diff --git a/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/candidates.tsv new file mode 100644 index 000000000..6db5d8134 --- /dev/null +++ b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/candidates.tsv @@ -0,0 +1 @@ +label as_iri uberon_id note diff --git a/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/errors.tsv new file mode 100644 index 000000000..5648fec10 --- /dev/null +++ b/bulk_ntr_workflow/outputs/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/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-palatine-tonsil-reports/input.tsv new file mode 100644 index 000000000..a8241bf1e --- /dev/null +++ b/bulk_ntr_workflow/outputs/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/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/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index eff1283ae..dec053015 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225757,6 +225757,98 @@ 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/3717" xsd:anyURI +[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:8930158 ! tonsil secondary follicle +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +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