From 708bddd83036757eb4b3c3ef4d58ccf58ef8e4bd Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Tue, 26 May 2026 13:36:26 -0400 Subject: [PATCH] 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