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Add HRA spleen NTR batch outputs and review reports #3722

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708bddd
Add HRA spleen NTR batch outputs and review reports
zhengj2007 May 26, 2026
d61ae4a
Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/
dosumis Jul 6, 2026
8f4cfd8
Update hra-spleen template and add new spleen terms to uberon-edit.obo
github-actions[bot] Jul 13, 2026
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2 changes: 2 additions & 0 deletions bulk_ntr_workflow/outputs/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 bulk_ntr_workflow/outputs/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 bulk_ntr_workflow/outputs/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 bulk_ntr_workflow/outputs/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 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"
125 changes: 125 additions & 0 deletions src/ontology/uberon-edit.obo
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Expand Up @@ -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
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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=|
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