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Add ovary-other NTR template and reports #3739

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57 changes: 57 additions & 0 deletions bulk_ntr_workflow/source_data/ovary-other.csv
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tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
ovary,https://purl.org/ccf/ASCTB-TEMP_antral-follicle,antral follicle,,,UBERON:0001305,ovarian follicle,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-inferior-antimesenteric-ovary,central inferior antimesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary,central inferior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-inferior-mesenteric-ovary,central inferior mesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary,central inferior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary,central inferior ovary,,,https://purl.org/ccf/ASCTB-TEMP_central-ovary,central ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-ovary,central ovary,,,UBERON:0000992,ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-superior-antimesenteric-ovary,central superior antimesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary,central superior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-superior-mesenteric-ovary,central superior mesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary,central superior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary,central superior ovary,,,https://purl.org/ccf/ASCTB-TEMP_central-ovary,central ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_corona-radiata,corona radiata,,,UBERON:0005170,granulosa cell layer,
ovary,https://purl.org/ccf/ASCTB-TEMP_corpus-luteum-granulosa-lutein-layer,corpus luteum granulosa lutein layer,,,UBERON:0002512,corpus luteum,
ovary,https://purl.org/ccf/ASCTB-TEMP_corpus-luteum-granulosa-theca-layer,corpus luteum granulosa theca layer,,,UBERON:0002512,corpus luteum,
ovary,https://purl.org/ccf/ASCTB-TEMP_cortical-blood-vessels,cortical blood vessels,,,UBERON:0013191,ovarian cortex,
ovary,https://purl.org/ccf/ASCTB-TEMP_cumulus-oophorus-oocyte-complex,cumulus oophorus oocyte complex,,,UBERON:0003982,mature ovarian follicle,"https://doi.org/10.1210/er.2018-00085, https://doi.org/10.1093/oxfordjournals.humrep.a136365"
ovary,https://purl.org/ccf/ASCTB-TEMP_dominance-antral-follicle,dominance antral follicle,,,https://purl.org/ccf/ASCTB-TEMP_antral-follicle,antral follicle,https://doi.org/10.1093/oxfordjournals.humrep.a136365
ovary,https://purl.org/ccf/ASCTB-TEMP_early-antral-follicle,early antral follicle,,,https://purl.org/ccf/ASCTB-TEMP_antral-follicle,antral follicle,https://doi.org/10.1093/oxfordjournals.humrep.a136365
ovary,https://purl.org/ccf/ASCTB-TEMP_hemorrhagic-anovulatory-follicle,hemorrhagic anovulatory follicle,,,UBERON:0001305,ovarian follicle,"https://doi.org/10.1093/oxfordjournals.humrep.a136365, https://doi.org/10.1210/er.2018-00085"
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-antimesenteric-ovary,lateral inferior antimesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary,lateral inferior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-mesenteric-ovary,lateral inferior mesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary,lateral inferior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary,lateral inferior ovary,,,https://purl.org/ccf/ASCTB-TEMP_lateral-ovary,lateral ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-ovary,lateral ovary,,,UBERON:0000992,ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-superior-antimesenteric-ovary,lateral superior antimesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary,lateral superior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-superior-mesenteric-ovary,lateral superior mesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary,lateral superior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary,lateral superior ovary,,,https://purl.org/ccf/ASCTB-TEMP_lateral-ovary,lateral ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_luteinized-unruptured-follicle,luteinized unruptured follicle,,,UBERON:0001305,ovarian follicle,"https://doi.org/10.1093/oxfordjournals.humrep.a136365, https://doi.org/10.1210/er.2018-00085"
ovary,https://purl.org/ccf/ASCTB-TEMP_lymphatic-vessel,lymphatic vessel,,,UBERON:0013192,ovarian medulla,
ovary,https://purl.org/ccf/ASCTB-TEMP_matrisome,matrisome,,,UBERON:0013192,ovarian medulla,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-inferior-antimesenteric-ovary,medial inferior antimesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary,medial inferior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-inferior-mesenteric-ovary,medial inferior mesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary,medial inferior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary,medial inferior ovary,,,https://purl.org/ccf/ASCTB-TEMP_medial-ovary,medial ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-ovary,medial ovary,,,UBERON:0000992,ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-superior-antimesenteric-ovary,medial superior antimesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary,medial superior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-superior-mesenteric-ovary,medial superior mesenteric ovary,,,https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary,medial superior ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary,medial superior ovary,,,https://purl.org/ccf/ASCTB-TEMP_medial-ovary,medial ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_multilayer-ovarian-follicle,multilayer ovarian follicle,,,https://purl.org/ccf/ASCTB-TEMP_preantral-follicle,preantral follicle,"https://doi.org/10.1093/oxfordjournals.humrep.a136365, https://doi.org/10.1210/er.2018-00085"
ovary,https://purl.org/ccf/ASCTB-TEMP_ovarian-corticomedullary-junction,ovarian corticomedullary junction,,,https://purl.org/ccf/ASCTB-TEMP_central-inferior-antimesenteric-ovary,central inferior antimesenteric ovary,
ovary,https://purl.org/ccf/ASCTB-TEMP_ovarian-medullary-vasculature,ovarian medullary vasculature,,,UBERON:0013192,ovarian medulla,
ovary,https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle,pre-selection antral follicle,,,https://purl.org/ccf/ASCTB-TEMP_antral-follicle,antral follicle,https://doi.org/10.1093/oxfordjournals.humrep.a136365
ovary,https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle,pre-selection antral follicle,,,https://purl.org/ccf/ASCTB-TEMP_antral-follicle,antral follicle,
ovary,https://purl.org/ccf/ASCTB-TEMP_preantral-follicle,preantral follicle,,,UBERON:0001305,ovarian follicle,
ovary,https://purl.org/ccf/ASCTB-TEMP_selection-antral-follicle,selection antral follicle,,,https://purl.org/ccf/ASCTB-TEMP_antral-follicle,antral follicle,https://doi.org/10.1093/oxfordjournals.humrep.a136365
ovary,https://purl.org/ccf/ASCTB-TEMP_transitional-primary-ovarian-follicle,transitional primary ovarian follicle,,,https://purl.org/ccf/ASCTB-TEMP_preantral-follicle,preantral follicle,"https://doi.org/10.1093/oxfordjournals.humrep.a136365, https://doi.org/10.1210/er.2018-00085"
ovary,https://purl.org/ccf/ASCTB-TEMP_transitional-primordial-ovarian-follicle,transitional primordial ovarian follicle,,,https://purl.org/ccf/ASCTB-TEMP_preantral-follicle,preantral follicle,"https://doi.org/10.1093/oxfordjournals.humrep.a136365, https://doi.org/10.1210/er.2018-00085"
pancreas,https://purl.org/ccf/ASCTB-TEMP_extracellular-matrix,pancreatic extracellular matrix,,,UBERON:0000482,basal lamina of epithelium,https://doi.org/10.48539/HBM336.TBNP.923
small-intestine,https://purl.org/ccf/ASCTB-TEMP_connective-tissue,connective tissue in small intestine ,,,UBERON:0003337,serosa of jejunum,"PMID: 20126587, PMID: 3310649"
small-intestine,https://purl.org/ccf/ASCTB-TEMP_circular-longitudinal-muscle,small intestine circular/longitudinal muscle,,,https://purl.org/ccf/ASCTB-TEMP_muscularis-externa,muscularis externa,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_endoethlial,small intestine endothelial,,,UBERON:0003332,submucosa of duodenum,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_epithelium,small intestine Epithelium,,,UBERON:0001213,intestinal villus,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_lamina-propria-gut-associated-lymphoid-tissue-galt-,small intestine Lamina propria/Gut associated lymphoid tissue (GALT),,,UBERON:0001213,intestinal villus,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_mucosa,small intestine mucosa,,,UBERON:0013644,duodenal ampulla,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_muscularis-externa,small intestine muscularis externa,,,UBERON:0002115,jejunum,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_muscularis-mucosa,small intestine muscularis mucosa,,,UBERON:0001213,intestinal villus,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_muscularis-propria,small intestine muscularis propria,,,UBERON:0013644,duodenal ampulla,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_myenteric-plexus-of-auerbach,small intestine myenteric plexus of Auerbach,,,UBERON:0012377,muscle layer of jejunum,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_serosa,small intestine serosa,,,UBERON:0013644,duodenal ampulla,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_submucosa,small intestine submucosa,,,UBERON:0013644,duodenal ampulla,
small-intestine,https://purl.org/ccf/ASCTB-TEMP_submucosal-plexus-of-meissner,small intestine submucosal plexus of Meissner,,,UBERON:0003332,submucosa of duodenum,
14 changes: 14 additions & 0 deletions src/templates/hra-ovary-other-reports/candidates.tsv
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label as_iri uberon_id note
small intestine Epithelium UBERON:0001902 confirmed_match (confidence: high)
small intestine muscularis mucosa UBERON:0001210 confirmed_match (confidence: high)
small intestine muscularis externa UBERON:0011201 confirmed_match (confidence: high)
small intestine submucosal plexus of Meissner UBERON:0005304 confirmed_match (confidence: high)
small intestine myenteric plexus of Auerbach UBERON:8410063 confirmed_match (confidence: high)
lymphatic vessel UBERON:0001473 confirmed_match (confidence: high)
small intestine mucosa UBERON:0001204 confirmed_match (confidence: high)
small intestine muscularis propria UBERON:0011201 confirmed_match (confidence: high)
small intestine serosa UBERON:0001206 confirmed_match (confidence: high)
small intestine submucosa UBERON:0001205 confirmed_match (confidence: high)
small intestine circular/longitudinal muscle UBERON:0011201 confirmed_match (confidence: high)
antral follicle UBERON:0000037 possible_match (UBERON:0000037 'tertiary ovarian follicle' has 'antral follicle' as a BROAD synonym, suggesting that 'antral follicle' may be a broader category than tertiary follicle alone. The literature may distinguish early vs late antral follicles, while UBERON:0000037 specifically refers to the most mature stage. Further investigation needed to determine if this is truly equivalent or if a broader antral follicle class is needed.)
preantral follicle UBERON:0000036 possible_match (UBERON:0000036 'secondary ovarian follicle' has 'preantral follicle' as an EXACT synonym. UBERON:0000035 'primary ovarian follicle' also has 'preantral follicle of ovary' as a RELATED synonym. The EXACT match to secondary follicle is more specific, making UBERON:0000036 the more likely match. However, the term may be used broadly in the literature to refer to both primary and secondary stages.)
29 changes: 29 additions & 0 deletions src/templates/hra-ovary-other-reports/errors.tsv
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label as_iri issue_type parent_id parent_label detail
central inferior antimesenteric ovary https://purl.org/ccf/ASCTB-TEMP_central-inferior-antimesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary central inferior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
central inferior mesenteric ovary https://purl.org/ccf/ASCTB-TEMP_central-inferior-mesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary central inferior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
central inferior ovary https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-ovary central ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
central superior antimesenteric ovary https://purl.org/ccf/ASCTB-TEMP_central-superior-antimesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary central superior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
central superior mesenteric ovary https://purl.org/ccf/ASCTB-TEMP_central-superior-mesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary central superior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
central superior ovary https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-ovary central ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
dominance antral follicle https://purl.org/ccf/ASCTB-TEMP_dominance-antral-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
early antral follicle https://purl.org/ccf/ASCTB-TEMP_early-antral-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
lateral inferior antimesenteric ovary https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-antimesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary lateral inferior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
lateral inferior mesenteric ovary https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-mesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary lateral inferior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
lateral inferior ovary https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-ovary lateral ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
lateral superior antimesenteric ovary https://purl.org/ccf/ASCTB-TEMP_lateral-superior-antimesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary lateral superior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
lateral superior mesenteric ovary https://purl.org/ccf/ASCTB-TEMP_lateral-superior-mesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary lateral superior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
lateral superior ovary https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_lateral-ovary lateral ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial inferior antimesenteric ovary https://purl.org/ccf/ASCTB-TEMP_medial-inferior-antimesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary medial inferior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial inferior mesenteric ovary https://purl.org/ccf/ASCTB-TEMP_medial-inferior-mesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary medial inferior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial inferior ovary https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_medial-ovary medial ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial superior antimesenteric ovary https://purl.org/ccf/ASCTB-TEMP_medial-superior-antimesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary medial superior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial superior mesenteric ovary https://purl.org/ccf/ASCTB-TEMP_medial-superior-mesenteric-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary medial superior ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
medial superior ovary https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_medial-ovary medial ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
multilayer ovarian follicle https://purl.org/ccf/ASCTB-TEMP_multilayer-ovarian-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_preantral-follicle preantral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
ovarian corticomedullary junction https://purl.org/ccf/ASCTB-TEMP_ovarian-corticomedullary-junction asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_central-inferior-antimesenteric-ovary central inferior antimesenteric ovary Parent not yet in UBERON; subagent should search OLS4 for correct parent
pre-selection antral follicle https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
pre-selection antral follicle https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
selection antral follicle https://purl.org/ccf/ASCTB-TEMP_selection-antral-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
transitional primary ovarian follicle https://purl.org/ccf/ASCTB-TEMP_transitional-primary-ovarian-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_preantral-follicle preantral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
transitional primordial ovarian follicle https://purl.org/ccf/ASCTB-TEMP_transitional-primordial-ovarian-follicle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_preantral-follicle preantral follicle Parent not yet in UBERON; subagent should search OLS4 for correct parent
small intestine circular/longitudinal muscle https://purl.org/ccf/ASCTB-TEMP_circular-longitudinal-muscle asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_muscularis-externa muscularis externa Parent not yet in UBERON; subagent should search OLS4 for correct parent
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