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18 changes: 18 additions & 0 deletions bulk_ntr_workflow/source_data/placenta.csv
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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,
2 changes: 2 additions & 0 deletions src/templates/hra-placenta-groups.template.tsv
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ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref
ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=|
17 changes: 17 additions & 0 deletions src/templates/hra-placenta-reports/candidates.tsv
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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.)
1 change: 1 addition & 0 deletions src/templates/hra-placenta-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
18 changes: 18 additions & 0 deletions src/templates/hra-placenta-reports/input.tsv
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table as_iri label uberon_id parent_id parent_label references term_type
https://purl.org/ccf/ASCTB-TEMP_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
3 changes: 3 additions & 0 deletions src/templates/hra-placenta-reports/name_corrections.tsv
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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.
4 changes: 4 additions & 0 deletions src/templates/hra-placenta.template.tsv
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ID LABEL Definition def_xref is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref
ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| SC % SC BFO:0000050 some % SC RO:0002202 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=|
http://purl.obolibrary.org/obo/UBERON_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
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