diff --git a/bulk_ntr_workflow/outputs/hra-spleen-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/candidates.tsv new file mode 100644 index 000000000..d6d558096 --- /dev/null +++ b/bulk_ntr_workflow/outputs/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/bulk_ntr_workflow/outputs/hra-spleen-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/errors.tsv new file mode 100644 index 000000000..7f20612cf --- /dev/null +++ b/bulk_ntr_workflow/outputs/hra-spleen-reports/errors.tsv @@ -0,0 +1 @@ +label as_iri issue_type parent_id parent_label detail diff --git a/bulk_ntr_workflow/outputs/hra-spleen-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/input.tsv new file mode 100644 index 000000000..16f64b9b6 --- /dev/null +++ b/bulk_ntr_workflow/outputs/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/bulk_ntr_workflow/outputs/hra-spleen-reports/name_corrections.tsv b/bulk_ntr_workflow/outputs/hra-spleen-reports/name_corrections.tsv new file mode 100644 index 000000000..67a599358 --- /dev/null +++ b/bulk_ntr_workflow/outputs/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/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/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index eff1283ae..35d29772d 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225757,6 +225757,136 @@ relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3717" xsd:anyURI +[Term] +id: UBERON: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:10.1111/imm.12469] +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 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: "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 +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 + +[Term] +id: UBERON:8930194 +name: outer periarterial lymphatic sheath of spleen +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 [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 +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 + +[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:37007998] +subset: added_by_HRA +xref: Wikipedia:Red_pulp +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 +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: 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 +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:10.1111/imm.12469] +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