonsil follicle' -> 'palatine tonsil follicle' - UBERON:8930157 (tonsil germinal center mantle zone): add part_of UBERON:8930158 (tonsil secondary follicle) - UBERON:8930159 (tonsil T cell zone): remove xref FMA:55221 Signed-off-by: @dragon-ai-agent --- 🤖 **Generated by @dragon-ai-agent** - Model: `claude-opus-4-7` - Agent harness: claude-code - Triggered by: @zhengj2007 - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/28964269531) --- src/templates/hra-palatine-tonsil-groups.template.tsv | 2 -- src/templates/hra-palatine-tonsil.template.tsv | 6 +++--- 2 files changed, 3 insertions(+), 5 deletions(-) delete mode 100644 src/templates/hra-palatine-tonsil-groups.template.tsv diff --git a/src/templates/hra-palatine-tonsil-groups.template.tsv b/src/templates/hra-palatine-tonsil-groups.template.tsv deleted file mode 100644 index dff359c07..000000000 --- a/src/templates/hra-palatine-tonsil-groups.template.tsv +++ /dev/null @@ -1,2 +0,0 @@ -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-palatine-tonsil.template.tsv b/src/templates/hra-palatine-tonsil.template.tsv index fbb512237..27d166515 100644 --- a/src/templates/hra-palatine-tonsil.template.tsv +++ b/src/templates/hra-palatine-tonsil.template.tsv @@ -1,9 +1,9 @@ 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_8930154 palatine 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_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 UBERON:8930158 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 +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 From c890b08ee63f3ce6a7708c18f5ef4dd0bf9f40c1 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 6 Jul 2026 16:04:45 +0100 Subject: [PATCH 3/5] Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/ Reports are review artifacts, not ODK templates, and should not live under src/templates/. Relocated to bulk_ntr_workflow/outputs/ to match the canonical layout used by the muscular branch (PR #3700). Signed-off-by: dragon-ai-agent --- .../outputs}/hra-palatine-tonsil-reports/candidates.tsv | 0 .../outputs}/hra-palatine-tonsil-reports/errors.tsv | 0 .../outputs}/hra-palatine-tonsil-reports/input.tsv | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename {src/templates => bulk_ntr_workflow/outputs}/hra-palatine-tonsil-reports/candidates.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-palatine-tonsil-reports/errors.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-palatine-tonsil-reports/input.tsv (100%) diff --git a/src/templates/hra-palatine-tonsil-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/candidates.tsv similarity index 100% rename from src/templates/hra-palatine-tonsil-reports/candidates.tsv rename to bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/candidates.tsv diff --git a/src/templates/hra-palatine-tonsil-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/errors.tsv similarity index 100% rename from src/templates/hra-palatine-tonsil-reports/errors.tsv rename to bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/errors.tsv diff --git a/src/templates/hra-palatine-tonsil-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/input.tsv similarity index 100% rename from src/templates/hra-palatine-tonsil-reports/input.tsv rename to bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/input.tsv From cebdb2fb5e9aea3b616207c204711e88941d4ec1 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 14:53:38 +0100 Subject: [PATCH 4/5] Add HRA palatine tonsil terms to uberon-edit.obo Hand-convert the 7 template rows into OBO stanzas (<20-term policy, as requested by @zhengj2007 on 2026-07-19) and remove the unregistered template, which was never built so the terms were not in the ontology. Modelling follows the existing lymph node analogues: - mantle zone: intersection_of secondary follicle corona + part_of tonsil, part_of tonsil secondary follicle, surrounds tonsil germinal center (cf. UBERON:0010420) - tonsil secondary follicle, tonsil T cell zone, palatine tonsil follicle: genus-differentia logical definitions (cf. UBERON:0010753, UBERON:0010417) - dark/light zone: is_a lymphoid tissue, part_of tonsil germinal center (cf. UBERON:8410052/8410053) - peritonsillar plexus of veins: located_in (not part_of) tonsillar fossa, since the fossa is an immaterial anatomical space (part_of would be unsatisfiable under material/immaterial disjointness). Also: ASCTB-TEMP IRIs moved from def xrefs to CCF: xrefs; DOI URLs as DOI: CURIEs; dropped Wikipedia xrefs pointing at different structures and a follicular-lymphoma (pathology) depiction image. Signed: @ai4c-agent Co-Authored-By: Claude Opus 5.5 (1M context) --- src/ontology/uberon-edit.obo | 93 +++++++++++++++++++ .../hra-palatine-tonsil.template.tsv | 9 -- 2 files changed, 93 insertions(+), 9 deletions(-) delete mode 100644 src/templates/hra-palatine-tonsil.template.tsv diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 7fa8a7506..10c529bc7 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225284,6 +225284,99 @@ is_a: UBERON:0006914 ! squamous epithelium relationship: has_part CL:4030023 ! respiratory tract hillock cell relationship: part_of UBERON:0007196 ! tracheobronchial tree +[Term] +id: UBERON:8930153 +name: peritonsillar plexus of veins +def: "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." [PMID:34430822] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_peritonsillar-plexus-of-veins +is_a: UBERON:0001593 ! venous plexus +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: located_in UBERON:0035228 ! tonsillar fossa +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + +[Term] +id: UBERON:8930154 +name: palatine tonsil follicle +def: "A lymphoid follicle that is part of a palatine tonsil." [PMID:11789984, PMID:417886] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_tonsil-follicle +intersection_of: UBERON:0000444 ! lymphoid follicle +intersection_of: part_of UBERON:0002373 ! palatine tonsil +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + +[Term] +id: UBERON:8930155 +name: tonsil germinal center dark zone +def: "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." [PMID:25656706, PMID:8011279] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_tonsil-germinal-center-dark-zone +is_a: UBERON:0001744 ! lymphoid tissue +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0013688 ! tonsil germinal center +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + +[Term] +id: UBERON:8930156 +name: tonsil germinal center light zone +def: "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 body macrophages, and T follicular helper cells, where B cell selection takes place." [PMID:25656706, PMID:8011279] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_tonsil-germinal-center-light-zone +is_a: UBERON:0001744 ! lymphoid tissue +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0013688 ! tonsil germinal center +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + +[Term] +id: UBERON:8930157 +name: tonsil germinal center mantle zone +def: "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." [PMID:25656706] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_tonsil-germinal-center-mantle-zone +intersection_of: UBERON:0010755 ! secondary follicle corona +intersection_of: part_of UBERON:0002372 ! tonsil +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:8930158 ! tonsil secondary follicle +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: surrounds UBERON:0013688 ! tonsil germinal center +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + +[Term] +id: UBERON:8930158 +name: tonsil secondary follicle +def: "A secondary follicle that is located in a tonsil." [DOI:10.1101/2022.06.24.497299, DOI:10.1126/sciimmunol.abh3768, PMID:28844822] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_tonsil-secondary-follicle +intersection_of: UBERON:0001745 ! secondary nodular lymphoid tissue +intersection_of: part_of UBERON:0002372 ! tonsil +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + +[Term] +id: UBERON:8930159 +name: tonsil T cell zone +def: "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." [PMID:30801022] +subset: added_by_HRA +xref: CCF:ASCTB-TEMP_tonsil-t-cell-zone +intersection_of: UBERON:0010393 ! T cell domain +intersection_of: part_of UBERON:0002372 ! tonsil +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3719" xsd:anyURI + [Typedef] id: aboral_to name: aboral to diff --git a/src/templates/hra-palatine-tonsil.template.tsv b/src/templates/hra-palatine-tonsil.template.tsv deleted file mode 100644 index 27d166515..000000000 --- a/src/templates/hra-palatine-tonsil.template.tsv +++ /dev/null @@ -1,9 +0,0 @@ -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 palatine 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 UBERON:8930158 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 From ff8bb10c4fd559812d058cccd48978160bbfbe73 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 16:39:37 +0100 Subject: [PATCH 5/5] Narrow mantle zone logical definition to tonsil secondary follicle tonsil germinal center mantle zone (UBERON:8930157): the logical definition used part_of tonsil (UBERON:0002372) while the text definition says "a part of the secondary follicle of the tonsil". The broad differentia risks over-classifying any secondary follicle corona that is part of a tonsil under this term. Change the differentia to part_of tonsil secondary follicle (UBERON:8930158) so the logical definition mirrors the text definition, and drop the now-redundant asserted part_of UBERON:8930158. ELK: no unsatisfiable classes; no new inferred subclasses of UBERON:8930157. Signed: @ai4c-agent Co-Authored-By: Claude Opus 5.5 (1M context) --- src/ontology/uberon-edit.obo | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index d7e0c0c32..078f6c1a4 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225789,9 +225789,8 @@ def: "A part of the secondary follicle of the tonsil in which naive B cells resi subset: added_by_HRA xref: CCF:ASCTB-TEMP_tonsil-germinal-center-mantle-zone intersection_of: UBERON:0010755 ! secondary follicle corona -intersection_of: part_of UBERON:0002372 ! tonsil +intersection_of: part_of UBERON:8930158 ! tonsil secondary follicle relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 -relationship: part_of UBERON:8930158 ! tonsil secondary follicle relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: surrounds UBERON:0013688 ! tonsil germinal center property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime