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11 changes: 11 additions & 0 deletions bulk_ntr_workflow/source_data/spleen.csv
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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"
2 changes: 2 additions & 0 deletions src/templates/hra-spleen-groups.template.tsv
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ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref
ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=|
2 changes: 2 additions & 0 deletions src/templates/hra-spleen-reports/candidates.tsv
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label as_iri uberon_id note
Connective tissue UBERON:0002384 confirmed_match (confidence: high)
1 change: 1 addition & 0 deletions src/templates/hra-spleen-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
11 changes: 11 additions & 0 deletions src/templates/hra-spleen-reports/input.tsv
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table as_iri label uberon_id parent_id parent_label references term_type
https://purl.org/ccf/ASCTB-TEMP_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
4 changes: 4 additions & 0 deletions src/templates/hra-spleen-reports/name_corrections.tsv
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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.
11 changes: 11 additions & 0 deletions src/templates/hra-spleen.template.tsv
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ID LABEL Definition def_xref is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref
ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| SC % SC BFO:0000050 some % SC RO:0002202 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=|
http://purl.obolibrary.org/obo/UBERON_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
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