From 9e74c35c6410cdbd9631d009d84cd0ce9d966702 Mon Sep 17 00:00:00 2001 From: zhengj2007 Date: Tue, 26 May 2026 12:02:49 -0400 Subject: [PATCH 1/3] Add HRA placenta NTR batch outputs and review reports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Generated via bulk_ntr_workflow from source_data/placenta.csv. Pipeline completed through Stage 4: - 2 new UBERON leaf terms in final template (endometrial lymphatic vessel, villous mesenchyme) - 0 group terms - 14 confirmed existing matches excluded - 2 possible matches identified (chorionic mesoderm→UBERON:0003265, others) - 0 out-of-scope terms - 0 manual-curation items Resolved final pending row (UBERON_8930179 chorionic mesoderm) by excluding as duplicate of UBERON:0003265 (chorionic mesenchyme). 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/ --- bulk_ntr_workflow/source_data/placenta.csv | 18 ++++++++++++++++++ src/templates/hra-placenta-groups.template.tsv | 2 ++ .../hra-placenta-reports/candidates.tsv | 17 +++++++++++++++++ src/templates/hra-placenta-reports/errors.tsv | 1 + src/templates/hra-placenta-reports/input.tsv | 18 ++++++++++++++++++ .../hra-placenta-reports/name_corrections.tsv | 3 +++ src/templates/hra-placenta.template.tsv | 4 ++++ 7 files changed, 63 insertions(+) create mode 100644 bulk_ntr_workflow/source_data/placenta.csv create mode 100644 src/templates/hra-placenta-groups.template.tsv create mode 100644 src/templates/hra-placenta-reports/candidates.tsv create mode 100644 src/templates/hra-placenta-reports/errors.tsv create mode 100644 src/templates/hra-placenta-reports/input.tsv create mode 100644 src/templates/hra-placenta-reports/name_corrections.tsv create mode 100644 src/templates/hra-placenta.template.tsv diff --git a/bulk_ntr_workflow/source_data/placenta.csv b/bulk_ntr_workflow/source_data/placenta.csv new file mode 100644 index 000000000..f3554c449 --- /dev/null +++ b/bulk_ntr_workflow/source_data/placenta.csv @@ -0,0 +1,18 @@ +tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references +placenta,https://purl.org/ccf/ASCTB-TEMP_cell-island,cell island,,,UBERON:0004027,chorionic plate,"https://doi.org/10.1016/0198-8859(93)90138-Q, https://doi.org/10.1016/j.jim.2003.03.001, https://doi.org/10.1053/plac.2000.0559, https://doi.org/10.1093/humrep/dem265, https://doi.org/10.1095/biolreprod.106.055244, https://doi.org/10.1155/2021/6662201, https://doi.org/10.1242/dev.148932, PMID:8804361, https://doi.org/10.1016/j.ajpath.2014.08.006, https://doi.org/10.1016/S0143-4004(05)80438-2, https://doi.org/10.1007/BF01628222, https://doi.org/10.1056/NEJM197007232830408, https://doi.org/10.1146/annurev.bi.50.070181.002341, https://doi.org/10.1093/oxfordjournals.humrep.a136040, https://doi.org/10.1371/journal.pone.0169849, https://doi.org/10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2, https://doi.org/10.1016/j.jcyt.2017.03.001, https://doi.org/10.1093/humrep/den051, https://doi.org/10.1095/biolreprod.108.075226, https://doi.org/10.1095/biolreprod51.4.739, https://doi.org/10.1182/blood.V74.2.751.751, https://doi.org/10.1186/s13287-017-0757-1, https://doi.org/10.3346/jkms.2012.27.8.857, https://doi.org/10.3390/cells1041061, https://doi.org/10.5966/sctm.2015-0022" +placenta,https://purl.org/ccf/ASCTB-TEMP_chorionic-ectoderm-from-chorion-,chorionic ectoderm (from chorion),,,UBERON:0003124,chorion membrane,"https://doi.org/10.1016/j.ajpath.2014.08.006, https://doi.org/10.1016/j.jim.2003.03.001, https://doi.org/10.1016/S0143-4004(05)80438-2, https://doi.org/10.1053/plac.2000.0559, https://doi.org/10.1095/biolreprod.106.055244, https://doi.org/10.1016/0198-8859(93)90138-Q, https://doi.org/10.1093/humrep/dem265, https://doi.org/10.1155/2021/6662201, https://doi.org/10.1242/dev.148932, PMID:8804361" +placenta,https://purl.org/ccf/ASCTB-TEMP_chorionic-ectoderm-from-chorionic-plate-,chorionic ectoderm (from chorionic plate),,,UBERON:0004027,chorionic plate,"https://doi.org/10.1016/j.ajpath.2014.08.006, https://doi.org/10.1016/j.jim.2003.03.001, https://doi.org/10.1016/S0143-4004(05)80438-2, https://doi.org/10.1053/plac.2000.0559, https://doi.org/10.1095/biolreprod.106.055244, https://doi.org/10.1007/BF01628222, https://doi.org/10.1056/NEJM197007232830408, https://doi.org/10.1146/annurev.bi.50.070181.002341, https://doi.org/10.1016/0198-8859(93)90138-Q, https://doi.org/10.1093/humrep/dem265, https://doi.org/10.1155/2021/6662201, https://doi.org/10.1242/dev.148932, PMID:8804361" +placenta,https://purl.org/ccf/ASCTB-TEMP_chorionic-mesoderm,chorionic mesoderm,,,UBERON:0003124,chorion membrane,"https://doi.org/10.1016/j.jcyt.2017.03.001, https://doi.org/10.1093/humrep/den051, https://doi.org/10.1095/biolreprod.108.075226, https://doi.org/10.1095/biolreprod51.4.739, https://doi.org/10.1182/blood.V74.2.751.751, https://doi.org/10.1186/s13287-017-0757-1, https://doi.org/10.3346/jkms.2012.27.8.857, https://doi.org/10.3390/cells1041061, https://doi.org/10.5966/sctm.2015-0022" +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_anchoring-villus,anchoring villus,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_chorionic-mesoderm-from-chorion-,chorionic mesoderm (from chorion),,,UBERON:0003124,chorion membrane, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_chorionic-mesoderm-from-chorionic-plate-,chorionic mesoderm (from chorionic plate),,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_endometrial-lymphatic-vessel,endometrial lymphatic vessel,,,UBERON:0001295,endometrium, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_floating-villus,floating villus,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_immature-intermediate-villus,immature intermediate villus,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_mature-intermediate-villus,mature intermediate villus,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_placental-disc,placental disc,,,UBERON:0001987,placenta, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_stem-villous-vessel,stem villous vessel,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_stem-villus,stem villus,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_terminal-villus,terminal villus,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_trophoblast-island,trophoblast island,,,UBERON:0004027,chorionic plate, +placenta-full-term,https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme,villous mesenchyme,,,UBERON:0001987,placenta, \ No newline at end of file diff --git a/src/templates/hra-placenta-groups.template.tsv b/src/templates/hra-placenta-groups.template.tsv new file mode 100644 index 000000000..dff359c07 --- /dev/null +++ b/src/templates/hra-placenta-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-placenta-reports/candidates.tsv b/src/templates/hra-placenta-reports/candidates.tsv new file mode 100644 index 000000000..4de905e1b --- /dev/null +++ b/src/templates/hra-placenta-reports/candidates.tsv @@ -0,0 +1,17 @@ +label as_iri uberon_id note +placental disc UBERON:8600038 confirmed_match (confidence: high) +chorionic ectoderm (from chorion) UBERON:0003374 confirmed_match (confidence: high) +chorionic mesoderm UBERON:0003265 confirmed_match (confidence: high) +chorionic mesoderm (from chorion) UBERON:0003265 confirmed_match (confidence: high) +cell island UBERON:8600050 confirmed_match (confidence: high) +chorionic ectoderm (from chorionic plate) UBERON:0003374 confirmed_match (confidence: high) +anchoring villus UBERON:8600033 confirmed_match (confidence: high) +floating villus UBERON:8600032 confirmed_match (confidence: high) +immature intermediate villus UBERON:8600029 confirmed_match (confidence: high) +mature intermediate villus UBERON:8600031 confirmed_match (confidence: high) +stem villous vessel UBERON:8600040 confirmed_match (confidence: high) +stem villus UBERON:8600027 confirmed_match (confidence: high) +terminal villus UBERON:8600030 confirmed_match (confidence: high) +trophoblast island UBERON:8600050 confirmed_match (confidence: high) +villous mesenchyme UBERON:8600023 possible_match (placental villous stroma (UBERON:8600023) is defined as 'A stroma that is part of a chorionic villus' and has synonym 'chorionic villous stroma'. This appears to be the same structure as villous mesenchyme, though stroma typically refers to mature connective tissue framework while mesenchyme refers to embryonic/developing connective tissue. In placental literature, these terms may be used somewhat interchangeably, but villous mesenchyme may specifically emphasize the embryonic/cellular aspect. Needs curator review to determine if this should be a synonym or a separate developmental stage.) +chorionic mesoderm (from chorionic plate) UBERON:0003265 possible_match (UBERON:0003265 is named 'chorionic mesenchyme' and has 'chorion mesoderm' as an EXACT synonym. The UBERON term is defined as 'A mesenchyme that is part of a chorion' which is broader than just the chorionic plate component. However, in placental anatomy, the chorionic plate is the primary chorionic structure, so these likely refer to the same tissue. The chorionic plate definition (UBERON:0004027) states it 'consists of the mesoderm that lines the chorionic vesicle', confirming the mesoderm is a component of the plate. Recommend curator review to determine if NTR term should be treated as exact match or if a more specific term for 'mesenchyme of chorionic plate' is needed.) diff --git a/src/templates/hra-placenta-reports/errors.tsv b/src/templates/hra-placenta-reports/errors.tsv new file mode 100644 index 000000000..7f20612cf --- /dev/null +++ b/src/templates/hra-placenta-reports/errors.tsv @@ -0,0 +1 @@ +label as_iri issue_type parent_id parent_label detail diff --git a/src/templates/hra-placenta-reports/input.tsv b/src/templates/hra-placenta-reports/input.tsv new file mode 100644 index 000000000..5bc1c37d9 --- /dev/null +++ b/src/templates/hra-placenta-reports/input.tsv @@ -0,0 +1,18 @@ +table as_iri label uberon_id parent_id parent_label references term_type + https://purl.org/ccf/ASCTB-TEMP_cell-island cell island UBERON:0004027 chorionic plate https://doi.org/10.1016/0198-8859(93)90138-Q, https://doi.org/10.1016/j.jim.2003.03.001, https://doi.org/10.1053/plac.2000.0559, https://doi.org/10.1093/humrep/dem265, https://doi.org/10.1095/biolreprod.106.055244, https://doi.org/10.1155/2021/6662201, https://doi.org/10.1242/dev.148932, PMID:8804361, https://doi.org/10.1016/j.ajpath.2014.08.006, https://doi.org/10.1016/S0143-4004(05)80438-2, https://doi.org/10.1007/BF01628222, https://doi.org/10.1056/NEJM197007232830408, https://doi.org/10.1146/annurev.bi.50.070181.002341, https://doi.org/10.1093/oxfordjournals.humrep.a136040, https://doi.org/10.1371/journal.pone.0169849, https://doi.org/10.1290/1071-2690(2001)037<0408:IOECFH>2.0.CO;2, https://doi.org/10.1016/j.jcyt.2017.03.001, https://doi.org/10.1093/humrep/den051, https://doi.org/10.1095/biolreprod.108.075226, https://doi.org/10.1095/biolreprod51.4.739, https://doi.org/10.1182/blood.V74.2.751.751, https://doi.org/10.1186/s13287-017-0757-1, https://doi.org/10.3346/jkms.2012.27.8.857, https://doi.org/10.3390/cells1041061, https://doi.org/10.5966/sctm.2015-0022 leaf + https://purl.org/ccf/ASCTB-TEMP_chorionic-ectoderm-from-chorion- chorionic ectoderm (from chorion) UBERON:0003124 chorion membrane https://doi.org/10.1016/j.ajpath.2014.08.006, https://doi.org/10.1016/j.jim.2003.03.001, https://doi.org/10.1016/S0143-4004(05)80438-2, https://doi.org/10.1053/plac.2000.0559, https://doi.org/10.1095/biolreprod.106.055244, https://doi.org/10.1016/0198-8859(93)90138-Q, https://doi.org/10.1093/humrep/dem265, https://doi.org/10.1155/2021/6662201, https://doi.org/10.1242/dev.148932, PMID:8804361 leaf + https://purl.org/ccf/ASCTB-TEMP_chorionic-ectoderm-from-chorionic-plate- chorionic ectoderm (from chorionic plate) UBERON:0004027 chorionic plate https://doi.org/10.1016/j.ajpath.2014.08.006, https://doi.org/10.1016/j.jim.2003.03.001, https://doi.org/10.1016/S0143-4004(05)80438-2, https://doi.org/10.1053/plac.2000.0559, https://doi.org/10.1095/biolreprod.106.055244, https://doi.org/10.1007/BF01628222, https://doi.org/10.1056/NEJM197007232830408, https://doi.org/10.1146/annurev.bi.50.070181.002341, https://doi.org/10.1016/0198-8859(93)90138-Q, https://doi.org/10.1093/humrep/dem265, https://doi.org/10.1155/2021/6662201, https://doi.org/10.1242/dev.148932, PMID:8804361 leaf + https://purl.org/ccf/ASCTB-TEMP_chorionic-mesoderm chorionic mesoderm UBERON:0003124 chorion membrane https://doi.org/10.1016/j.jcyt.2017.03.001, https://doi.org/10.1093/humrep/den051, https://doi.org/10.1095/biolreprod.108.075226, https://doi.org/10.1095/biolreprod51.4.739, https://doi.org/10.1182/blood.V74.2.751.751, https://doi.org/10.1186/s13287-017-0757-1, https://doi.org/10.3346/jkms.2012.27.8.857, https://doi.org/10.3390/cells1041061, https://doi.org/10.5966/sctm.2015-0022 leaf + https://purl.org/ccf/ASCTB-TEMP_anchoring-villus anchoring villus UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_chorionic-mesoderm-from-chorion- chorionic mesoderm (from chorion) UBERON:0003124 chorion membrane leaf + https://purl.org/ccf/ASCTB-TEMP_chorionic-mesoderm-from-chorionic-plate- chorionic mesoderm (from chorionic plate) UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_endometrial-lymphatic-vessel endometrial lymphatic vessel UBERON:0001295 endometrium leaf + https://purl.org/ccf/ASCTB-TEMP_floating-villus floating villus UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_immature-intermediate-villus immature intermediate villus UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_mature-intermediate-villus mature intermediate villus UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_placental-disc placental disc UBERON:0001987 placenta leaf + https://purl.org/ccf/ASCTB-TEMP_stem-villous-vessel stem villous vessel UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_stem-villus stem villus UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_terminal-villus terminal villus UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_trophoblast-island trophoblast island UBERON:0004027 chorionic plate leaf + https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme villous mesenchyme UBERON:0001987 placenta leaf diff --git a/src/templates/hra-placenta-reports/name_corrections.tsv b/src/templates/hra-placenta-reports/name_corrections.tsv new file mode 100644 index 000000000..f7d6b385b --- /dev/null +++ b/src/templates/hra-placenta-reports/name_corrections.tsv @@ -0,0 +1,3 @@ +source_label corrected_label reason +chorionic ectoderm (from chorion) chorionic ectoderm The '(from chorion)' qualifier is redundant. Chorionic ectoderm is by definition the ectodermal layer of the chorion membrane. UBERON:0003374 already captures this relationship via 'part_of UBERON:0003124 ! chorion membrane'. The source label should be kept as a synonym if needed, but the primary label should follow standard anatomical nomenclature. +chorionic mesoderm (from chorion) chorionic mesoderm The '(from chorion)' qualifier is redundant. Chorionic mesoderm/mesenchyme is by definition the mesodermal layer of the chorion membrane. UBERON:0003265 already captures this relationship. The qualifier does not add meaningful anatomical distinction. diff --git a/src/templates/hra-placenta.template.tsv b/src/templates/hra-placenta.template.tsv new file mode 100644 index 000000000..e3586f3b7 --- /dev/null +++ b/src/templates/hra-placenta.template.tsv @@ -0,0 +1,4 @@ +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_8930180 endometrial lymphatic vessel A lymphatic vessel that is part of the endometrium. Endometrial lymphatic vessels participate in tissue drainage and immune cell trafficking, with lymphangiogenesis occurring during different phases of the menstrual cycle under the regulation of vascular endothelial growth factors. https://purl.org/ccf/ASCTB-TEMP_endometrial-lymphatic-vessel|PMID:19001552|PMID:17981324|PMID:17347164 UBERON:0001473 UBERON:0001295 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:Endometrium +http://purl.obolibrary.org/obo/UBERON_8930189 villous mesenchyme A mesenchyme that is part of a chorionic villus. The villous mesenchyme forms the connective tissue core of the chorionic villus, supporting fetal capillaries and the overlying trophoblast layers. https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme|PMID:42146334|PMID:42048630 UBERON:0003104 UBERON:0007106 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:Chorionic_villi From 2305b60517a9b9e24d11a8c7189f5300a29d20e6 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Mon, 6 Jul 2026 16:04:45 +0100 Subject: [PATCH 2/3] Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/ Reports are review artifacts, not ODK templates, and should not live under src/templates/. Relocated to bulk_ntr_workflow/outputs/ to match the canonical layout used by the muscular branch (PR #3700). Signed-off-by: dragon-ai-agent --- .../outputs}/hra-placenta-reports/candidates.tsv | 0 .../outputs}/hra-placenta-reports/errors.tsv | 0 .../outputs}/hra-placenta-reports/input.tsv | 0 .../outputs}/hra-placenta-reports/name_corrections.tsv | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename {src/templates => bulk_ntr_workflow/outputs}/hra-placenta-reports/candidates.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-placenta-reports/errors.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-placenta-reports/input.tsv (100%) rename {src/templates => bulk_ntr_workflow/outputs}/hra-placenta-reports/name_corrections.tsv (100%) diff --git a/src/templates/hra-placenta-reports/candidates.tsv b/bulk_ntr_workflow/outputs/hra-placenta-reports/candidates.tsv similarity index 100% rename from src/templates/hra-placenta-reports/candidates.tsv rename to bulk_ntr_workflow/outputs/hra-placenta-reports/candidates.tsv diff --git a/src/templates/hra-placenta-reports/errors.tsv b/bulk_ntr_workflow/outputs/hra-placenta-reports/errors.tsv similarity index 100% rename from src/templates/hra-placenta-reports/errors.tsv rename to bulk_ntr_workflow/outputs/hra-placenta-reports/errors.tsv diff --git a/src/templates/hra-placenta-reports/input.tsv b/bulk_ntr_workflow/outputs/hra-placenta-reports/input.tsv similarity index 100% rename from src/templates/hra-placenta-reports/input.tsv rename to bulk_ntr_workflow/outputs/hra-placenta-reports/input.tsv diff --git a/src/templates/hra-placenta-reports/name_corrections.tsv b/bulk_ntr_workflow/outputs/hra-placenta-reports/name_corrections.tsv similarity index 100% rename from src/templates/hra-placenta-reports/name_corrections.tsv rename to bulk_ntr_workflow/outputs/hra-placenta-reports/name_corrections.tsv From b10c1c6db5c351574ad42946217c56cf7c756a43 Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Mon, 13 Jul 2026 16:56:40 +0000 Subject: [PATCH 3/3] Add UBERON:8930180 (endometrial lymphatic vessel) and UBERON:8930181 (villous mesenchyme); revert accidental file changes MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Add two new HRA-requested placenta NTR terms to uberon-edit.obo: - UBERON:8930180 endometrial lymphatic vessel - UBERON:8930181 villous mesenchyme (with a distinguishing comment vs. UBERON:8600023 placental villous stroma; previously staged as 8930189 in the template and reassigned to 8930181 per request). - Update src/templates/hra-placenta.template.tsv to use UBERON:8930181 for villous mesenchyme (was UBERON:8930189). - Reset src/mappings/biomappings.sssom.tsv and src/ontology/uberon.Makefile to master to undo accidental modifications. - Delete empty src/templates/hra-placenta-groups.template.tsv. Signed-off-by: @dragon-ai-agent --- 🤖 **Generated by @dragon-ai-agent** - Model: `claude-opus-4-7` - Agent harness: claude-code - Triggered by: @zhengj2007 - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/29267642486) --- src/mappings/biomappings.sssom.tsv | 557 +++++++++--------- src/ontology/uberon-edit.obo | 29 + src/ontology/uberon.Makefile | 15 +- .../hra-placenta-groups.template.tsv | 2 - src/templates/hra-placenta.template.tsv | 2 +- 5 files changed, 316 insertions(+), 289 deletions(-) delete mode 100644 src/templates/hra-placenta-groups.template.tsv diff --git a/src/mappings/biomappings.sssom.tsv b/src/mappings/biomappings.sssom.tsv index 6aba2fd8c..791c2a0b5 100644 --- a/src/mappings/biomappings.sssom.tsv +++ b/src/mappings/biomappings.sssom.tsv @@ -6,285 +6,290 @@ # mesh: http://id.nlm.nih.gov/mesh/ # orcid: https://orcid.org/ #mapping_set_id: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv -#mapping_set_version: 0.5.0-dev-528eae3f +#mapping_set_version: 0.5.1-dev-ec7849df #mapping_set_title: Biomappings #mapping_set_description: Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings. #creator_id: # - orcid:0000-0003-4423-4370 #license: https://creativecommons.org/publicdomain/zero/1.0/ #issue_tracker: https://github.com/biopragmatics/bioregistry/issues -subject_id subject_label predicate_id predicate_modifier object_id object_label mapping_justification author_id mapping_tool confidence -UBERON:0000016 endocrine pancreas skos:exactMatch mesh:D007515 Islets of Langerhans semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0000017 exocrine pancreas skos:exactMatch mesh:D046790 Pancreas, Exocrine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000018 compound eye skos:exactMatch IDOMAL:0002421 compound eye semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0000044 dorsal root ganglion skos:exactMatch mesh:D005727 Ganglia, Spinal semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0000066 fully formed stage skos:exactMatch IDOMAL:0001253 adult stage semapv:LexicalMatching mira 0.556 -UBERON:0000076 external ectoderm skos:exactMatch BTO:0006242 external ectoderm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0000104 life cycle skos:exactMatch Not mesh:D008018 Life Cycle Stages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000105 life cycle stage skos:exactMatch mesh:D008018 Life Cycle Stages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000106 zygote stage skos:exactMatch IDOMAL:0000302 zygote stage semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -UBERON:0000113 post-juvenile adult stage skos:exactMatch IDOMAL:0001253 adult stage semapv:LexicalMatching mira 0.556 -UBERON:0000120 blood brain barrier skos:exactMatch mesh:D001812 Blood-Brain Barrier semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000127 facial nucleus skos:exactMatch mesh:D065828 Facial Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000159 anal canal skos:exactMatch mesh:D001003 Anal Canal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000167 oral cavity skos:exactMatch mesh:D009055 Mouth semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0000175 pleural effusion skos:exactMatch mesh:D010996 Pleural Effusion semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000220 atlanto-occipital joint skos:exactMatch mesh:D001269 Atlanto-Occipital Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000341 throat skos:exactMatch mesh:D010614 Pharynx semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0000353 parenchyma skos:exactMatch BTO:0001539 parenchyma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0000353 parenchyma skos:exactMatch Not BTO:0000999 plant parenchyma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0000387 meniscus skos:exactMatch mesh:D000072600 Meniscus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000467 anatomical system skos:exactMatch IDOMAL:0002460 anatomical system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0000477 anatomical cluster skos:exactMatch IDOMAL:0002461 anatomical cluster semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0000480 anatomical group skos:exactMatch IDOMAL:0002459 anatomical group semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0000569 ileocecal valve skos:exactMatch mesh:D007080 Ileocecal Valve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000922 embryo skos:exactMatch IDOMAL:0000646 embryo semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0000939 imaginal disc skos:exactMatch mesh:D060227 Imaginal Discs semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0000990 reproductive system skos:exactMatch mesh:D005835 Genitalia semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001009 circulatory system skos:exactMatch mesh:D002319 Cardiovascular System semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001049 neural tube skos:exactMatch mesh:D054259 Neural Tube semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001156 ascending colon skos:exactMatch mesh:D044682 Colon, Ascending semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001157 transverse colon skos:exactMatch mesh:D044684 Colon, Transverse semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001158 descending colon skos:exactMatch mesh:D044683 Colon, Descending semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001173 biliary tree skos:exactMatch mesh:D001659 Biliary Tract semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001263 pancreatic acinus skos:exactMatch Not BTO:0000028 pancreatic acinar cell semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0001268 peritoneal fluid skos:exactMatch mesh:D001202 Ascitic Fluid semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001347 white adipose tissue skos:exactMatch mesh:D052436 Adipose Tissue, White semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001377 quadriceps femoris skos:exactMatch mesh:D052097 Quadriceps Muscle semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001439 compact bone tissue skos:exactMatch mesh:D000071538 Cortical Bone semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001473 lymphatic vessel skos:exactMatch mesh:D042601 Lymphatic Vessels semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001555 digestive tract skos:exactMatch mesh:D041981 Gastrointestinal Tract semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001601 extra-ocular muscle skos:exactMatch mesh:D009801 Oculomotor Muscles semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001642 superior sagittal sinus skos:exactMatch mesh:D054063 Superior Sagittal Sinus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001683 jugal bone skos:exactMatch mesh:D015050 Zygoma semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001715 oculomotor nuclear complex skos:exactMatch mesh:D065838 Oculomotor Nuclear Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001742 epiglottic cartilage skos:exactMatch mesh:D004825 Epiglottis semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001797 vitreous humor skos:exactMatch mesh:D014822 Vitreous Body semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001806 sympathetic ganglion skos:exactMatch mesh:D005728 Ganglia, Sympathetic semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001808 parasympathetic ganglion skos:exactMatch mesh:D005726 Ganglia, Parasympathetic semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001823 nasal cartilage skos:exactMatch mesh:D055171 Nasal Cartilages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001856 semicircular duct skos:exactMatch mesh:D054776 Semicircular Ducts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001862 vestibular labyrinth skos:exactMatch mesh:D014722 Vestibule, Labyrinth semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001863 scala vestibuli skos:exactMatch mesh:D054738 Scala Vestibuli semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001870 frontal cortex skos:exactMatch mesh:D005625 Frontal Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001883 olfactory tubercle skos:exactMatch mesh:D066208 Olfactory Tubercle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001886 choroid plexus skos:exactMatch Not VO:0011021 CP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0001907 zona incerta skos:exactMatch mesh:D065820 Zona Incerta semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001931 lateral preoptic nucleus skos:exactMatch BTO:0006166 nucleus preopticus lateralis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0001943 midbrain tegmentum skos:exactMatch mesh:D013681 Tegmentum Mesencephali semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001944 pretectal region skos:exactMatch mesh:D066250 Pretectal Region semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001947 red nucleus skos:exactMatch BTO:0006329 red nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0001965 substantia nigra pars compacta skos:exactMatch mesh:D065842 Pars Compacta semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001966 substantia nigra pars reticulata skos:exactMatch mesh:D065841 Pars Reticulata semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0001977 blood serum skos:exactMatch mesh:D044967 Serum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0001995 fibrocartilage skos:exactMatch mesh:D051445 Fibrocartilage semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002020 gray matter skos:exactMatch mesh:D066128 Gray Matter semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002035 medial preoptic nucleus skos:exactMatch BTO:0006167 nucleus preopticus medialis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0002043 dorsal raphe nucleus skos:exactMatch mesh:D065847 Dorsal Raphe Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002062 endocardial cushion skos:exactMatch mesh:D054089 Endocardial Cushions semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002072 hypodermis skos:exactMatch mesh:D040521 Subcutaneous Tissue semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002090 postcranial axial skeleton skos:exactMatch mesh:D013131 Spine semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002101 limb skos:exactMatch mesh:D005121 Extremities semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002120 pronephros skos:exactMatch mesh:D060910 Pronephros semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002128 superior olivary complex skos:exactMatch mesh:D065832 Superior Olivary Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002141 parvocellular oculomotor nucleus skos:exactMatch mesh:D065839 Edinger-Westphal Nucleus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002142 pedunculopontine tegmental nucleus skos:exactMatch mesh:D045042 Pedunculopontine Tegmental Nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -UBERON:0002145 interpeduncular nucleus skos:exactMatch mesh:D066268 Interpeduncular Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002152 middle cerebellar peduncle skos:exactMatch mesh:D065837 Middle Cerebellar Peduncle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002156 nucleus raphe magnus skos:exactMatch mesh:D065846 Nucleus Raphe Magnus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002157 nucleus raphe pallidus skos:exactMatch mesh:D065848 Nucleus Raphe Pallidus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002186 bronchiole skos:exactMatch mesh:D055745 Bronchioles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002190 subcutaneous adipose tissue skos:exactMatch mesh:D015434 Panniculitis semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002207 xiphoid process skos:exactMatch mesh:D014989 Xiphoid Bone semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002219 subfornical organ skos:exactMatch BTO:0006266 subfornical organ semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002228 rib skos:exactMatch Not VO:0012403 Rib semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -UBERON:0002236 costal cartilage skos:exactMatch mesh:D066186 Costal Cartilage semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002242 nucleus pulposus skos:exactMatch mesh:D000070614 Nucleus Pulposus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002262 celiac ganglion skos:exactMatch BTO:0006296 celiac ganglion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002295 scala media skos:exactMatch mesh:D003053 Cochlear Duct semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002316 white matter skos:exactMatch mesh:D066127 White Matter semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002373 palatine tonsil skos:exactMatch mesh:D014066 Palatine Tonsil semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002393 pharyngotympanic tube skos:exactMatch mesh:D005064 Eustachian Tube semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002396 vomer skos:exactMatch mesh:D055172 Vomer semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002409 pericardial fluid skos:exactMatch mesh:D000069236 Pericardial Fluid semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002410 autonomic nervous system skos:exactMatch IDOMAL:0002126 visceral nervous system semapv:LexicalMatching mira 0.556 -UBERON:0002412 vertebra skos:exactMatch BTO:0006196 vertebra semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002430 lateral hypothalamic area skos:exactMatch BTO:0006481 lateral hypothalamus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0002469 esophagus mucosa skos:exactMatch mesh:D000071041 Esophageal Mucosa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002493 uterine artery skos:exactMatch mesh:D055988 Uterine Artery semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002540 lateral line system skos:exactMatch mesh:D053403 Lateral Line System semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002548 larva skos:exactMatch mesh:D007814 Larva semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002590 prepyriform area skos:exactMatch mesh:D066195 Piriform Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002600 limbic lobe skos:exactMatch mesh:D065726 Limbic Lobe semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002623 cerebral peduncle skos:exactMatch mesh:D065850 Cerebral Peduncle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002625 median preoptic nucleus skos:exactMatch BTO:0006168 nucleus preopticus medianus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0002631 cerebral crus skos:exactMatch mesh:D065843 Cerebral Crus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002633 motor nucleus of trigeminal nerve skos:exactMatch mesh:D066266 Trigeminal Motor Nucleus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002639 midbrain reticular formation skos:exactMatch mesh:D066265 Midbrain Reticular Formation semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002656 periamygdaloid area skos:exactMatch mesh:D066277 Periamygdaloid Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002682 abducens nucleus skos:exactMatch mesh:D065827 Abducens Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002684 nucleus raphe obscurus skos:exactMatch mesh:D065849 Nucleus Raphe Obscurus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002689 supraoptic crest skos:exactMatch mesh:D066278 Organum Vasculosum semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002689 supraoptic crest skos:exactMatch BTO:0006268 organum vasculosum laminae terminalis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0002704 metathalamus skos:exactMatch mesh:D005829 Geniculate Bodies semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002705 midline nuclear group skos:exactMatch mesh:D020644 Midline Thalamic Nuclei semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002707 corticospinal tract skos:exactMatch BTO:0006132 corticospinal tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002714 rubrospinal tract skos:exactMatch BTO:0006159 rubrospinal tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002726 cervical spinal cord skos:exactMatch mesh:D066193 Cervical Cord semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002743 basal forebrain skos:exactMatch mesh:D066187 Basal Forebrain semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002751 inferior temporal gyrus skos:exactMatch BTO:0006175 inferior temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002752 olivocerebellar tract skos:exactMatch BTO:0006157 olivocerebellar fiber system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0002754 predorsal bundle skos:exactMatch mesh:D065844 Tectospinal Fibers semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002769 superior temporal gyrus skos:exactMatch BTO:0006177 superior temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002771 middle temporal gyrus skos:exactMatch BTO:0006176 middle temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0002776 ventral nuclear group skos:exactMatch mesh:D020651 Ventral Thalamic Nuclei semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002883 central amygdaloid nucleus skos:exactMatch mesh:D066274 Central Amygdaloid Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002894 olfactory cortex skos:exactMatch mesh:D066194 Olfactory Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002895 secondary olfactory cortex skos:exactMatch mesh:D018728 Entorhinal Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0002932 trapezoid body skos:exactMatch mesh:D065833 Trapezoid Body semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0002967 cingulate gyrus skos:exactMatch mesh:D006179 Gyrus Cinguli semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0003011 facial motor nucleus skos:exactMatch mesh:D065828 Facial Nucleus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0003023 pontine tegmentum skos:exactMatch mesh:D065821 Pontine Tegmentum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003044 uncinate fasciculus skos:exactMatch mesh:D000083382 Uncinate Fasciculus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003050 olfactory placode skos:exactMatch BTO:0006222 olfactory placode semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003055 periderm skos:exactMatch BTO:0003377 periderm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003060 pronephric duct skos:exactMatch BTO:0005991 pronephric duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003074 mesonephric duct skos:exactMatch BTO:0005990 mesonephric duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003075 neural plate skos:exactMatch mesh:D054258 Neural Plate semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003089 sclerotome skos:exactMatch BTO:0006255 sclerotome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003128 cranium skos:exactMatch mesh:D012886 Skull semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0003143 pupa skos:exactMatch mesh:D011679 Pupa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003209 blood nerve barrier skos:exactMatch mesh:D049428 Blood-Nerve Barrier semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003460 arm bone skos:exactMatch mesh:D050280 Arm Bones semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003462 facial bone skos:exactMatch mesh:D005147 Facial Bones semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003679 mouth floor skos:exactMatch BTO:0006184 mouth floor semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003687 foramen magnum skos:exactMatch BTO:0006035 foramen magnum semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003823 hindlimb zeugopod skos:exactMatch Not VO:0010971 SurA semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0003881 CA1 field of hippocampus skos:exactMatch mesh:D056547 CA1 Region, Hippocampal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003882 CA2 field of hippocampus skos:exactMatch mesh:D056651 CA2 Region, Hippocampal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003883 CA3 field of hippocampus skos:exactMatch mesh:D056654 CA3 Region, Hippocampal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0003911 choroid plexus epithelium skos:exactMatch BTO:0006008 choroid plexus epithelium semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0003937 reproductive gland skos:exactMatch BTO:0006162 reproductive gland semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0004016 dermatome skos:exactMatch BTO:0006248 dermatome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0004035 cortical subplate skos:exactMatch Not VO:0011276 SP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -UBERON:0004199 S-shaped body skos:exactMatch Not VO:0010896 Ssb semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -UBERON:0004341 primitive streak skos:exactMatch mesh:D054240 Primitive Streak semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0004550 gastroesophageal sphincter skos:exactMatch mesh:D049630 Esophageal Sphincter, Lower semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0004637 otic capsule skos:exactMatch BTO:0005981 auditory capsule semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0004676 spinal cord lateral horn skos:exactMatch mesh:D066152 Spinal Cord Lateral Horn semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0004720 cerebellar vermis skos:exactMatch mesh:D065814 Cerebellar Vermis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0004725 piriform cortex skos:exactMatch mesh:D066195 Piriform Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0004749 blastodisc skos:exactMatch mesh:D054239 Blastodisc semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005290 myelencephalon skos:exactMatch mesh:D054024 Myelencephalon semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005335 chorioallantoic membrane skos:exactMatch mesh:D049033 Chorioallantoic Membrane semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005343 cortical plate skos:exactMatch mesh:D002540 Cerebral Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0005343 cortical plate skos:exactMatch Not VO:0011021 CP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira -UBERON:0005366 olfactory lobe skos:exactMatch mesh:D066194 Olfactory Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0005403 ventral striatum skos:exactMatch mesh:D066328 Ventral Striatum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005408 circumventricular organ skos:exactMatch mesh:D066280 Circumventricular Organs semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005408 circumventricular organ skos:exactMatch BTO:0006267 circumventricular organ semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0005438 coronary sinus skos:exactMatch mesh:D054326 Coronary Sinus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005456 jugular foramen skos:exactMatch mesh:D000080869 Jugular Foramina semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005498 primitive heart tube skos:exactMatch BTO:0006179 cardiac tube semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0005631 extraembryonic membrane skos:exactMatch mesh:D005321 Extraembryonic Membranes semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005742 adventitia skos:exactMatch mesh:D063194 Adventitia semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005777 glomerular basement membrane skos:exactMatch mesh:D050533 Glomerular Basement Membrane semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0005902 occipital region skos:exactMatch mesh:D009778 Occipital Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0006083 perirhinal cortex skos:exactMatch mesh:D000071039 Perirhinal Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006098 basal nuclear complex skos:exactMatch mesh:D001479 Basal Ganglia semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0006108 corticomedial nuclear complex skos:exactMatch mesh:D066276 Corticomedial Nuclear Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006444 annulus fibrosus skos:exactMatch mesh:D000070616 Annulus Fibrosus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006514 pallidum skos:exactMatch mesh:D005917 Globus Pallidus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0006562 pharynx skos:exactMatch mesh:D010614 Pharynx semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006588 round ligament of liver skos:exactMatch mesh:D000069592 Round Ligament of Liver semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006589 round ligament of uterus skos:exactMatch mesh:D012404 Round Ligament of Uterus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006614 aponeurosis skos:exactMatch mesh:D000070606 Aponeurosis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006657 glenoid fossa skos:exactMatch mesh:D061165 Glenoid Cavity semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0006675 venous valve skos:exactMatch mesh:D055422 Venous Valves semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0006692 vertebral canal skos:exactMatch mesh:D013115 Spinal Canal semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0006810 olecranon skos:exactMatch mesh:D056740 Olecranon Process semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0006812 mental foramen skos:exactMatch mesh:D000080383 Mental Foramen semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007109 meconium skos:exactMatch mesh:D008470 Meconium semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007132 head kidney skos:exactMatch mesh:D060226 Head Kidney semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007251 preoptic nucleus skos:exactMatch mesh:D011301 Preoptic Area semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0007268 upper esophageal sphincter skos:exactMatch mesh:D049631 Esophageal Sphincter, Upper semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007329 pancreatic duct skos:exactMatch mesh:D010183 Pancreatic Ducts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007380 dermal scale skos:exactMatch mesh:D000075342 Animal Scales semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0007381 epidermal scale skos:exactMatch mesh:D000075342 Animal Scales semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0007412 midbrain raphe nuclei skos:exactMatch mesh:D066267 Midbrain Raphe Nuclei semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007632 Barrington's nucleus skos:exactMatch mesh:D065835 Barrington's Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007634 parabrachial nucleus skos:exactMatch mesh:D065823 Parabrachial Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007641 trigeminal nuclear complex skos:exactMatch mesh:D014278 Trigeminal Nuclei semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0007703 spinothalamic tract skos:exactMatch mesh:D013133 Spinothalamic Tracts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0007703 spinothalamic tract skos:exactMatch BTO:0006128 spinothalamic tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0008266 periodontal ligament skos:exactMatch mesh:D010513 Periodontal Ligament semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0008269 nacre skos:exactMatch mesh:D060734 Nacre semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0008275 carapace skos:exactMatch mesh:D060105 Animal Shells semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0008826 pulmonary surfactant skos:exactMatch mesh:D011663 Pulmonary Surfactants semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0008904 neuromast skos:exactMatch BTO:0006219 neuromast semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0008969 dental follicle skos:exactMatch mesh:D003795 Dental Sac semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0008974 apocrine gland skos:exactMatch mesh:D001050 Apocrine Glands semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0009040 deep circumflex iliac artery skos:exactMatch mesh:D007083 Iliac Artery semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0009097 gravid organism skos:exactMatch IDOMAL:0000443 gravid semapv:LexicalMatching mira 0.556 -UBERON:0009127 epibranchial ganglion skos:exactMatch BTO:0006250 epibranchial ganglion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0009755 spermaceti skos:exactMatch mesh:C009301 spermaceti semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0009757 ambergris skos:exactMatch mesh:D018648 Ambergris semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0009951 main olfactory bulb skos:exactMatch mesh:D009830 Olfactory Bulb semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0010264 hepatopancreas skos:exactMatch mesh:D043143 Hepatopancreas semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0010361 synostosis skos:exactMatch mesh:D013580 Synostosis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0010725 accessory navicular bone skos:exactMatch mesh:C536002 Accessory navicular bone semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0011004 pharyngeal arch cartilage skos:exactMatch BTO:0006051 pharyngeal arch cartilage semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0011117 superior tibiofibular joint skos:exactMatch mesh:D007719 Knee Joint semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0011119 carpometacarpal joint skos:exactMatch mesh:D052737 Carpometacarpal Joints semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0011132 intercarpal joint skos:exactMatch mesh:D050824 Carpal Joints semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0011166 patellofemoral joint skos:exactMatch mesh:D057071 Patellofemoral Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0011390 pudendal nerve skos:exactMatch mesh:D060525 Pudendal Nerve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0011895 endomysium skos:exactMatch BTO:0006241 endomysium semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0011905 plantaris skos:exactMatch BTO:0006312 plantaris muscle semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0012245 silk skos:exactMatch mesh:D047011 Silk semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0012245 silk skos:exactMatch Not BTO:0002854 corn silk semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:0013218 rete mirabile skos:exactMatch BTO:0006363 rete mirabile semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0013422 infratemporal fossa skos:exactMatch mesh:D000080884 Infratemporal Fossa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0013755 arterial blood skos:exactMatch BTO:0006188 arterial blood semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0013756 venous blood skos:exactMatch BTO:0006187 venous blood semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0014374 embryoid body skos:exactMatch mesh:D058732 Embryoid Bodies semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0014398 respiratory muscle skos:exactMatch mesh:D012132 Respiratory Muscles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0014537 periamygdaloid cortex skos:exactMatch mesh:D066277 Periamygdaloid Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0014621 cervical spinal cord ventral horn skos:exactMatch mesh:D066151 Spinal Cord Ventral Horn semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0015169 tapetum skos:exactMatch BTO:0001350 tapetum semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0015488 sural nerve skos:exactMatch mesh:D013497 Sural Nerve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0016435 chest wall skos:exactMatch mesh:D035441 Thoracic Wall semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0016530 parietal cortex skos:exactMatch mesh:D010296 Parietal Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0016538 temporal cortex skos:exactMatch mesh:D013702 Temporal Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0016884 shoulder joint skos:exactMatch mesh:D012785 Shoulder Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0018141 anterior perforated substance skos:exactMatch mesh:D066208 Olfactory Tubercle semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:0018144 cervical rib skos:exactMatch mesh:D057070 Cervical Rib semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0018388 cercaria skos:exactMatch mesh:D058487 Cercaria semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0022469 primary olfactory cortex skos:exactMatch Not mesh:D066194 Olfactory Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0034921 multi organ part structure skos:exactMatch IDOMAL:0002461 anatomical cluster semapv:LexicalMatching mira 0.556 -UBERON:0034971 aortic body skos:exactMatch mesh:D001016 Aortic Bodies semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0034971 aortic body skos:exactMatch BTO:0006193 aortic body semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0035032 abdominal oblique muscle skos:exactMatch mesh:D000071596 Abdominal Oblique Muscles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0035050 excretory duct skos:exactMatch BTO:0006341 excretory duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:0035618 parapharyngeal space skos:exactMatch mesh:D000080886 Parapharyngeal Space semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0036016 honey skos:exactMatch mesh:D006722 Honey semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0036145 glymphatic system skos:exactMatch mesh:D000077502 Glymphatic System semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:0036243 vaginal fluid skos:exactMatch BTO:0003084 vaginal fluid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:1000010 mole skos:exactMatch mesh:D009506 Nevus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:2000006 ball skos:exactMatch mesh:D015452 Precursor B-Cell Lymphoblastic Leukemia-Lymphoma semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:2000188 corpus cerebelli skos:exactMatch mesh:D002531 Cerebellum semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 -UBERON:2000293 synencephalon skos:exactMatch BTO:0006476 synencephalon semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:2000297 vagal lobe skos:exactMatch BTO:0006431 vagal lobe semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:2000356 gill raker skos:exactMatch BTO:0002149 gill raker semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:2001553 manubrium skos:exactMatch mesh:D008371 Manubrium semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:2001977 pad skos:exactMatch Not mesh:D058729 Peripheral Arterial Disease semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:3010463 animal cap skos:exactMatch BTO:0004724 animal cap semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:3010586 vasa efferentia skos:exactMatch BTO:0002254 vas efferens semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:4000104 ganoine skos:exactMatch mesh:C067951 ganoine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:4000163 anal fin skos:exactMatch BTO:0004652 anal fin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:4000164 caudal fin skos:exactMatch BTO:0001827 tail fin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:4200215 suture skos:exactMatch mesh:D013537 Sutures semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -UBERON:4300194 photophore skos:exactMatch BTO:0001477 photophore semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:8440012 cerebral nuclei skos:exactMatch BTO:0006534 cerebral nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py -UBERON:8450002 excretory system skos:exactMatch BTO:0006338 excretory system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py -UBERON:8480040 ovarian fluid skos:exactMatch BTO:0004569 ovarian fluid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +subject_id subject_label predicate_id predicate_modifier object_id object_label mapping_justification author_id reviewer_id mapping_tool confidence +UBERON:0000016 endocrine pancreas skos:exactMatch mesh:D007515 Islets of Langerhans semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0000017 exocrine pancreas skos:exactMatch mesh:D046790 Pancreas, Exocrine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000018 compound eye skos:exactMatch IDOMAL:0002421 compound eye semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0000044 dorsal root ganglion skos:exactMatch mesh:D005727 Ganglia, Spinal semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0000066 fully formed stage skos:exactMatch IDOMAL:0001253 adult stage semapv:LexicalMatching mira 0.556 +UBERON:0000076 external ectoderm skos:exactMatch BTO:0006242 external ectoderm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0000104 life cycle skos:exactMatch Not mesh:D008018 Life Cycle Stages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000105 life cycle stage skos:exactMatch mesh:D008018 Life Cycle Stages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000106 zygote stage skos:exactMatch IDOMAL:0000302 zygote stage semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +UBERON:0000113 post-juvenile adult stage skos:exactMatch IDOMAL:0001253 adult stage semapv:LexicalMatching mira 0.556 +UBERON:0000120 blood brain barrier skos:exactMatch mesh:D001812 Blood-Brain Barrier semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000127 facial nucleus skos:exactMatch mesh:D065828 Facial Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000159 anal canal skos:exactMatch mesh:D001003 Anal Canal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000167 oral cavity skos:exactMatch mesh:D009055 Mouth semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0000175 pleural effusion skos:exactMatch mesh:D010996 Pleural Effusion semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000220 atlanto-occipital joint skos:exactMatch mesh:D001269 Atlanto-Occipital Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000341 throat skos:exactMatch mesh:D010614 Pharynx semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0000353 parenchyma skos:exactMatch BTO:0001539 parenchyma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0000353 parenchyma skos:exactMatch Not BTO:0000999 plant parenchyma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0000387 meniscus skos:exactMatch mesh:D000072600 Meniscus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000467 anatomical system skos:exactMatch IDOMAL:0002460 anatomical system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0000477 anatomical cluster skos:exactMatch IDOMAL:0002461 anatomical cluster semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0000480 anatomical group skos:exactMatch IDOMAL:0002459 anatomical group semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0000569 ileocecal valve skos:exactMatch mesh:D007080 Ileocecal Valve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000922 embryo skos:exactMatch IDOMAL:0000646 embryo semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0000939 imaginal disc skos:exactMatch mesh:D060227 Imaginal Discs semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000990 reproductive system skos:exactMatch mesh:D005835 Genitalia semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001009 circulatory system skos:exactMatch mesh:D002319 Cardiovascular System semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001049 neural tube skos:exactMatch mesh:D054259 Neural Tube semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001156 ascending colon skos:exactMatch mesh:D044682 Colon, Ascending semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001157 transverse colon skos:exactMatch mesh:D044684 Colon, Transverse semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001158 descending colon skos:exactMatch mesh:D044683 Colon, Descending semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001173 biliary tree skos:exactMatch mesh:D001659 Biliary Tract semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001263 pancreatic acinus skos:exactMatch Not BTO:0000028 pancreatic acinar cell semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0001268 peritoneal fluid skos:exactMatch mesh:D001202 Ascitic Fluid semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001347 white adipose tissue skos:exactMatch mesh:D052436 Adipose Tissue, White semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001377 quadriceps femoris skos:exactMatch mesh:D052097 Quadriceps Muscle semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001439 compact bone tissue skos:exactMatch mesh:D000071538 Cortical Bone semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001473 lymphatic vessel skos:exactMatch mesh:D042601 Lymphatic Vessels semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001555 digestive tract skos:exactMatch mesh:D041981 Gastrointestinal Tract semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001601 extra-ocular muscle skos:exactMatch mesh:D009801 Oculomotor Muscles semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001642 superior sagittal sinus skos:exactMatch mesh:D054063 Superior Sagittal Sinus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001683 jugal bone skos:exactMatch mesh:D015050 Zygoma semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001715 oculomotor nuclear complex skos:exactMatch mesh:D065838 Oculomotor Nuclear Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001742 epiglottic cartilage skos:exactMatch mesh:D004825 Epiglottis semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001797 vitreous humor skos:exactMatch mesh:D014822 Vitreous Body semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001806 sympathetic ganglion skos:exactMatch mesh:D005728 Ganglia, Sympathetic semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001808 parasympathetic ganglion skos:exactMatch mesh:D005726 Ganglia, Parasympathetic semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001823 nasal cartilage skos:exactMatch mesh:D055171 Nasal Cartilages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001856 semicircular duct skos:exactMatch mesh:D054776 Semicircular Ducts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001862 vestibular labyrinth skos:exactMatch mesh:D014722 Vestibule, Labyrinth semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001863 scala vestibuli skos:exactMatch mesh:D054738 Scala Vestibuli semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001870 frontal cortex skos:exactMatch mesh:D005625 Frontal Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001883 olfactory tubercle skos:exactMatch mesh:D066208 Olfactory Tubercle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001886 choroid plexus skos:exactMatch Not VO:0011021 CP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0001907 zona incerta skos:exactMatch mesh:D065820 Zona Incerta semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001931 lateral preoptic nucleus skos:exactMatch BTO:0006166 nucleus preopticus lateralis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0001943 midbrain tegmentum skos:exactMatch mesh:D013681 Tegmentum Mesencephali semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001944 pretectal region skos:exactMatch mesh:D066250 Pretectal Region semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001947 red nucleus skos:exactMatch BTO:0006329 red nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0001965 substantia nigra pars compacta skos:exactMatch mesh:D065842 Pars Compacta semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001966 substantia nigra pars reticulata skos:exactMatch mesh:D065841 Pars Reticulata semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0001977 blood serum skos:exactMatch mesh:D044967 Serum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001995 fibrocartilage skos:exactMatch mesh:D051445 Fibrocartilage semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002020 gray matter skos:exactMatch mesh:D066128 Gray Matter semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002035 medial preoptic nucleus skos:exactMatch BTO:0006167 nucleus preopticus medialis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002043 dorsal raphe nucleus skos:exactMatch mesh:D065847 Dorsal Raphe Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002062 endocardial cushion skos:exactMatch mesh:D054089 Endocardial Cushions semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002072 hypodermis skos:exactMatch mesh:D040521 Subcutaneous Tissue semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002090 postcranial axial skeleton skos:exactMatch mesh:D013131 Spine semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002101 limb skos:exactMatch mesh:D005121 Extremities semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002120 pronephros skos:exactMatch mesh:D060910 Pronephros semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002128 superior olivary complex skos:exactMatch mesh:D065832 Superior Olivary Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002141 parvocellular oculomotor nucleus skos:exactMatch mesh:D065839 Edinger-Westphal Nucleus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002142 pedunculopontine tegmental nucleus skos:exactMatch mesh:D045042 Pedunculopontine Tegmental Nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +UBERON:0002145 interpeduncular nucleus skos:exactMatch mesh:D066268 Interpeduncular Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002152 middle cerebellar peduncle skos:exactMatch mesh:D065837 Middle Cerebellar Peduncle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002156 nucleus raphe magnus skos:exactMatch mesh:D065846 Nucleus Raphe Magnus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002157 nucleus raphe pallidus skos:exactMatch mesh:D065848 Nucleus Raphe Pallidus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002186 bronchiole skos:exactMatch mesh:D055745 Bronchioles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002190 subcutaneous adipose tissue skos:exactMatch mesh:D015434 Panniculitis semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002207 xiphoid process skos:exactMatch mesh:D014989 Xiphoid Bone semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002219 subfornical organ skos:exactMatch BTO:0006266 subfornical organ semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002228 rib skos:exactMatch Not VO:0012403 Rib semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +UBERON:0002236 costal cartilage skos:exactMatch mesh:D066186 Costal Cartilage semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002242 nucleus pulposus skos:exactMatch mesh:D000070614 Nucleus Pulposus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002262 celiac ganglion skos:exactMatch BTO:0006296 celiac ganglion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002295 scala media skos:exactMatch mesh:D003053 Cochlear Duct semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002316 white matter skos:exactMatch mesh:D066127 White Matter semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002373 palatine tonsil skos:exactMatch mesh:D014066 Palatine Tonsil semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002393 pharyngotympanic tube skos:exactMatch mesh:D005064 Eustachian Tube semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002396 vomer skos:exactMatch mesh:D055172 Vomer semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002397 maxilla skos:exactMatch BTO:0006516 invertebrate maxilla semapv:LexicalMatching orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002409 pericardial fluid skos:exactMatch mesh:D000069236 Pericardial Fluid semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002410 autonomic nervous system skos:exactMatch IDOMAL:0002126 visceral nervous system semapv:LexicalMatching mira 0.556 +UBERON:0002412 vertebra skos:exactMatch BTO:0006196 vertebra semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002430 lateral hypothalamic area skos:exactMatch BTO:0006481 lateral hypothalamus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002469 esophagus mucosa skos:exactMatch mesh:D000071041 Esophageal Mucosa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002493 uterine artery skos:exactMatch mesh:D055988 Uterine Artery semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002540 lateral line system skos:exactMatch mesh:D053403 Lateral Line System semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002548 larva skos:exactMatch mesh:D007814 Larva semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002590 prepyriform area skos:exactMatch mesh:D066195 Piriform Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002600 limbic lobe skos:exactMatch mesh:D065726 Limbic Lobe semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002623 cerebral peduncle skos:exactMatch mesh:D065850 Cerebral Peduncle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002625 median preoptic nucleus skos:exactMatch BTO:0006168 nucleus preopticus medianus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002631 cerebral crus skos:exactMatch mesh:D065843 Cerebral Crus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002633 motor nucleus of trigeminal nerve skos:exactMatch mesh:D066266 Trigeminal Motor Nucleus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002639 midbrain reticular formation skos:exactMatch mesh:D066265 Midbrain Reticular Formation semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002656 periamygdaloid area skos:exactMatch mesh:D066277 Periamygdaloid Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002682 abducens nucleus skos:exactMatch mesh:D065827 Abducens Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002684 nucleus raphe obscurus skos:exactMatch mesh:D065849 Nucleus Raphe Obscurus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002689 supraoptic crest skos:exactMatch mesh:D066278 Organum Vasculosum semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002689 supraoptic crest skos:exactMatch BTO:0006268 organum vasculosum laminae terminalis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002704 metathalamus skos:exactMatch mesh:D005829 Geniculate Bodies semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002705 midline nuclear group skos:exactMatch mesh:D020644 Midline Thalamic Nuclei semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002707 corticospinal tract skos:exactMatch BTO:0006132 corticospinal tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002714 rubrospinal tract skos:exactMatch BTO:0006159 rubrospinal tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002726 cervical spinal cord skos:exactMatch mesh:D066193 Cervical Cord semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002743 basal forebrain skos:exactMatch mesh:D066187 Basal Forebrain semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002751 inferior temporal gyrus skos:exactMatch BTO:0006175 inferior temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002752 olivocerebellar tract skos:exactMatch BTO:0006157 olivocerebellar fiber system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002754 predorsal bundle skos:exactMatch mesh:D065844 Tectospinal Fibers semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002769 superior temporal gyrus skos:exactMatch BTO:0006177 superior temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002771 middle temporal gyrus skos:exactMatch BTO:0006176 middle temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0002776 ventral nuclear group skos:exactMatch mesh:D020651 Ventral Thalamic Nuclei semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002883 central amygdaloid nucleus skos:exactMatch mesh:D066274 Central Amygdaloid Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002894 olfactory cortex skos:exactMatch mesh:D066194 Olfactory Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002895 secondary olfactory cortex skos:exactMatch mesh:D018728 Entorhinal Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0002932 trapezoid body skos:exactMatch mesh:D065833 Trapezoid Body semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002967 cingulate gyrus skos:exactMatch mesh:D006179 Gyrus Cinguli semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0003011 facial motor nucleus skos:exactMatch mesh:D065828 Facial Nucleus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0003023 pontine tegmentum skos:exactMatch mesh:D065821 Pontine Tegmentum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003044 uncinate fasciculus skos:exactMatch mesh:D000083382 Uncinate Fasciculus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003050 olfactory placode skos:exactMatch BTO:0006222 olfactory placode semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0003055 periderm skos:exactMatch BTO:0003377 periderm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0003060 pronephric duct skos:exactMatch BTO:0005991 pronephric duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0003074 mesonephric duct skos:exactMatch BTO:0005990 mesonephric duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0003075 neural plate skos:exactMatch mesh:D054258 Neural Plate semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003089 sclerotome skos:exactMatch BTO:0006255 sclerotome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0003128 cranium skos:exactMatch mesh:D012886 Skull semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0003143 pupa skos:exactMatch mesh:D011679 Pupa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003209 blood nerve barrier skos:exactMatch mesh:D049428 Blood-Nerve Barrier semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003460 arm bone skos:exactMatch mesh:D050280 Arm Bones semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003462 facial bone skos:exactMatch mesh:D005147 Facial Bones semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003679 mouth floor skos:exactMatch BTO:0006184 mouth floor semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0003687 foramen magnum skos:exactMatch BTO:0006035 foramen magnum semapv:ManualMappingCuration 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+UBERON:0004016 dermatome skos:exactMatch BTO:0006248 dermatome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0004035 cortical subplate skos:exactMatch Not VO:0011276 SP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +UBERON:0004199 S-shaped body skos:exactMatch Not VO:0010896 Ssb semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +UBERON:0004341 primitive streak skos:exactMatch mesh:D054240 Primitive Streak semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004550 gastroesophageal sphincter skos:exactMatch mesh:D049630 Esophageal Sphincter, Lower semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0004637 otic capsule skos:exactMatch BTO:0005981 auditory capsule semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0004676 spinal cord lateral horn skos:exactMatch mesh:D066152 Spinal Cord Lateral Horn semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004720 cerebellar vermis skos:exactMatch mesh:D065814 Cerebellar Vermis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004725 piriform cortex skos:exactMatch mesh:D066195 Piriform Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004749 blastodisc skos:exactMatch mesh:D054239 Blastodisc semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005290 myelencephalon skos:exactMatch mesh:D054024 Myelencephalon semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005335 chorioallantoic membrane skos:exactMatch mesh:D049033 Chorioallantoic Membrane semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005343 cortical plate skos:exactMatch mesh:D002540 Cerebral Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0005343 cortical plate skos:exactMatch Not VO:0011021 CP semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mira +UBERON:0005366 olfactory lobe skos:exactMatch mesh:D066194 Olfactory Cortex semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0005403 ventral striatum skos:exactMatch mesh:D066328 Ventral Striatum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005408 circumventricular organ skos:exactMatch mesh:D066280 Circumventricular Organs semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005408 circumventricular organ skos:exactMatch BTO:0006267 circumventricular organ semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0005438 coronary sinus skos:exactMatch mesh:D054326 Coronary Sinus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005456 jugular foramen skos:exactMatch mesh:D000080869 Jugular Foramina semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005498 primitive heart tube skos:exactMatch BTO:0006179 cardiac tube semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0005631 extraembryonic membrane skos:exactMatch mesh:D005321 Extraembryonic Membranes semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005742 adventitia skos:exactMatch mesh:D063194 Adventitia semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005777 glomerular basement membrane skos:exactMatch mesh:D050533 Glomerular Basement Membrane semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005902 occipital region skos:exactMatch mesh:D009778 Occipital Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0006083 perirhinal cortex skos:exactMatch mesh:D000071039 Perirhinal Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006098 basal nuclear complex skos:exactMatch mesh:D001479 Basal Ganglia semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0006108 corticomedial nuclear complex skos:exactMatch mesh:D066276 Corticomedial Nuclear Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006444 annulus fibrosus skos:exactMatch mesh:D000070616 Annulus Fibrosus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006514 pallidum skos:exactMatch mesh:D005917 Globus Pallidus semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0006562 pharynx skos:exactMatch mesh:D010614 Pharynx semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006588 round ligament of liver skos:exactMatch mesh:D000069592 Round Ligament of Liver semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006589 round ligament of uterus skos:exactMatch mesh:D012404 Round Ligament of Uterus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006614 aponeurosis skos:exactMatch mesh:D000070606 Aponeurosis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006657 glenoid fossa skos:exactMatch mesh:D061165 Glenoid Cavity 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Parabrachial Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0007641 trigeminal nuclear complex skos:exactMatch mesh:D014278 Trigeminal Nuclei semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0007703 spinothalamic tract skos:exactMatch mesh:D013133 Spinothalamic Tracts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0007703 spinothalamic tract skos:exactMatch BTO:0006128 spinothalamic tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0008266 periodontal ligament skos:exactMatch mesh:D010513 Periodontal Ligament semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008269 nacre skos:exactMatch mesh:D060734 Nacre semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008275 carapace skos:exactMatch mesh:D060105 Animal Shells semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0008826 pulmonary surfactant skos:exactMatch mesh:D011663 Pulmonary Surfactants semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008904 neuromast skos:exactMatch BTO:0006219 neuromast semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0008969 dental follicle skos:exactMatch mesh:D003795 Dental Sac semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0008974 apocrine gland skos:exactMatch mesh:D001050 Apocrine Glands semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0009040 deep circumflex iliac artery skos:exactMatch mesh:D007083 Iliac Artery semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0009097 gravid organism skos:exactMatch IDOMAL:0000443 gravid semapv:LexicalMatching mira 0.556 +UBERON:0009127 epibranchial ganglion skos:exactMatch BTO:0006250 epibranchial ganglion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0009201 nephric duct skos:exactMatch BTO:0005990 mesonephric duct semapv:LexicalMatching orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0009755 spermaceti skos:exactMatch mesh:C009301 spermaceti semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0009757 ambergris skos:exactMatch mesh:D018648 Ambergris semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0009951 main olfactory bulb skos:exactMatch mesh:D009830 Olfactory Bulb semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0010264 hepatopancreas skos:exactMatch mesh:D043143 Hepatopancreas semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0010361 synostosis skos:exactMatch mesh:D013580 Synostosis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0010725 accessory navicular bone skos:exactMatch mesh:C536002 Accessory navicular bone semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011004 pharyngeal arch cartilage skos:exactMatch BTO:0006051 pharyngeal arch cartilage semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0011117 superior tibiofibular joint skos:exactMatch mesh:D007719 Knee Joint semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0011119 carpometacarpal joint skos:exactMatch mesh:D052737 Carpometacarpal Joints semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011132 intercarpal joint skos:exactMatch mesh:D050824 Carpal Joints semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0011166 patellofemoral joint skos:exactMatch mesh:D057071 Patellofemoral Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011390 pudendal nerve skos:exactMatch mesh:D060525 Pudendal Nerve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011895 endomysium skos:exactMatch BTO:0006241 endomysium semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0011905 plantaris 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venous blood skos:exactMatch BTO:0006187 venous blood semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0014374 embryoid body skos:exactMatch mesh:D058732 Embryoid Bodies semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0014398 respiratory muscle skos:exactMatch mesh:D012132 Respiratory Muscles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0014537 periamygdaloid cortex skos:exactMatch mesh:D066277 Periamygdaloid Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0014621 cervical spinal cord ventral horn skos:exactMatch mesh:D066151 Spinal Cord Ventral Horn semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0015169 tapetum skos:exactMatch BTO:0001350 tapetum semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:0015488 sural nerve skos:exactMatch mesh:D013497 Sural Nerve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0016435 chest wall skos:exactMatch mesh:D035441 Thoracic Wall semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0016530 parietal cortex skos:exactMatch mesh:D010296 Parietal Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0016538 temporal cortex skos:exactMatch mesh:D013702 Temporal Lobe semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0016884 shoulder joint skos:exactMatch mesh:D012785 Shoulder Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0018141 anterior perforated substance skos:exactMatch mesh:D066208 Olfactory Tubercle semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:0018144 cervical rib skos:exactMatch mesh:D057070 Cervical Rib semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0018388 cercaria skos:exactMatch mesh:D058487 Cercaria semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0022469 primary olfactory cortex skos:exactMatch Not 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mesh:D006722 Honey semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0036145 glymphatic system skos:exactMatch mesh:D000077502 Glymphatic System semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0036243 vaginal fluid skos:exactMatch BTO:0003084 vaginal fluid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:1000010 mole skos:exactMatch mesh:D009506 Nevus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:2000006 ball skos:exactMatch mesh:D015452 Precursor B-Cell Lymphoblastic Leukemia-Lymphoma semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:2000188 corpus cerebelli skos:exactMatch mesh:D002531 Cerebellum semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9 +UBERON:2000293 synencephalon skos:exactMatch BTO:0006476 synencephalon semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:2000297 vagal lobe skos:exactMatch BTO:0006431 vagal lobe semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:2000356 gill raker skos:exactMatch BTO:0002149 gill raker semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:2001553 manubrium skos:exactMatch mesh:D008371 Manubrium semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:2001977 pad skos:exactMatch Not mesh:D058729 Peripheral Arterial Disease semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:2002053 bony plate skos:exactMatch BTO:0000967 osseous plate semapv:LexicalMatching orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:2002116 epibranchial organ skos:exactMatch BTO:0004195 pharyngeal organ semapv:LexicalMatching orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:3010463 animal cap skos:exactMatch BTO:0004724 animal cap semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:3010586 vasa efferentia skos:exactMatch BTO:0002254 vas efferens semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:4000104 ganoine skos:exactMatch mesh:C067951 ganoine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:4000163 anal fin skos:exactMatch BTO:0004652 anal fin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:4000164 caudal fin skos:exactMatch BTO:0001827 tail fin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:4200215 suture skos:exactMatch mesh:D013537 Sutures semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:4300194 photophore skos:exactMatch BTO:0001477 photophore semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:8440012 cerebral nuclei skos:exactMatch BTO:0006534 cerebral nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:8450002 excretory system skos:exactMatch BTO:0006338 excretory system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py +UBERON:8480040 ovarian fluid skos:exactMatch BTO:0004569 ovarian fluid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 generate_uberon_bto_mappings.py diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index d867d5049..b829e98c9 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225211,6 +225211,35 @@ 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:8930180 +name: endometrial lymphatic vessel +def: "A lymphatic vessel that is part of the endometrium. Endometrial lymphatic vessels participate in tissue drainage and immune cell trafficking, with lymphangiogenesis occurring during different phases of the menstrual cycle under the regulation of vascular endothelial growth factors." [https://purl.org/ccf/ASCTB-TEMP_endometrial-lymphatic-vessel, PMID:17347164, PMID:17981324, PMID:19001552] +subset: added_by_HRA +xref: Wikipedia:Endometrium +is_a: UBERON:0001473 ! lymphatic vessel +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: part_of UBERON:0001295 ! endometrium +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3721" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930181 +name: villous mesenchyme +def: "A mesenchyme that is part of a chorionic villus. The villous mesenchyme forms the connective tissue core of the chorionic villus, supporting fetal capillaries and the overlying trophoblast layers." [https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme, PMID:42048630, PMID:42146334] +comment: Villous mesenchyme refers to the embryonic connective tissue core of the developing chorionic villus; distinct from placental villous stroma (UBERON:8600023) which denotes the mature stromal compartment. +subset: added_by_HRA +xref: Wikipedia:Chorionic_villi +is_a: UBERON:0003104 ! mesenchyme +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: part_of UBERON:0007106 ! chorionic villus +property_value: dcterms-date "2026-05-26T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3721" xsd:anyURI +created_by: dragon-ai-agent + [Typedef] id: aboral_to name: aboral to diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index a6cf8c391..096a415bf 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -1200,6 +1200,8 @@ composite-diff: reports/release-diff-composite.txt # Saves someone the hassle of typing 'make composite-metazoan.obo composite-vertebrate.obo' composites: composite-metazoan.obo composite-vertebrate.obo +# So you can run `make biomappings` +biomappings: $(MAPPINGDIR)/biomappings.sssom.tsv # ---------------------------------------- # SSSOM MAPPINGS @@ -1265,13 +1267,9 @@ $(MAPPINGDIR)/sslso.sssom.tsv: .FORCE wget "https://github.com/obophenotype/developmental-stage-ontologies/releases/latest/download/life-stages.sssom.tsv" -O $@ # Biomappings mapping set. Nominally a simple mirror, but we need a -# custom rule for two reasons: -# - the set is provided with the metadata in a separate file, which the -# ODK mirroring code does not support; -# - we want to filter out anything anything that has nothing to do with -# Uberon to keep the file to a reasonable size. -$(MAPPINGDIR)/biomappings.sssom.tsv: $(TMPDIR)/biomappings.sssom.tsv \ - $(TMPDIR)/biomappings.sssom.yml +# custom rule because we want to filter out anything anything that has nothing +# to do with Uberon to keep the file to a reasonable size. +$(MAPPINGDIR)/biomappings.sssom.tsv: $(TMPDIR)/biomappings.sssom.tsv sssom-cli --input $< --prefix 'UBERON=http://purl.obolibrary.org/obo/UBERON_' \ --rule '!(subject==UBERON:* || object==UBERON:*) -> stop()' \ --rule 'object==UBERON:* -> invert()' \ @@ -1282,9 +1280,6 @@ $(MAPPINGDIR)/biomappings.sssom.tsv: $(TMPDIR)/biomappings.sssom.tsv \ $(TMPDIR)/biomappings.sssom.tsv: wget -O $@ https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv -$(TMPDIR)/biomappings.sssom.yml: - wget -O $@ https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.yml - endif diff --git a/src/templates/hra-placenta-groups.template.tsv b/src/templates/hra-placenta-groups.template.tsv deleted file mode 100644 index dff359c07..000000000 --- a/src/templates/hra-placenta-groups.template.tsv +++ /dev/null @@ -1,2 +0,0 @@ -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-placenta.template.tsv b/src/templates/hra-placenta.template.tsv index e3586f3b7..e89d6fe37 100644 --- a/src/templates/hra-placenta.template.tsv +++ b/src/templates/hra-placenta.template.tsv @@ -1,4 +1,4 @@ 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_8930180 endometrial lymphatic vessel A lymphatic vessel that is part of the endometrium. Endometrial lymphatic vessels participate in tissue drainage and immune cell trafficking, with lymphangiogenesis occurring during different phases of the menstrual cycle under the regulation of vascular endothelial growth factors. https://purl.org/ccf/ASCTB-TEMP_endometrial-lymphatic-vessel|PMID:19001552|PMID:17981324|PMID:17347164 UBERON:0001473 UBERON:0001295 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:Endometrium -http://purl.obolibrary.org/obo/UBERON_8930189 villous mesenchyme A mesenchyme that is part of a chorionic villus. The villous mesenchyme forms the connective tissue core of the chorionic villus, supporting fetal capillaries and the overlying trophoblast layers. https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme|PMID:42146334|PMID:42048630 UBERON:0003104 UBERON:0007106 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:Chorionic_villi +http://purl.obolibrary.org/obo/UBERON_8930181 villous mesenchyme A mesenchyme that is part of a chorionic villus. The villous mesenchyme forms the connective tissue core of the chorionic villus, supporting fetal capillaries and the overlying trophoblast layers. https://purl.org/ccf/ASCTB-TEMP_villous-mesenchyme|PMID:42146334|PMID:42048630 UBERON:0003104 UBERON:0007106 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:Chorionic_villi