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 7fa8a7506..ccaa4aec4 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225284,6 +225284,131 @@ 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:10.1111/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 +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 +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 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 +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: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