From 708bddd83036757eb4b3c3ef4d58ccf58ef8e4bd Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Tue, 26 May 2026 13:36:26 -0400 Subject: [PATCH 1/9] Add HRA spleen NTR batch outputs and review reports Generated via bulk_ntr_workflow from source_data/spleen.csv. Pipeline completed through Stage 4: - 9 new UBERON leaf terms in final template - 0 group terms - 1 confirmed existing match excluded - 0 possible matches identified - 0 out-of-scope terms - 0 manual-curation items QC status: - 0 [PENDING] definitions - 0 INFER/UNRESOLVABLE/NEEDS_MAPPING markers Includes: - Template and groups TSVs in src/templates/ - Detailed review reports: candidates, errors, input, name_corrections - Source data snapshot in bulk_ntr_workflow/source_data/ Signed-off-by: @dragon-ai-agent --- bulk_ntr_workflow/source_data/spleen.csv | 11 +++++++++++ src/templates/hra-spleen-groups.template.tsv | 2 ++ src/templates/hra-spleen-reports/candidates.tsv | 2 ++ src/templates/hra-spleen-reports/errors.tsv | 1 + src/templates/hra-spleen-reports/input.tsv | 11 +++++++++++ src/templates/hra-spleen-reports/name_corrections.tsv | 4 ++++ src/templates/hra-spleen.template.tsv | 11 +++++++++++ 7 files changed, 42 insertions(+) create mode 100644 bulk_ntr_workflow/source_data/spleen.csv create mode 100644 src/templates/hra-spleen-groups.template.tsv create mode 100644 src/templates/hra-spleen-reports/candidates.tsv create mode 100644 src/templates/hra-spleen-reports/errors.tsv create mode 100644 src/templates/hra-spleen-reports/input.tsv create mode 100644 src/templates/hra-spleen-reports/name_corrections.tsv create mode 100644 src/templates/hra-spleen.template.tsv diff --git a/bulk_ntr_workflow/source_data/spleen.csv b/bulk_ntr_workflow/source_data/spleen.csv new file mode 100644 index 000000000..30b6a5375 --- /dev/null +++ b/bulk_ntr_workflow/source_data/spleen.csv @@ -0,0 +1,11 @@ +tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references +spleen,https://purl.org/ccf/ASCTB-TEMP_connective-tissue,Connective tissue,,Connective tissue of serosa of spleen,UBERON:0004641,spleen capsule,"PMID: 20126587, PMID: 3310649" +spleen,https://purl.org/ccf/ASCTB-TEMP_arterial-capillary,Arterial Capillary,,,UBERON:0001250,red pulp of spleen,"https://doi.org/ 10.1182/ bloodadvances.2017015073, https://doi.org/10.1007/s00418-007-0320-8" +spleen,https://purl.org/ccf/ASCTB-TEMP_inner-mantle-zone,Inner Mantle Zone,,,UBERON:0010421,spleen B cell corona,"https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1111/imm.12469, https://doi.org/10.1111/imm.12325, https://doi.org/10.1093/intimm/14.2.157, https://doi.org/10.1038/s41467-019-09728-3, https://doi.org/10.1007/s00418-007-0320-8, https://doi.org/10.1016/j.aanat.2019.05.004, https://doi.org/10.1182/bloodadvances.2017015073, https://doi.org/10.1007/s00418-020-01924-3, https://doi.org/10.1371/journal.pone.0191019" +spleen,https://purl.org/ccf/ASCTB-TEMP_inner-pals,Inner PALS,,,UBERON:0010401,spleen central arteriole,"https://doi.org/10.1007/s00418-007-0320-8, https://doi.org/10.1111/j.1365-2559.1985.tb02841.x, https://doi.org/10.1111/j.1365-2559.1986.tb02482.x, https://doi.org/10.1182/bloodadvances.2017015073, https://doi.org/10.1111/imm.12469, https://doi.org/10.1016/j.bbi.2018.12.009, https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1126/sciimmunol.aau6085, https://doi.org/10.1007/s00262-015-1729-x, https://doi.org/10.1016/j.immuni.2012.09.020, https://doi.org/10.1038/s41467-019-09728-3, https://doi.org/10.55418/9781933477060., https://doi.org/10.1309/M95G-7DQ2-TLQL-7Q11, https://doi.org/10.1369%2Fjhc.4A6514.2005, PMID:16515224" +spleen,https://purl.org/ccf/ASCTB-TEMP_outer-pals,Outer PALS,,,UBERON:0001960,periarterial lymphatic sheath,"https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1126/sciimmunol.aau6085, https://doi.org/10.1007/s00262-015-1729-x, https://doi.org/10.1016/j.immuni.2012.09.020, https://doi.org/10.1038/s41467-019-09728-3, https://doi.org/10.1111/imm.12469, https://doi.org/10.55418/9781933477060., https://doi.org/10.1038/s41421-020-0157-z, https://doi.org/10.1093/intimm/14.2.157" +spleen,https://purl.org/ccf/ASCTB-TEMP_ring-fiber,Ring Fiber,,,UBERON:0003910,splenic sinusoid,"https://doi.org/10.1111/j.1365-2559.1986.tb02483.x, https://doi.org/10.2478/s11756-009-0193-5" +spleen,https://purl.org/ccf/ASCTB-TEMP_splenic-red-pulp-stroma,Splenic Red Pulp Stroma,,,UBERON:0003910,splenic sinusoid,https://doi.org/10.1002/eji.200425442 +spleen,https://purl.org/ccf/ASCTB-TEMP_subcapsule,Subcapsule,,,UBERON:0004641,spleen capsule,https://doi.org/10.1111/j.1365-2249.2008.03734.x +spleen,https://purl.org/ccf/ASCTB-TEMP_superficial-mantle-zone,Superficial Mantle Zone,,,UBERON:0010421,spleen B cell corona,"https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1111/imm.12469, https://doi.org/10.1111/j.1365-2567.2005.02242.x, https://doi.org/10.1038/s41467-019-09728-3, PMID: 20126587, https://doi.org/10.1007/s00418-020-01924-3, https://doi.org/10.1371/journal.pone.0191019, https://doi.org/10.1007/s00418-007-0320-8, https://doi.org/10.1016/j.aanat.2019.05.004, https://doi.org/10.1182/bloodadvances.2017015073" +spleen,https://purl.org/ccf/ASCTB-TEMP_white-pulp-lymphatic-vessels,White Pulp Lymphatic Vessels,,,UBERON:0001959,white pulp of spleen,"https://doi.org/10.1369/jhc.4A6514.2005, PMID:16515224" \ No newline at end of file diff --git a/src/templates/hra-spleen-groups.template.tsv b/src/templates/hra-spleen-groups.template.tsv new file mode 100644 index 000000000..dff359c07 --- /dev/null +++ b/src/templates/hra-spleen-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-spleen-reports/candidates.tsv b/src/templates/hra-spleen-reports/candidates.tsv new file mode 100644 index 000000000..d6d558096 --- /dev/null +++ b/src/templates/hra-spleen-reports/candidates.tsv @@ -0,0 +1,2 @@ +label as_iri uberon_id note +Connective tissue UBERON:0002384 confirmed_match (confidence: high) diff --git a/src/templates/hra-spleen-reports/errors.tsv b/src/templates/hra-spleen-reports/errors.tsv new file mode 100644 index 000000000..7f20612cf --- /dev/null +++ b/src/templates/hra-spleen-reports/errors.tsv @@ -0,0 +1 @@ +label as_iri issue_type parent_id parent_label detail diff --git a/src/templates/hra-spleen-reports/input.tsv b/src/templates/hra-spleen-reports/input.tsv new file mode 100644 index 000000000..16f64b9b6 --- /dev/null +++ b/src/templates/hra-spleen-reports/input.tsv @@ -0,0 +1,11 @@ +table as_iri label uberon_id parent_id parent_label references term_type + https://purl.org/ccf/ASCTB-TEMP_connective-tissue Connective tissue UBERON:0004641 spleen capsule PMID: 20126587, PMID: 3310649 leaf + https://purl.org/ccf/ASCTB-TEMP_arterial-capillary Arterial Capillary UBERON:0001250 red pulp of spleen https://doi.org/ 10.1182/ bloodadvances.2017015073, https://doi.org/10.1007/s00418-007-0320-8 leaf + https://purl.org/ccf/ASCTB-TEMP_inner-mantle-zone Inner Mantle Zone UBERON:0010421 spleen B cell corona https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1111/imm.12469, https://doi.org/10.1111/imm.12325, https://doi.org/10.1093/intimm/14.2.157, https://doi.org/10.1038/s41467-019-09728-3, https://doi.org/10.1007/s00418-007-0320-8, https://doi.org/10.1016/j.aanat.2019.05.004, https://doi.org/10.1182/bloodadvances.2017015073, https://doi.org/10.1007/s00418-020-01924-3, https://doi.org/10.1371/journal.pone.0191019 leaf + https://purl.org/ccf/ASCTB-TEMP_inner-pals Inner PALS UBERON:0010401 spleen central arteriole https://doi.org/10.1007/s00418-007-0320-8, https://doi.org/10.1111/j.1365-2559.1985.tb02841.x, https://doi.org/10.1111/j.1365-2559.1986.tb02482.x, https://doi.org/10.1182/bloodadvances.2017015073, https://doi.org/10.1111/imm.12469, https://doi.org/10.1016/j.bbi.2018.12.009, https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1126/sciimmunol.aau6085, https://doi.org/10.1007/s00262-015-1729-x, https://doi.org/10.1016/j.immuni.2012.09.020, https://doi.org/10.1038/s41467-019-09728-3, https://doi.org/10.55418/9781933477060., https://doi.org/10.1309/M95G-7DQ2-TLQL-7Q11, https://doi.org/10.1369%2Fjhc.4A6514.2005, PMID:16515224 leaf + https://purl.org/ccf/ASCTB-TEMP_outer-pals Outer PALS UBERON:0001960 periarterial lymphatic sheath https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1126/sciimmunol.aau6085, https://doi.org/10.1007/s00262-015-1729-x, https://doi.org/10.1016/j.immuni.2012.09.020, https://doi.org/10.1038/s41467-019-09728-3, https://doi.org/10.1111/imm.12469, https://doi.org/10.55418/9781933477060., https://doi.org/10.1038/s41421-020-0157-z, https://doi.org/10.1093/intimm/14.2.157 leaf + https://purl.org/ccf/ASCTB-TEMP_ring-fiber Ring Fiber UBERON:0003910 splenic sinusoid https://doi.org/10.1111/j.1365-2559.1986.tb02483.x, https://doi.org/10.2478/s11756-009-0193-5 leaf + https://purl.org/ccf/ASCTB-TEMP_splenic-red-pulp-stroma Splenic Red Pulp Stroma UBERON:0003910 splenic sinusoid https://doi.org/10.1002/eji.200425442 leaf + https://purl.org/ccf/ASCTB-TEMP_subcapsule Subcapsule UBERON:0004641 spleen capsule https://doi.org/10.1111/j.1365-2249.2008.03734.x leaf + https://purl.org/ccf/ASCTB-TEMP_superficial-mantle-zone Superficial Mantle Zone UBERON:0010421 spleen B cell corona https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1111/imm.12469, https://doi.org/10.1111/j.1365-2567.2005.02242.x, https://doi.org/10.1038/s41467-019-09728-3, PMID: 20126587, https://doi.org/10.1007/s00418-020-01924-3, https://doi.org/10.1371/journal.pone.0191019, https://doi.org/10.1007/s00418-007-0320-8, https://doi.org/10.1016/j.aanat.2019.05.004, https://doi.org/10.1182/bloodadvances.2017015073 leaf + https://purl.org/ccf/ASCTB-TEMP_white-pulp-lymphatic-vessels White Pulp Lymphatic Vessels UBERON:0001959 white pulp of spleen https://doi.org/10.1369/jhc.4A6514.2005, PMID:16515224 leaf diff --git a/src/templates/hra-spleen-reports/name_corrections.tsv b/src/templates/hra-spleen-reports/name_corrections.tsv new file mode 100644 index 000000000..67a599358 --- /dev/null +++ b/src/templates/hra-spleen-reports/name_corrections.tsv @@ -0,0 +1,4 @@ +source_label corrected_label reason +Arterial Capillary arterial capillary Standard anatomical nomenclature uses lowercase. Keep source name 'Arterial Capillary' as synonym. +White Pulp Lymphatic Vessels white pulp lymphatic vessel UBERON convention uses lowercase for anatomical terms; 'vessel' should be singular to match pattern of similar terms like 'facial lymphatic vessel' (UBERON:0001422). Original capitalization and plural form from source should be added as synonyms. +Subcapsule subcapsular zone Anatomical terminology typically uses 'subcapsular' as the adjective form. However, the structure's relationship to spleen capsule (parent) is unclear - 'sub-' means 'under/below', suggesting this structure lies beneath the capsule rather than being part of it. More context needed to determine if this should be 'subcapsular zone of spleen' (part_of spleen, adjacent_to spleen capsule) or a layer within the capsule itself. diff --git a/src/templates/hra-spleen.template.tsv b/src/templates/hra-spleen.template.tsv new file mode 100644 index 000000000..adf0af0c3 --- /dev/null +++ b/src/templates/hra-spleen.template.tsv @@ -0,0 +1,11 @@ +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_8930191 arterial capillary A capillary that receives blood from an arteriole and represents the arterial end of the capillary bed, characterized by higher hydrostatic pressure that promotes filtration of fluid and nutrients from the blood into the surrounding interstitial tissue. https://doi.org/ 10.1182/ bloodadvances.2017015073|https://doi.org/10.1007/s00418-007-0320-8|https://purl.org/ccf/ASCTB-TEMP_arterial-capillary|DOI:10.1182/bloodadvances.2017015073|DOI:10.1007/s00418-007-0320-8 UBERON:0001982 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:Capillary +http://purl.obolibrary.org/obo/UBERON_8930192 Inner Mantle Zone A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/imm.12325|https://doi.org/10.1093/intimm/14.2.157|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://purl.org/ccf/ASCTB-TEMP_inner-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone +http://purl.obolibrary.org/obo/UBERON_8930193 Inner PALS The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation. https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1111/j.1365-2559.1985.tb02841.x|https://doi.org/10.1111/j.1365-2559.1986.tb02482.x|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1111/imm.12469|https://doi.org/10.1016/j.bbi.2018.12.009|https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1309/M95G-7DQ2-TLQL-7Q11|https://doi.org/10.1369%2Fjhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_inner-pals UBERON:0000064 UBERON:0001960 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:White_pulp +http://purl.obolibrary.org/obo/UBERON_8930194 Outer PALS An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1111/imm.12469|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1038/s41421-020-0157-z|https://doi.org/10.1093/intimm/14.2.157|https://purl.org/ccf/ASCTB-TEMP_outer-pals UBERON:0000064 UBERON:0001960 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_8930195 Ring Fiber A circumferential reticular fiber that encircles a splenic sinusoid, forming part of the sinusoidal basement membrane and providing structural support to the vessel wall. https://doi.org/10.1111/j.1365-2559.1986.tb02483.x|https://doi.org/10.2478/s11756-009-0193-5|https://purl.org/ccf/ASCTB-TEMP_ring-fiber|PMID:15258183|PMID:2424311|PMID:6194184 UBERON:0006804 UBERON:0003910 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_8930196 Splenic Red Pulp Stroma The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids. https://doi.org/10.1002/eji.200425442|https://purl.org/ccf/ASCTB-TEMP_splenic-red-pulp-stroma|PMID:16914502|PMID:37007998|PMID:32393414 UBERON:0003891 UBERON:0001250 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:Red_pulp +http://purl.obolibrary.org/obo/UBERON_8930197 subcapsular zone An anatomical compartment that lies immediately beneath the fibrous capsule of an organ, typically containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma. https://doi.org/10.1111/j.1365-2249.2008.03734.x|https://purl.org/ccf/ASCTB-TEMP_subcapsule UBERON:0000064 UBERON:0002106 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_8930198 Superficial Mantle Zone A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/j.1365-2567.2005.02242.x|https://doi.org/10.1038/s41467-019-09728-3|PMID: 20126587|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://purl.org/ccf/ASCTB-TEMP_superficial-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|PMID:20126587|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone +http://purl.obolibrary.org/obo/UBERON_8930199 white pulp lymphatic vessel A lymphatic vessel that is part of the white pulp of the spleen. https://doi.org/10.1369/jhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_white-pulp-lymphatic-vessels UBERON:0001473 UBERON:0001959 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:White_pulp From d61ae4a5c25ea4c3d65ace2b92780dc120474ec9 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 6 Jul 2026 16:04:45 +0100 Subject: [PATCH 2/9] 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-spleen-reports/candidates.tsv | 0 .../outputs}/hra-spleen-reports/errors.tsv | 0 .../outputs}/hra-spleen-reports/input.tsv | 0 .../outputs}/hra-spleen-reports/name_corrections.tsv | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename {src/templates => bulk_ntr_workflow/outputs}/hra-spleen-reports/candidates.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-spleen-reports/errors.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-spleen-reports/input.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-spleen-reports/name_corrections.tsv (100%) diff --git a/src/templates/hra-spleen-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/candidates.tsv similarity index 100% rename from src/templates/hra-spleen-reports/candidates.tsv rename to bulk_ntr_workflow/outputs/hra-spleen-reports/candidates.tsv diff --git a/src/templates/hra-spleen-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/errors.tsv similarity index 100% rename from src/templates/hra-spleen-reports/errors.tsv rename to bulk_ntr_workflow/outputs/hra-spleen-reports/errors.tsv diff --git a/src/templates/hra-spleen-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/input.tsv similarity index 100% rename from src/templates/hra-spleen-reports/input.tsv rename to bulk_ntr_workflow/outputs/hra-spleen-reports/input.tsv diff --git a/src/templates/hra-spleen-reports/name_corrections.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/name_corrections.tsv similarity index 100% rename from src/templates/hra-spleen-reports/name_corrections.tsv rename to bulk_ntr_workflow/outputs/hra-spleen-reports/name_corrections.tsv From 8f4cfd8bd3d5e4c6e622dfcab8cf56bb1b967a69 Mon Sep 17 00:00:00 2001 From: "claude[bot]" <41898282+claude[bot]@users.noreply.github.com> Date: Mon, 13 Jul 2026 23:20:52 +0000 Subject: [PATCH 3/9] Update hra-spleen template and add new spleen terms to uberon-edit.obo MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updated src/templates/hra-spleen.template.tsv per curator review: - Lowercased labels: inner mantle zone, superficial mantle zone, ring fiber, splenic red pulp stroma - Renamed 'Inner PALS' -> 'inner periarterial lymphatic sheath' (adds exact synonym 'inner PALS') - Renamed 'Outer PALS' -> 'outer periarterial lymphatic sheath' (adds exact synonym 'outer PALS') - Renamed 'Ring Fiber' -> 'ring fiber' (adds exact synonym 'annular fiber') - Replaced 'arterial capillary' (UBERON:8930191) with 'spleen connective tissue': new definition, def_xref PMID:20126587|PMID:3310649, is_a UBERON:0002384, removed xref, added equivalent class axiom 'connective tissue and (part_of some spleen)' - Fixed 'PMID: 20126587' -> 'PMID:20126587' (removed space) - Added Synonym and equivalent_class columns to template header Added 9 new terms (UBERON:8930191-UBERON:8930199) to src/ontology/uberon-edit.obo with definitions, provenance (dc-contributor, dcterms-date, term_tracker_item, created_by) and taxonomic scope (present_in_taxon Homo sapiens). 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/29292174485) Co-Authored-By: Claude Opus 4.7 --- src/ontology/uberon-edit.obo | 125 ++++++++++++++++++++++++++ src/templates/hra-spleen.template.tsv | 22 ++--- 2 files changed, 136 insertions(+), 11 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index d867d5049..5d9aea993 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225211,6 +225211,131 @@ 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:8930191 +name: spleen connective tissue +def: "A portion of connective tissue that is part of a spleen." [PMID:20126587, PMID:3310649] +subset: added_by_HRA +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0002106 ! spleen +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930192 +name: inner mantle zone +def: "A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells." [doi:10.1007/s00418-007-0320-8, doi:10.1007/s00418-020-01924-3, doi:10.1016/j.aanat.2019.05.004, doi:10.1038/s41467-019-09728-3, doi:10.1093/intimm/14.2.157, doi:10.1111/imm.12325, doi:10.1111/imm.12469, doi:10.1182/bloodadvances.2017015073, doi:10.1186/s13059-019-1906-x, doi:10.1371/journal.pone.0191019] +subset: added_by_HRA +xref: Wikipedia:Mantle_zone +is_a: UBERON:0001744 ! lymphoid tissue +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0010421 ! spleen B cell corona +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930193 +name: inner periarterial lymphatic sheath +def: "The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation." [doi:10.1007/s00262-015-1729-x, doi:10.1007/s00418-007-0320-8, doi:10.1016/j.bbi.2018.12.009, doi:10.1016/j.immuni.2012.09.020, doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2559.1985.tb02841.x, doi:10.1111/j.1365-2559.1986.tb02482.x, doi:10.1126/sciimmunol.aau6085, doi:10.1182/bloodadvances.2017015073, doi:10.1186/s13059-019-1906-x, PMID:16515224] +subset: added_by_HRA +synonym: "inner PALS" EXACT [] +xref: Wikipedia:White_pulp +is_a: UBERON:0000064 ! organ part +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930194 +name: outer periarterial lymphatic sheath +def: "An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp." [doi:10.1007/s00262-015-1729-x, doi:10.1016/j.immuni.2012.09.020, doi:10.1038/s41421-020-0157-z, doi:10.1038/s41467-019-09728-3, doi:10.1093/intimm/14.2.157, doi:10.1111/imm.12469, doi:10.1126/sciimmunol.aau6085, doi:10.1186/s13059-019-1906-x] +subset: added_by_HRA +synonym: "outer PALS" EXACT [] +is_a: UBERON:0000064 ! organ part +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930195 +name: ring fiber +def: "A circumferential reticular fiber that encircles a splenic sinusoid, forming part of the sinusoidal basement membrane and providing structural support to the vessel wall." [doi:10.1111/j.1365-2559.1986.tb02483.x, doi:10.2478/s11756-009-0193-5, PMID:15258183, PMID:2424311, PMID:6194184] +subset: added_by_HRA +synonym: "annular fiber" EXACT [] +is_a: UBERON:0006804 ! reticular tissue +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0003910 ! splenic sinusoid +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930196 +name: splenic red pulp stroma +def: "The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids." [doi:10.1002/eji.200425442, PMID:16914502, PMID:32393414, PMID:37007998] +subset: added_by_HRA +xref: Wikipedia:Red_pulp +is_a: UBERON:0003891 ! stroma +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0001250 ! red pulp of spleen +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930197 +name: subcapsular zone +def: "An anatomical compartment that lies immediately beneath the fibrous capsule of an organ, typically containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma." [doi:10.1111/j.1365-2249.2008.03734.x] +subset: added_by_HRA +is_a: UBERON:0000064 ! organ part +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0002106 ! spleen +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930198 +name: superficial mantle zone +def: "A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes." [doi:10.1007/s00418-007-0320-8, doi:10.1007/s00418-020-01924-3, doi:10.1016/j.aanat.2019.05.004, doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2567.2005.02242.x, doi:10.1182/bloodadvances.2017015073, doi:10.1186/s13059-019-1906-x, doi:10.1371/journal.pone.0191019, PMID:20126587] +subset: added_by_HRA +xref: Wikipedia:Mantle_zone +is_a: UBERON:0001744 ! lymphoid tissue +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0010421 ! spleen B cell corona +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/3722" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930199 +name: white pulp lymphatic vessel +def: "A lymphatic vessel that is part of the white pulp of the spleen." [doi:10.1369/jhc.4A6514.2005, PMID:16515224] +subset: added_by_HRA +xref: Wikipedia:White_pulp +is_a: UBERON:0001473 ! lymphatic vessel +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0001959 ! white pulp of spleen +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/3722" xsd:anyURI +created_by: dragon-ai-agent + [Typedef] id: aboral_to name: aboral to diff --git a/src/templates/hra-spleen.template.tsv b/src/templates/hra-spleen.template.tsv index adf0af0c3..1a76ce377 100644 --- a/src/templates/hra-spleen.template.tsv +++ b/src/templates/hra-spleen.template.tsv @@ -1,11 +1,11 @@ -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_8930191 arterial capillary A capillary that receives blood from an arteriole and represents the arterial end of the capillary bed, characterized by higher hydrostatic pressure that promotes filtration of fluid and nutrients from the blood into the surrounding interstitial tissue. https://doi.org/ 10.1182/ bloodadvances.2017015073|https://doi.org/10.1007/s00418-007-0320-8|https://purl.org/ccf/ASCTB-TEMP_arterial-capillary|DOI:10.1182/bloodadvances.2017015073|DOI:10.1007/s00418-007-0320-8 UBERON:0001982 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:Capillary -http://purl.obolibrary.org/obo/UBERON_8930192 Inner Mantle Zone A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/imm.12325|https://doi.org/10.1093/intimm/14.2.157|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://purl.org/ccf/ASCTB-TEMP_inner-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone -http://purl.obolibrary.org/obo/UBERON_8930193 Inner PALS The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation. https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1111/j.1365-2559.1985.tb02841.x|https://doi.org/10.1111/j.1365-2559.1986.tb02482.x|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1111/imm.12469|https://doi.org/10.1016/j.bbi.2018.12.009|https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1309/M95G-7DQ2-TLQL-7Q11|https://doi.org/10.1369%2Fjhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_inner-pals UBERON:0000064 UBERON:0001960 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:White_pulp -http://purl.obolibrary.org/obo/UBERON_8930194 Outer PALS An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1111/imm.12469|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1038/s41421-020-0157-z|https://doi.org/10.1093/intimm/14.2.157|https://purl.org/ccf/ASCTB-TEMP_outer-pals UBERON:0000064 UBERON:0001960 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_8930195 Ring Fiber A circumferential reticular fiber that encircles a splenic sinusoid, forming part of the sinusoidal basement membrane and providing structural support to the vessel wall. https://doi.org/10.1111/j.1365-2559.1986.tb02483.x|https://doi.org/10.2478/s11756-009-0193-5|https://purl.org/ccf/ASCTB-TEMP_ring-fiber|PMID:15258183|PMID:2424311|PMID:6194184 UBERON:0006804 UBERON:0003910 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_8930196 Splenic Red Pulp Stroma The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids. https://doi.org/10.1002/eji.200425442|https://purl.org/ccf/ASCTB-TEMP_splenic-red-pulp-stroma|PMID:16914502|PMID:37007998|PMID:32393414 UBERON:0003891 UBERON:0001250 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:Red_pulp -http://purl.obolibrary.org/obo/UBERON_8930197 subcapsular zone An anatomical compartment that lies immediately beneath the fibrous capsule of an organ, typically containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma. https://doi.org/10.1111/j.1365-2249.2008.03734.x|https://purl.org/ccf/ASCTB-TEMP_subcapsule UBERON:0000064 UBERON:0002106 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_8930198 Superficial Mantle Zone A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/j.1365-2567.2005.02242.x|https://doi.org/10.1038/s41467-019-09728-3|PMID: 20126587|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://purl.org/ccf/ASCTB-TEMP_superficial-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|PMID:20126587|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone -http://purl.obolibrary.org/obo/UBERON_8930199 white pulp lymphatic vessel A lymphatic vessel that is part of the white pulp of the spleen. https://doi.org/10.1369/jhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_white-pulp-lymphatic-vessels UBERON:0001473 UBERON:0001959 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:White_pulp +ID LABEL Definition def_xref Synonym is_a equivalent_class part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| A oboInOwl:hasExactSynonym SPLIT=| SC % EC % 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_8930191 spleen connective tissue A portion of connective tissue that is part of a spleen. PMID:20126587|PMID:3310649 UBERON:0002384 UBERON:0002384 and (BFO:0000050 some UBERON:0002106) 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_8930192 inner mantle zone A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/imm.12325|https://doi.org/10.1093/intimm/14.2.157|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://purl.org/ccf/ASCTB-TEMP_inner-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone +http://purl.obolibrary.org/obo/UBERON_8930193 inner periarterial lymphatic sheath The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation. https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1111/j.1365-2559.1985.tb02841.x|https://doi.org/10.1111/j.1365-2559.1986.tb02482.x|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1111/imm.12469|https://doi.org/10.1016/j.bbi.2018.12.009|https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1309/M95G-7DQ2-TLQL-7Q11|https://doi.org/10.1369%2Fjhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_inner-pals inner PALS UBERON:0000064 UBERON:0001960 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:White_pulp +http://purl.obolibrary.org/obo/UBERON_8930194 outer periarterial lymphatic sheath An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1111/imm.12469|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1038/s41421-020-0157-z|https://doi.org/10.1093/intimm/14.2.157|https://purl.org/ccf/ASCTB-TEMP_outer-pals outer PALS UBERON:0000064 UBERON:0001960 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_8930195 ring fiber A circumferential reticular fiber that encircles a splenic sinusoid, forming part of the sinusoidal basement membrane and providing structural support to the vessel wall. https://doi.org/10.1111/j.1365-2559.1986.tb02483.x|https://doi.org/10.2478/s11756-009-0193-5|https://purl.org/ccf/ASCTB-TEMP_ring-fiber|PMID:15258183|PMID:2424311|PMID:6194184 annular fiber UBERON:0006804 UBERON:0003910 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_8930196 splenic red pulp stroma The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids. https://doi.org/10.1002/eji.200425442|https://purl.org/ccf/ASCTB-TEMP_splenic-red-pulp-stroma|PMID:16914502|PMID:37007998|PMID:32393414 UBERON:0003891 UBERON:0001250 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:Red_pulp +http://purl.obolibrary.org/obo/UBERON_8930197 subcapsular zone An anatomical compartment that lies immediately beneath the fibrous capsule of an organ, typically containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma. https://doi.org/10.1111/j.1365-2249.2008.03734.x|https://purl.org/ccf/ASCTB-TEMP_subcapsule UBERON:0000064 UBERON:0002106 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_8930198 superficial mantle zone A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/j.1365-2567.2005.02242.x|https://doi.org/10.1038/s41467-019-09728-3|PMID:20126587|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://purl.org/ccf/ASCTB-TEMP_superficial-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone +http://purl.obolibrary.org/obo/UBERON_8930199 white pulp lymphatic vessel A lymphatic vessel that is part of the white pulp of the spleen. https://doi.org/10.1369/jhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_white-pulp-lymphatic-vessels UBERON:0001473 UBERON:0001959 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:White_pulp From 11b94df7126fd032056003bd04c63186804704a0 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 14:54:18 +0100 Subject: [PATCH 4/9] Update uberon-edit.obo Trimmed references --- src/ontology/uberon-edit.obo | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5d9aea993..a3b050205 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225227,7 +225227,7 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930192 name: inner mantle zone -def: "A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells." [doi:10.1007/s00418-007-0320-8, doi:10.1007/s00418-020-01924-3, doi:10.1016/j.aanat.2019.05.004, doi:10.1038/s41467-019-09728-3, doi:10.1093/intimm/14.2.157, doi:10.1111/imm.12325, doi:10.1111/imm.12469, doi:10.1182/bloodadvances.2017015073, doi:10.1186/s13059-019-1906-x, doi:10.1371/journal.pone.0191019] +def: "A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells." [doi:10.1111/imm.12469] subset: added_by_HRA xref: Wikipedia:Mantle_zone is_a: UBERON:0001744 ! lymphoid tissue @@ -225241,7 +225241,7 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930193 name: inner periarterial lymphatic sheath -def: "The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation." [doi:10.1007/s00262-015-1729-x, doi:10.1007/s00418-007-0320-8, doi:10.1016/j.bbi.2018.12.009, doi:10.1016/j.immuni.2012.09.020, doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2559.1985.tb02841.x, doi:10.1111/j.1365-2559.1986.tb02482.x, doi:10.1126/sciimmunol.aau6085, doi:10.1182/bloodadvances.2017015073, doi:10.1186/s13059-019-1906-x, PMID:16515224] +def: "The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation." [doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2559.1985.tb02841.x, doi:10.1111/j.1365-2559.1986.tb02482.x, doi:10.1126/sciimmunol.aau6085, doi:10.1182/bloodadvances.2017015073] subset: added_by_HRA synonym: "inner PALS" EXACT [] xref: Wikipedia:White_pulp @@ -225255,8 +225255,8 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930194 -name: outer periarterial lymphatic sheath -def: "An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp." [doi:10.1007/s00262-015-1729-x, doi:10.1016/j.immuni.2012.09.020, doi:10.1038/s41421-020-0157-z, doi:10.1038/s41467-019-09728-3, doi:10.1093/intimm/14.2.157, doi:10.1111/imm.12469, doi:10.1126/sciimmunol.aau6085, doi:10.1186/s13059-019-1906-x] +name: outer periarterial lymphatic sheath of spleen +def: "An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp." [DOI:10.1007/BF00225103] subset: added_by_HRA synonym: "outer PALS" EXACT [] is_a: UBERON:0000064 ! organ part @@ -225284,10 +225284,10 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930196 name: splenic red pulp stroma -def: "The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids." [doi:10.1002/eji.200425442, PMID:16914502, PMID:32393414, PMID:37007998] +def: "The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids." [doi:10.1002/eji.200425442, PMID:37007998] subset: added_by_HRA xref: Wikipedia:Red_pulp -is_a: UBERON:0003891 ! stroma +is_a: UBERON:0002384 ! connective tissue relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 relationship: part_of UBERON:0001250 ! red pulp of spleen relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens @@ -225297,8 +225297,8 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930197 -name: subcapsular zone -def: "An anatomical compartment that lies immediately beneath the fibrous capsule of an organ, typically containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma." [doi:10.1111/j.1365-2249.2008.03734.x] +name: spleen subcapsular zone +def: "An anatomical compartment that lies immediately beneath the fibrous capsule of the spleen containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma." [doi:10.1111/j.1365-2249.2008.03734.x] subset: added_by_HRA is_a: UBERON:0000064 ! organ part relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 @@ -225311,7 +225311,7 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930198 name: superficial mantle zone -def: "A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes." [doi:10.1007/s00418-007-0320-8, doi:10.1007/s00418-020-01924-3, doi:10.1016/j.aanat.2019.05.004, doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2567.2005.02242.x, doi:10.1182/bloodadvances.2017015073, doi:10.1186/s13059-019-1906-x, doi:10.1371/journal.pone.0191019, PMID:20126587] +def: "A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes." [doi:10.1111/imm.12469] subset: added_by_HRA xref: Wikipedia:Mantle_zone is_a: UBERON:0001744 ! lymphoid tissue From c96a0f93fd4522e6f5e253edbad8c3b3eb843c76 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 16:12:45 +0100 Subject: [PATCH 5/9] Delete src/templates/hra-spleen.template.tsv terms moved to edit file --- src/templates/hra-spleen.template.tsv | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 src/templates/hra-spleen.template.tsv diff --git a/src/templates/hra-spleen.template.tsv b/src/templates/hra-spleen.template.tsv deleted file mode 100644 index 1a76ce377..000000000 --- a/src/templates/hra-spleen.template.tsv +++ /dev/null @@ -1,11 +0,0 @@ -ID LABEL Definition def_xref Synonym is_a equivalent_class part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref -ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| A oboInOwl:hasExactSynonym SPLIT=| SC % EC % 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_8930191 spleen connective tissue A portion of connective tissue that is part of a spleen. PMID:20126587|PMID:3310649 UBERON:0002384 UBERON:0002384 and (BFO:0000050 some UBERON:0002106) 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_8930192 inner mantle zone A lymphoid tissue zone within the spleen B cell corona that is positioned adjacent to the germinal center and contains a heterogeneous population of B lymphocytes, including recently activated and transitional B cells. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/imm.12325|https://doi.org/10.1093/intimm/14.2.157|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://purl.org/ccf/ASCTB-TEMP_inner-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone -http://purl.obolibrary.org/obo/UBERON_8930193 inner periarterial lymphatic sheath The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation. https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1111/j.1365-2559.1985.tb02841.x|https://doi.org/10.1111/j.1365-2559.1986.tb02482.x|https://doi.org/10.1182/bloodadvances.2017015073|https://doi.org/10.1111/imm.12469|https://doi.org/10.1016/j.bbi.2018.12.009|https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1309/M95G-7DQ2-TLQL-7Q11|https://doi.org/10.1369%2Fjhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_inner-pals inner PALS UBERON:0000064 UBERON:0001960 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:White_pulp -http://purl.obolibrary.org/obo/UBERON_8930194 outer periarterial lymphatic sheath An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1126/sciimmunol.aau6085|https://doi.org/10.1007/s00262-015-1729-x|https://doi.org/10.1016/j.immuni.2012.09.020|https://doi.org/10.1038/s41467-019-09728-3|https://doi.org/10.1111/imm.12469|https://doi.org/10.55418/9781933477060.|https://doi.org/10.1038/s41421-020-0157-z|https://doi.org/10.1093/intimm/14.2.157|https://purl.org/ccf/ASCTB-TEMP_outer-pals outer PALS UBERON:0000064 UBERON:0001960 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_8930195 ring fiber A circumferential reticular fiber that encircles a splenic sinusoid, forming part of the sinusoidal basement membrane and providing structural support to the vessel wall. https://doi.org/10.1111/j.1365-2559.1986.tb02483.x|https://doi.org/10.2478/s11756-009-0193-5|https://purl.org/ccf/ASCTB-TEMP_ring-fiber|PMID:15258183|PMID:2424311|PMID:6194184 annular fiber UBERON:0006804 UBERON:0003910 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_8930196 splenic red pulp stroma The connective tissue framework of the red pulp of the spleen, consisting of reticular fibers and stromal cells that support the splenic cords and sinusoids. https://doi.org/10.1002/eji.200425442|https://purl.org/ccf/ASCTB-TEMP_splenic-red-pulp-stroma|PMID:16914502|PMID:37007998|PMID:32393414 UBERON:0003891 UBERON:0001250 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:Red_pulp -http://purl.obolibrary.org/obo/UBERON_8930197 subcapsular zone An anatomical compartment that lies immediately beneath the fibrous capsule of an organ, typically containing supporting connective tissue, blood vessels, and early-arriving lymphocytes or immune cells before they migrate into the organ parenchyma. https://doi.org/10.1111/j.1365-2249.2008.03734.x|https://purl.org/ccf/ASCTB-TEMP_subcapsule UBERON:0000064 UBERON:0002106 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_8930198 superficial mantle zone A lymphoid tissue zone forming the outermost layer of the spleen B cell corona, distal to the germinal center, that predominantly harbors naive and small resting B lymphocytes. https://doi.org/10.1186/s13059-019-1906-x|https://doi.org/10.1111/imm.12469|https://doi.org/10.1111/j.1365-2567.2005.02242.x|https://doi.org/10.1038/s41467-019-09728-3|PMID:20126587|https://doi.org/10.1007/s00418-020-01924-3|https://doi.org/10.1371/journal.pone.0191019|https://doi.org/10.1007/s00418-007-0320-8|https://doi.org/10.1016/j.aanat.2019.05.004|https://doi.org/10.1182/bloodadvances.2017015073|https://purl.org/ccf/ASCTB-TEMP_superficial-mantle-zone|doi:10.1186/s13059-019-1906-x|doi:10.1111/imm.12469|doi:10.1038/s41467-019-09728-3 UBERON:0001744 UBERON:0010421 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:Mantle_zone -http://purl.obolibrary.org/obo/UBERON_8930199 white pulp lymphatic vessel A lymphatic vessel that is part of the white pulp of the spleen. https://doi.org/10.1369/jhc.4A6514.2005|PMID:16515224|https://purl.org/ccf/ASCTB-TEMP_white-pulp-lymphatic-vessels UBERON:0001473 UBERON:0001959 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:White_pulp From 32f07e00e70616b16bc62308f060c801376bdcfd Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 16:13:12 +0100 Subject: [PATCH 6/9] Delete src/templates/hra-spleen-groups.template.tsv terms moved to edit file --- src/templates/hra-spleen-groups.template.tsv | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 src/templates/hra-spleen-groups.template.tsv diff --git a/src/templates/hra-spleen-groups.template.tsv b/src/templates/hra-spleen-groups.template.tsv deleted file mode 100644 index dff359c07..000000000 --- a/src/templates/hra-spleen-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=| From 588151c5fd4498a2cc439c9ce7b48e1ae21e1d2c Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 21:57:51 +0100 Subject: [PATCH 7/9] Inner/outer PALS: rodent-only taxon + explanatory comment inner periarterial lymphatic sheath (UBERON:8930193) and outer periarterial lymphatic sheath of spleen (UBERON:8930194): - present_in_taxon Homo sapiens -> Rodentia (NCBITaxon:9989). The inner/outer PALS subdivision is described in rat and mouse; adult human spleen lacks rodent-type PALS architecture. - Add comment explaining this, citing Veerman & van Ewijk 1975 (doi:10.1007/BF00225103), van Krieken et al. 1985 (doi:10.1111/j.1365-2559.1985.tb02841.x) and Steiniger, Ruettinger & Barth 2003 (doi:10.1177/002215540305100511). Requested by @dosumis. Signed: @ai4c-agent Co-Authored-By: Claude Opus 5.5 (1M context) --- src/ontology/uberon-edit.obo | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index ccaa4aec4..71db5bac9 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225315,13 +225315,14 @@ created_by: dragon-ai-agent id: UBERON:8930193 name: inner periarterial lymphatic sheath def: "The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation." [doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2559.1985.tb02841.x, doi:10.1111/j.1365-2559.1986.tb02482.x, doi:10.1126/sciimmunol.aau6085, doi:10.1182/bloodadvances.2017015073] +comment: Inner/outer PALS subdivision is described in rat and mouse (Veerman & van Ewijk 1975, doi:10.1007/BF00225103). In adult human spleen the T-cell regions are discontinuous and lack rodent-type PALS architecture (van Krieken et al. 1985, doi:10.1111/j.1365-2559.1985.tb02841.x; Steiniger, Rüttinger & Barth 2003, doi:10.1177/002215540305100511); no inner/outer subdivision has been demonstrated in humans. subset: added_by_HRA synonym: "inner PALS" EXACT [] xref: Wikipedia:White_pulp is_a: UBERON:0000064 ! organ part relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: present_in_taxon NCBITaxon:9989 ! Rodentia property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3722" xsd:anyURI created_by: dragon-ai-agent @@ -225330,12 +225331,13 @@ created_by: dragon-ai-agent id: UBERON:8930194 name: outer periarterial lymphatic sheath of spleen def: "An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp." [DOI:10.1007/BF00225103] +comment: Inner/outer PALS subdivision is described in rat and mouse (Veerman & van Ewijk 1975, doi:10.1007/BF00225103). In adult human spleen the T-cell regions are discontinuous and lack rodent-type PALS architecture (van Krieken et al. 1985, doi:10.1111/j.1365-2559.1985.tb02841.x; Steiniger, Rüttinger & Barth 2003, doi:10.1177/002215540305100511); no inner/outer subdivision has been demonstrated in humans. subset: added_by_HRA synonym: "outer PALS" EXACT [] is_a: UBERON:0000064 ! organ part relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: present_in_taxon NCBITaxon:9989 ! Rodentia property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3722" xsd:anyURI created_by: dragon-ai-agent From a5efc36b02c36bbde8ad37c46df0dc69fec5afe8 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 28 Sep 2026 22:13:17 +0100 Subject: [PATCH 8/9] Inner/outer PALS: 'of spleen' labels; defs and refs aligned to rodent literature inner periarterial lymphatic sheath of spleen (UBERON:8930193): - Relabel from 'inner periarterial lymphatic sheath' (kept as EXACT synonym) to match 'outer periarterial lymphatic sheath of spleen'. - Rewrite def to what Veerman & van Ewijk 1975 support (central PALS: thymus-dependent area, largely devoid of reticulum cells, IDCs in close contact with T cells). Replace 6 def refs (human/general or unrelated, e.g. myelofibrosis vessel-lining cells; two human papers argue against the structure) with rodent refs: DOI:10.1007/BF00225103, DOI:10.1002/ar.1092320103 (Sasou & Sugai 1992, central region), DOI:10.1007/BF00217084 (Eikelenboom et al. 1982, 'inner PALS'). - Synonyms 'central PALS' (Veerman 1975), 'inner PALS' now referenced. - Drop Wikipedia:White_pulp xref (broader structure). outer periarterial lymphatic sheath of spleen (UBERON:8930194): - Rewrite def: the previous 'containing activated T cells' is not supported; refs describe T and B lymphocytes, T-B interaction (Veerman 1975), antigen-induced proliferation / AFC clusters (Matsuno et al. 1989, DOI:10.1007/BF00221456) and the start of the IgM plasmablast response with migration to red pulp (Eikelenboom 1982). - Synonym 'peripheral PALS' (Veerman 1975); 'outer PALS' referenced. All DOIs verified against Crossref; claims checked against PubMed abstracts (PMIDs 1078994, 1536460, 2790931, 6751549). Signed: @ai4c-agent Co-Authored-By: Claude Opus 5.5 (1M context) --- src/ontology/uberon-edit.obo | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 71db5bac9..3315aa570 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225313,12 +225313,13 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930193 -name: inner periarterial lymphatic sheath -def: "The region of the periarterial lymphatic sheath that is immediately adjacent to the spleen central arteriole, characterized by a high density of T lymphocytes and specialized antigen-presenting cells that participate in T cell activation and differentiation." [doi:10.1038/s41467-019-09728-3, doi:10.1111/imm.12469, doi:10.1111/j.1365-2559.1985.tb02841.x, doi:10.1111/j.1365-2559.1986.tb02482.x, doi:10.1126/sciimmunol.aau6085, doi:10.1182/bloodadvances.2017015073] +name: inner periarterial lymphatic sheath of spleen +def: "The central region of the periarterial lymphatic sheath of the spleen, immediately surrounding the central arteriole. It forms the thymus-dependent (T cell) area of the splenic white pulp, is largely devoid of reticulum cells, and contains interdigitating cells in close contact with T lymphocytes." [DOI:10.1002/ar.1092320103, DOI:10.1007/BF00217084, DOI:10.1007/BF00225103] comment: Inner/outer PALS subdivision is described in rat and mouse (Veerman & van Ewijk 1975, doi:10.1007/BF00225103). In adult human spleen the T-cell regions are discontinuous and lack rodent-type PALS architecture (van Krieken et al. 1985, doi:10.1111/j.1365-2559.1985.tb02841.x; Steiniger, Rüttinger & Barth 2003, doi:10.1177/002215540305100511); no inner/outer subdivision has been demonstrated in humans. subset: added_by_HRA -synonym: "inner PALS" EXACT [] -xref: Wikipedia:White_pulp +synonym: "central PALS" EXACT [DOI:10.1007/BF00225103] +synonym: "inner PALS" EXACT [DOI:10.1007/BF00217084] +synonym: "inner periarterial lymphatic sheath" EXACT [] is_a: UBERON:0000064 ! organ part relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath @@ -225330,10 +225331,11 @@ created_by: dragon-ai-agent [Term] id: UBERON:8930194 name: outer periarterial lymphatic sheath of spleen -def: "An anatomical zone of the periarterial lymphatic sheath that forms the peripheral region surrounding the inner T cell zone, containing activated T cells and serving as an interface between the T cell domain and the adjacent B cell follicles in the splenic white pulp." [DOI:10.1007/BF00225103] +def: "The peripheral region of the periarterial lymphatic sheath of the spleen, surrounding the inner periarterial lymphatic sheath of spleen, in which reticulum cells are arranged in cylindrical shells. It contains both T and B lymphocytes and is a site of T-B cell interaction and of antigen-induced B cell proliferation and early plasmablast development, from where plasmablasts migrate towards the red pulp." [DOI:10.1007/BF00217084, DOI:10.1007/BF00221456, DOI:10.1007/BF00225103] comment: Inner/outer PALS subdivision is described in rat and mouse (Veerman & van Ewijk 1975, doi:10.1007/BF00225103). In adult human spleen the T-cell regions are discontinuous and lack rodent-type PALS architecture (van Krieken et al. 1985, doi:10.1111/j.1365-2559.1985.tb02841.x; Steiniger, Rüttinger & Barth 2003, doi:10.1177/002215540305100511); no inner/outer subdivision has been demonstrated in humans. subset: added_by_HRA -synonym: "outer PALS" EXACT [] +synonym: "outer PALS" EXACT [DOI:10.1007/BF00217084, DOI:10.1007/BF00221456] +synonym: "peripheral PALS" EXACT [DOI:10.1007/BF00225103] is_a: UBERON:0000064 ! organ part relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath From 663467d820341748e68520804f8aac5656a95f59 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Tue, 29 Sep 2026 08:48:19 +0100 Subject: [PATCH 9/9] Outer PALS surrounds inner PALS outer periarterial lymphatic sheath of spleen (UBERON:8930194): add relationship: surrounds UBERON:8930193 (inner periarterial lymphatic sheath of spleen), matching the text definition and Veerman & van Ewijk 1975 (DOI:10.1007/BF00225103: peripheral area of the PALS around the central area). ELK: no unsatisfiable classes. Signed: @ai4c-agent Co-Authored-By: Claude Opus 5.5 (1M context) --- src/ontology/uberon-edit.obo | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 3315aa570..59ceb0bc7 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225340,6 +225340,7 @@ is_a: UBERON:0000064 ! organ part relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 relationship: part_of UBERON:0001960 ! periarterial lymphatic sheath relationship: present_in_taxon NCBITaxon:9989 ! Rodentia +relationship: surrounds UBERON:8930193 ! inner periarterial lymphatic sheath of spleen property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3722" xsd:anyURI created_by: dragon-ai-agent