diff --git a/bulk_ntr_workflow/source_data/ovary-other.csv b/bulk_ntr_workflow/source_data/ovary-other.csv new file mode 100644 index 000000000..f4d477f96 --- /dev/null +++ b/bulk_ntr_workflow/source_data/ovary-other.csv @@ -0,0 +1,57 @@ +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, \ No newline at end of file diff --git a/src/templates/hra-ovary-other-reports/candidates.tsv b/src/templates/hra-ovary-other-reports/candidates.tsv new file mode 100644 index 000000000..048b7ed3d --- /dev/null +++ b/src/templates/hra-ovary-other-reports/candidates.tsv @@ -0,0 +1,14 @@ +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.) diff --git a/src/templates/hra-ovary-other-reports/errors.tsv b/src/templates/hra-ovary-other-reports/errors.tsv new file mode 100644 index 000000000..0224e20c5 --- /dev/null +++ b/src/templates/hra-ovary-other-reports/errors.tsv @@ -0,0 +1,29 @@ +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 diff --git a/src/templates/hra-ovary-other-reports/input.tsv b/src/templates/hra-ovary-other-reports/input.tsv new file mode 100644 index 000000000..d1e23d746 --- /dev/null +++ b/src/templates/hra-ovary-other-reports/input.tsv @@ -0,0 +1,57 @@ +table as_iri label uberon_id parent_id parent_label references term_type + https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle UBERON:0001305 ovarian follicle leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary central inferior ovary https://purl.org/ccf/ASCTB-TEMP_central-ovary central ovary leaf + https://purl.org/ccf/ASCTB-TEMP_central-ovary central ovary UBERON:0000992 ovary leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary central superior ovary https://purl.org/ccf/ASCTB-TEMP_central-ovary central ovary leaf + https://purl.org/ccf/ASCTB-TEMP_corona-radiata corona radiata UBERON:0005170 granulosa cell layer leaf + https://purl.org/ccf/ASCTB-TEMP_corpus-luteum-granulosa-lutein-layer corpus luteum granulosa lutein layer UBERON:0002512 corpus luteum leaf + https://purl.org/ccf/ASCTB-TEMP_corpus-luteum-granulosa-theca-layer corpus luteum granulosa theca layer UBERON:0002512 corpus luteum leaf + https://purl.org/ccf/ASCTB-TEMP_cortical-blood-vessels cortical blood vessels UBERON:0013191 ovarian cortex leaf + 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 leaf + 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 leaf + 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 leaf + 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 leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-ovary lateral inferior ovary https://purl.org/ccf/ASCTB-TEMP_lateral-ovary lateral ovary leaf + https://purl.org/ccf/ASCTB-TEMP_lateral-ovary lateral ovary UBERON:0000992 ovary leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_lateral-superior-ovary lateral superior ovary https://purl.org/ccf/ASCTB-TEMP_lateral-ovary lateral ovary leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_lymphatic-vessel lymphatic vessel UBERON:0013192 ovarian medulla leaf + https://purl.org/ccf/ASCTB-TEMP_matrisome matrisome UBERON:0013192 ovarian medulla leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary medial inferior ovary https://purl.org/ccf/ASCTB-TEMP_medial-ovary medial ovary leaf + https://purl.org/ccf/ASCTB-TEMP_medial-ovary medial ovary UBERON:0000992 ovary leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary medial superior ovary https://purl.org/ccf/ASCTB-TEMP_medial-ovary medial ovary leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_ovarian-medullary-vasculature ovarian medullary vasculature UBERON:0013192 ovarian medulla leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle pre-selection antral follicle https://purl.org/ccf/ASCTB-TEMP_antral-follicle antral follicle leaf + https://purl.org/ccf/ASCTB-TEMP_preantral-follicle preantral follicle UBERON:0001305 ovarian follicle leaf + 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 leaf + 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 leaf + 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 leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_connective-tissue connective tissue in small intestine UBERON:0003337 serosa of jejunum PMID: 20126587, PMID: 3310649 leaf + https://purl.org/ccf/ASCTB-TEMP_circular-longitudinal-muscle small intestine circular/longitudinal muscle https://purl.org/ccf/ASCTB-TEMP_muscularis-externa muscularis externa leaf + https://purl.org/ccf/ASCTB-TEMP_endoethlial small intestine endothelial UBERON:0003332 submucosa of duodenum leaf + https://purl.org/ccf/ASCTB-TEMP_epithelium small intestine Epithelium UBERON:0001213 intestinal villus leaf + 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 leaf + https://purl.org/ccf/ASCTB-TEMP_mucosa small intestine mucosa UBERON:0013644 duodenal ampulla leaf + https://purl.org/ccf/ASCTB-TEMP_muscularis-externa small intestine muscularis externa UBERON:0002115 jejunum leaf + https://purl.org/ccf/ASCTB-TEMP_muscularis-mucosa small intestine muscularis mucosa UBERON:0001213 intestinal villus leaf + https://purl.org/ccf/ASCTB-TEMP_muscularis-propria small intestine muscularis propria UBERON:0013644 duodenal ampulla leaf + https://purl.org/ccf/ASCTB-TEMP_myenteric-plexus-of-auerbach small intestine myenteric plexus of Auerbach UBERON:0012377 muscle layer of jejunum leaf + https://purl.org/ccf/ASCTB-TEMP_serosa small intestine serosa UBERON:0013644 duodenal ampulla leaf + https://purl.org/ccf/ASCTB-TEMP_submucosa small intestine submucosa UBERON:0013644 duodenal ampulla leaf + https://purl.org/ccf/ASCTB-TEMP_submucosal-plexus-of-meissner small intestine submucosal plexus of Meissner UBERON:0003332 submucosa of duodenum leaf diff --git a/src/templates/hra-ovary-other-reports/manual_curation.tsv b/src/templates/hra-ovary-other-reports/manual_curation.tsv new file mode 100644 index 000000000..1527925c7 --- /dev/null +++ b/src/templates/hra-ovary-other-reports/manual_curation.tsv @@ -0,0 +1,13 @@ +label definition reason similar_terms suggestion +small intestine Lamina propria/Gut associated lymphoid tissue (GALT) Not written - composite term flagged for name correction Composite slash term violates UBERON naming conventions. Cannot determine which single structure the source intends to reference. Both 'lamina propria of small intestine' (UBERON:0001204) and 'gut-associated lymphoid tissue' (UBERON:0001962) already exist as separate, well-defined terms. UBERON:0001204=lamina propria of small intestine; UBERON:0001962=gut-associated lymphoid tissue; UBERON:0003454=small intestine Peyer's patch Curator should: (1) Contact ASCTB source to clarify intent and correct the slash notation. (2) If they mean GALT in small intestine, consider creating 'gut-associated lymphoid tissue of small intestine' as intersection_of: UBERON:0001962 ! GALT + part_of UBERON:0002108 ! small intestine. (3) If they mean both structures, split into two separate term requests. (4) If they mean specifically lymphoid tissue within the lamina propria, use existing UBERON:0001204 and note that it contains lymphoid tissue in its definition. +small intestine endothelial INCOMPLETE TERM NAME - likely intended as 'endothelium of small intestine vasculature' or referring to an endothelial cell type. In UBERON, endothelium terms follow the pattern 'endothelium of X' (e.g., UBERON:0001917 'endothelium of artery', UBERON:0001915 'endothelium of capillary') with logical definition: genus UBERON:0001986 (endothelium) and part_of the containing structure. If this refers to a cell type, it belongs in Cell Ontology (CL:0000115 endothelial cell), not UBERON anatomical structures. Term name is incomplete and ambiguous. Parent assignment to 'submucosa of duodenum' (UBERON:0003332) is anatomically incorrect - endothelium is part of blood vessels, not a direct component of submucosa layers. The term cannot be properly classified without clarification of whether it refers to: (1) endothelium tissue of small intestine vasculature, (2) endothelium of a specific vessel type (arteries, veins, capillaries), or (3) a cell type that belongs in Cell Ontology. UBERON:0001986=endothelium; UBERON:0001915=endothelium of capillary; UBERON:0001917=endothelium of artery; UBERON:0001919=endothelium of vein Request clarification from submitter. If tissue structure intended, create regional term following UBERON pattern: 'endothelium of small intestine vasculature' or more specific terms like 'endothelium of small intestine artery', 'endothelium of small intestine capillary', etc. with appropriate genus and part_of axioms. If cell type intended, redirect to Cell Ontology for 'endothelial cell' with appropriate location qualifiers. +central inferior antimesenteric ovary An anatomical space of the ovary located in the central-inferior region on the antimesenteric border, which is the side of the ovary facing away from the mesovarium attachment. Very fine-grained spatial subdivision without distinct histological or functional characteristics. UBERON typically models structures with biological distinctiveness rather than pure coordinate-based spatial zones. These terms appear to be created for detailed cell mapping (HRA ASCTB project) and may be better represented in a spatial reference system or coordinate annotation framework. UBERON:0000992=ovary; UBERON:0001342=mesovarium; UBERON:0006960=ovary stroma Curator should decide whether: (1) to add these as anatomical_space subclasses with part_of ovary, (2) to handle via a separate spatial annotation or coordinate system for the HRA project, or (3) to mark as out-of-scope for UBERON if they lack biological significance beyond spatial positioning. If added, consider creating intermediate grouping classes like 'inferior region of ovary', 'mesenteric border of ovary', etc., to organize the hierarchy rather than adding many individual fine-grained zones directly under ovary. +central inferior mesenteric ovary An anatomical space of the ovary located in the central-inferior region on the mesenteric border, which is the side of the ovary facing toward the mesovarium attachment. Very fine-grained spatial subdivision without distinct histological or functional characteristics. UBERON typically models structures with biological distinctiveness rather than pure coordinate-based spatial zones. These terms appear to be created for detailed cell mapping (HRA ASCTB project) and may be better represented in a spatial reference system or coordinate annotation framework. UBERON:0000992=ovary; UBERON:0001342=mesovarium; UBERON:0006960=ovary stroma Curator should decide whether: (1) to add these as anatomical_space subclasses with part_of ovary, (2) to handle via a separate spatial annotation or coordinate system for the HRA project, or (3) to mark as out-of-scope for UBERON if they lack biological significance beyond spatial positioning. If added, consider creating intermediate grouping classes like 'inferior region of ovary', 'mesenteric border of ovary', etc., to organize the hierarchy rather than adding many individual fine-grained zones directly under ovary. +central superior ovary (parent term) The parent term 'central superior ovary' does not exist in UBERON and must be created before these child terms can be added. This represents a novel fine-grained spatial parcellation scheme for the ovary. The entire ovarian spatial parcellation system (medial/central/lateral × superior/inferior × mesenteric/antimesenteric) appears to be an HRA-specific 3D coordinate reference framework. UBERON currently has only cortex/medulla subdivisions of the ovary. Before adding these terms, the curators should: (1) Decide if this level of spatial granularity is appropriate for UBERON or if it belongs in a separate spatial reference ontology; (2) If accepted, create the full hierarchy: central ovary → central superior ovary → central superior mesenteric/antimesenteric ovary; (3) Establish clear anatomical boundaries and measurement criteria for each zone; (4) Find published anatomical literature supporting these spatial divisions. +lateral inferior ovary The inferior portion of the lateral aspect of the ovary, a region of the ovary that faces the lateral pelvic wall and extends from the ovarian ligament attachment to the inferior pole. The terms 'lateral ovary', 'lateral inferior ovary', and 'lateral superior ovary' do not appear in standard anatomical literature (Gray's Anatomy, Terminologia Anatomica), Wikipedia, or UBERON. The ovary has recognized subdivisions (cortex, medulla, germinal epithelium) and surfaces (lateral surface facing pelvic wall, medial surface facing uterus), but 'lateral ovary' as a named substructure is not established in classical anatomy. These terms may originate from HRA ASCTB table-specific spatial subdivision schemes or imaging protocols rather than classical anatomical nomenclature. Curator should: (1) Verify the source and intended meaning of these terms in the HRA ASCTB context. (2) Consider whether these represent valid spatial subdivisions that should be added to UBERON (e.g., 'lateral surface of ovary' with superior/inferior regions), or whether they should be modeled using spatial relation ontology (BSPO) qualifiers instead of creating new anatomical structure terms. (3) If these are imaging-specific regional designations rather than anatomically distinct structures, consider representing them as qualities or spatial regions rather than anatomical entities. (4) Consult TA2 (Terminologia Anatomica 2nd ed.) and FMA for any precedent for dividing the ovarian surface into named regions. +lateral superior ovary The superior portion of the lateral aspect of the ovary, a region of the ovary that faces the lateral pelvic wall and extends from the superior pole toward the ovarian ligament attachment. Same as lateral inferior ovary - non-standard anatomical term not found in classical anatomy references. Same curation workflow as lateral inferior ovary. These two terms form a pair and should be curated together. +lateral superior antimesenteric ovary A region of the ovary located in the lateral and superior portion along the antimesenteric border, representing the free border opposite to the mesovarium attachment site. Very granular spatial subdivision. ASCTB has created an 18-region 3D grid system (3 mediolateral × 3 craniocaudal × 2 mesenteric/antimesenteric) for tissue mapping. While 'mesenteric' and 'antimesenteric' borders are valid anatomical concepts (mesovarium attachment vs free border), the specific fine-grained regional subdivisions are not established in standard anatomical literature (Gray's Anatomy, TA2). UBERON typically includes histologically or functionally distinct regions (e.g., ovarian cortex, medulla) rather than arbitrary spatial grid cells. UBERON:0013191=ovarian cortex; UBERON:0013192=ovarian medulla; UBERON:0001342=mesovarium Curator should evaluate whether UBERON's scope includes tissue-mapping spatial subdivisions. If yes: 1) Consider creating intermediate regional terms for consistency. 2) Add definitions emphasizing these are spatial subdivisions, not histologically distinct regions. 3) Consider adding relationships like 'adjacent_to UBERON:0001342 ! mesovarium' for the mesenteric terms. If no: Mark as out-of-scope and suggest spatial annotation approach using BSPO (spatial ontology) terms instead. +lateral superior mesenteric ovary A region of the ovary located in the lateral and superior portion along the mesenteric border, at or near the site where the mesovarium attaches to suspend the ovary. Same as above - very granular spatial subdivision from ASCTB 3D grid system, not established in standard anatomical literature. UBERON:0013191=ovarian cortex; UBERON:0013192=ovarian medulla; UBERON:0001342=mesovarium Same as above. Additionally, consider that the mesovarium attachment site (ovarian hilum) might be a more appropriate UBERON term to create instead of these grid subdivisions. +medial inferior antimesenteric ovary An anatomical region of the ovary located on the medial inferior aspect on the side opposite the mesovarium attachment, corresponding to the antimesenteric (free lateral) border of the ovary in its inferior medial quadrant. This term represents a highly granular spatial subdivision of the ovary that is not found in standard anatomical ontologies. The parent 'medial inferior ovary' itself is not in UBERON. UBERON contains only one ovary subdivision pattern for laterality (left/right ovary) and basic structural parts (cortex, medulla, capsule, etc.), not fine-grained spatial quadrants. The mesovarium (UBERON:0013771) exists as the mesentery of the ovary, but UBERON does not subdivide the ovary into mesenteric vs antimesenteric regions or medial/lateral/inferior/superior quadrants. DECISION REQUIRED: The curator must decide whether: (1) UBERON should expand to include such fine-grained spatial subdivisions of the ovary to support HRA mapping needs, which would require adding the entire hierarchy (medial ovary, medial inferior ovary, and their mesenteric/antimesenteric subdivisions); (2) These terms should be kept in a separate HRA-specific extension/module rather than core UBERON; (3) A different modeling approach should be used (e.g., using spatial relation properties like 'in medial inferior part of' rather than creating named anatomical entities for every possible spatial region). If option (1) is chosen, similar subdivisions would need to be considered for consistency: lateral ovary, superior ovary, lateral superior/inferior ovary, etc., which could lead to a combinatorial explosion of terms. Standard anatomical practice uses compositional descriptions (e.g., 'cells in the medial aspect of the ovarian cortex') rather than named regions for such granular locations. +medial inferior mesenteric ovary An anatomical region of the ovary located on the medial inferior aspect at the mesovarium attachment site, corresponding to the mesenteric (medially attached) border of the ovary in its inferior medial quadrant. Same as medial inferior antimesenteric ovary - highly granular spatial subdivision not found in standard anatomical ontologies, with parent term not in UBERON. Same curatorial decision needed as for medial inferior antimesenteric ovary. These two terms represent opposite sides of the same spatial quadrant and should be considered together. +medial ovary (parent term) ASCTB uses a coordinate-based spatial subdivision system (medial/lateral, superior/inferior, mesenteric/antimesenteric) that differs from UBERON's focus on named anatomical structures. Standard ovary subdivisions include: cortex (UBERON has ovary stroma UBERON:0003902), medulla, hilum, tunica albuginea. Curator should evaluate whether ASCTB spatial coordinate terms should be included in UBERON or whether a different approach (e.g., using spatial relationships or a separate spatial reference system) would be more appropriate. If included, consider creating a 'medial ovary' grouping term as an intermediate, but note this is non-standard anatomical nomenclature. diff --git a/src/templates/hra-ovary-other-reports/name_corrections.tsv b/src/templates/hra-ovary-other-reports/name_corrections.tsv new file mode 100644 index 000000000..150df46e9 --- /dev/null +++ b/src/templates/hra-ovary-other-reports/name_corrections.tsv @@ -0,0 +1,7 @@ +source_label corrected_label reason +small intestine Lamina propria/Gut associated lymphoid tissue (GALT) Requires curator decision: split into two separate terms OR clarify intent Composite term using slash notation combining two distinct anatomical structures: (1) lamina propria of small intestine (UBERON:0001204 already exists) and (2) gut-associated lymphoid tissue (UBERON:0001962 already exists). UBERON naming conventions prohibit slash-delimited composite terms. The source may intend: (a) GALT structures within the lamina propria, (b) both structures as separate entries, or (c) a new term for 'gut-associated lymphoid tissue of small intestine' (which would be intersection_of GALT and part_of small intestine, similar to existing 'small intestine Peyer's patch' UBERON:0003454). +corpus luteum granulosa theca layer corpus luteum theca lutein layer The term should refer to 'theca lutein' cells (not 'granulosa theca'). Theca lutein cells are luteinized theca cells, parallel to granulosa lutein cells. The current name conflates granulosa and theca nomenclature. +small intestine endothelial endothelium of small intestine [or endothelium of small intestine vasculature] Source term is grammatically incomplete - 'endothelial' is an adjective without a noun. UBERON pattern for endothelium structures uses 'endothelium of X' format (not 'X endothelial'). Examples: UBERON:0001917 'endothelium of artery', UBERON:0001915 'endothelium of capillary', UBERON:0002042 'lymphatic vessel endothelium'. If a cell type was intended rather than tissue, this belongs in Cell Ontology (CL) not UBERON. +connective tissue in small intestine small intestine connective tissue UBERON uses '[organ] connective tissue' pattern (e.g., lung connective tissue UBERON:0000114, head connective tissue UBERON:0003566). The suggested name matches this established naming convention. +dominance antral follicle dominant antral follicle Standard anatomical terminology uses 'dominant' (adjective) rather than 'dominance' (noun). The term should describe the follicle that is dominant, not a follicle of dominance. +small intestine circular/longitudinal muscle muscle layer of small intestine The '/' notation is non-standard in anatomical nomenclature. UBERON uses 'muscle layer of small intestine' with synonyms 'muscularis externa of small intestine' and 'muscular coat of small intestine'. The source name could be retained as a related synonym if needed for mapping purposes. diff --git a/src/templates/hra-ovary-other-reports/out_of_scope.tsv b/src/templates/hra-ovary-other-reports/out_of_scope.tsv new file mode 100644 index 000000000..1ea77c717 --- /dev/null +++ b/src/templates/hra-ovary-other-reports/out_of_scope.tsv @@ -0,0 +1,4 @@ +label reason suggestion +hemorrhagic anovulatory follicle Describes a pathological/dysfunctional state (hemorrhagic + anovulatory = failed to ovulate with bleeding). UBERON covers normal anatomy only; pathological structures belong in MONDO or as PATO-qualified terms. Consider MONDO or create a PATO-qualified term for this abnormal follicle state. The existing DOI references (10.1093/oxfordjournals.humrep.a136365, 10.1210/er.2018-00085) may be useful for documenting the pathological condition in the appropriate ontology. +luteinized unruptured follicle Describes a pathological/dysfunctional state (luteinized but unruptured = failed to rupture and release oocyte despite luteinization). UBERON covers normal anatomy only; this represents ovulatory dysfunction. Consider MONDO or create a PATO-qualified term for this abnormal follicle state. This condition is also known as luteinized unruptured follicle syndrome (LUFS). The existing DOI references (10.1093/oxfordjournals.humrep.a136365, 10.1210/er.2018-00085) document this pathological condition. +matrisome The matrisome is a molecular/proteomic concept referring to the complete set of extracellular matrix (ECM) proteins and ECM-associated proteins in a tissue or organism, not an anatomical structure. UBERON is an anatomy ontology focused on structural entities. This term belongs in a protein ontology (PRO - Protein Ontology) or a molecular function/component ontology (GO - Gene Ontology). The term was coined in 2009-2010 by the Hynes laboratory to describe the ECM proteome. While ECM is an important component of many anatomical structures in UBERON, the matrisome as a conceptual collection of proteins is outside UBERON's scope. diff --git a/src/templates/hra-ovary-other.template.tsv b/src/templates/hra-ovary-other.template.tsv new file mode 100644 index 000000000..531f1b825 --- /dev/null +++ b/src/templates/hra-ovary-other.template.tsv @@ -0,0 +1,34 @@ +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_9900001 antral follicle An ovarian follicle characterized by the presence of a fluid-filled cavity called the antrum that develops during folliculogenesis. https://purl.org/ccf/ASCTB-TEMP_antral-follicle|PMID:42484017|PMID:42483999 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 FMA:18641 +http://purl.obolibrary.org/obo/UBERON_9900004 central inferior ovary An anatomical subdivision of the ovarian medulla that is located in the inferior (lower) portion of the central ovarian region, containing vascular stroma, blood vessels, lymphatic vessels, and nerves. https://purl.org/ccf/ASCTB-TEMP_central-inferior-ovary|PMID:17999378|PMID:22666170 UBERON:0013192 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Medulla_of_ovary +http://purl.obolibrary.org/obo/UBERON_9900005 central ovary An organ part that is the central region of the ovary, positioned between the lateral and medial aspects and encompassing tissue from both cortex and medulla in the mid-region of the organ. https://purl.org/ccf/ASCTB-TEMP_central-ovary|PMID:17999378|PMID:22666170 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900006 central superior antimesenteric ovary An anatomical region of the ovary corresponding to the central-mediolateral and superior-inferosuperior portion of the free border (antimesenteric side) opposite to the mesovarium attachment. https://purl.org/ccf/ASCTB-TEMP_central-superior-antimesenteric-ovary|PMID:41985840|PMID:41813503 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/thumb/f/f5/Ovary.png/330px-Ovary.png Wikipedia:Ovary|Wikipedia:Mesovarium +http://purl.obolibrary.org/obo/UBERON_9900007 central superior mesenteric ovary An anatomical region of the ovary corresponding to the central-mediolateral and superior-inferosuperior portion of the hilar border (mesenteric side) adjacent to the mesovarium attachment. https://purl.org/ccf/ASCTB-TEMP_central-superior-mesenteric-ovary|PMID:41985840|PMID:41813503 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/thumb/f/f5/Ovary.png/330px-Ovary.png Wikipedia:Ovary|Wikipedia:Mesovarium +http://purl.obolibrary.org/obo/UBERON_9900008 central superior ovary An anatomical subdivision of the ovarian medulla that is located in the superior (upper) portion of the central ovarian region, containing vascular stroma, blood vessels, lymphatic vessels, and nerves. https://purl.org/ccf/ASCTB-TEMP_central-superior-ovary|PMID:17999378|PMID:22666170 UBERON:0013192 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Medulla_of_ovary +http://purl.obolibrary.org/obo/UBERON_9900009 corona radiata A cell layer of granulosa cells that radiates outward from the zona pellucida surrounding the oocyte within an ovarian follicle. The corona radiata consists of specialized granulosa cells arranged in a radial pattern, forming the outermost cellular layer directly adjacent to the zona pellucida. This structure is expelled with the oocyte during ovulation and must be penetrated by sperm for successful fertilization to occur. https://purl.org/ccf/ASCTB-TEMP_corona-radiata|PMID:40604261|PMID:35499777|PMID:34967955 UBERON:0000119 UBERON:0005170 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900010 corpus luteum granulosa lutein layer A cell layer of the corpus luteum that consists of large luteinized granulosa cells derived from the granulosa cell layer of the preovulatory follicle and forms the inner layer of the corpus luteum. https://purl.org/ccf/ASCTB-TEMP_corpus-luteum-granulosa-lutein-layer|PMID:20959416 UBERON:0000119 UBERON:0002512 UBERON:0005170 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg Wikipedia:Corpus_luteum +http://purl.obolibrary.org/obo/UBERON_9900011 corpus luteum theca lutein layer A cell layer of the corpus luteum that consists of luteinized theca cells derived from the theca cell layer of the preovulatory follicle and forms the outer layer of the corpus luteum. https://purl.org/ccf/ASCTB-TEMP_corpus-luteum-granulosa-theca-layer|PMID:20959416 UBERON:0000119 UBERON:0002512 UBERON:0000155 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg Wikipedia:Corpus_luteum +http://purl.obolibrary.org/obo/UBERON_9900012 cortical blood vessels A blood vessel that is located in the ovarian cortex, supplying oxygenated blood to the follicles and connective tissue stroma within the cortical region of the ovary. https://purl.org/ccf/ASCTB-TEMP_cortical-blood-vessels|PMID:42079177|PMID:41840688 UBERON:0001981 UBERON:0013191 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900013 cumulus oophorus oocyte complex A multicellular anatomical structure consisting of an oocyte surrounded by layers of cumulus oophorus cells (cumulus cells) within the ovarian follicle, released as a functional unit during ovulation and required for fertilization. https://doi.org/10.1210/er.2018-00085|https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://purl.org/ccf/ASCTB-TEMP_cumulus-oophorus-oocyte-complex|PMID:15219785|PMID:16944419|PMID:11315942 UBERON:0010000 UBERON:0001305 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg Wikipedia:Oocyte|Wikipedia:Cumulus_oophorus|FMA:18659 +http://purl.obolibrary.org/obo/UBERON_9900014 dominant antral follicle A tertiary ovarian follicle that has been selected for continued growth and maturation through preferential responsiveness to follicle-stimulating hormone, typically becoming the single follicle that will ovulate during a menstrual cycle. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://purl.org/ccf/ASCTB-TEMP_dominance-antral-follicle|PMID:16928805|PMID:11157797 UBERON:0000037 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovarian_follicle +http://purl.obolibrary.org/obo/UBERON_9900015 early antral follicle A tertiary ovarian follicle at the initial stage of antrum formation, characterized by the presence of small fluid-filled spaces between granulosa cells that have begun to coalesce. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://purl.org/ccf/ASCTB-TEMP_early-antral-follicle|PMID:18063620|PMID:11157797 UBERON:0000037 UBERON:0000036 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovarian_follicle +http://purl.obolibrary.org/obo/UBERON_9900017 lateral inferior antimesenteric ovary An anatomical subdivision of the ovary located in the lateral and inferior region, specifically on the antimesenteric side (the side opposite to the mesovarium, the peritoneal fold that attaches the ovary to the broad ligament). https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-antimesenteric-ovary|PMID:32123174|PMID:42435003 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovary +http://purl.obolibrary.org/obo/UBERON_9900018 lateral inferior mesenteric ovary An anatomical subdivision of the ovary located in the lateral and inferior region, specifically on the mesenteric side (the side adjacent to the mesovarium, the peritoneal fold that attaches the ovary to the broad ligament). https://purl.org/ccf/ASCTB-TEMP_lateral-inferior-mesenteric-ovary|PMID:32123174|PMID:42435003 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovary +http://purl.obolibrary.org/obo/UBERON_9900020 lateral ovary An organ part that is the lateral region of the ovary, comprising the outer aspect of the organ oriented away from the midline of the body. https://purl.org/ccf/ASCTB-TEMP_lateral-ovary|PMID:17999378|PMID:22666170 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900029 medial inferior ovary A spatial subdivision of the ovary representing the inferior (caudal) region of its medial (midline-facing) surface, defined by coordinate-based anatomical mapping rather than distinct histological or functional boundaries. https://purl.org/ccf/ASCTB-TEMP_medial-inferior-ovary|PMID:42479259 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovary +http://purl.obolibrary.org/obo/UBERON_9900030 medial ovary An organ part that is the medial region of the ovary, comprising the inner aspect of the organ oriented toward the midline of the body. https://purl.org/ccf/ASCTB-TEMP_medial-ovary|PMID:17999378|PMID:22666170 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900031 medial superior antimesenteric ovary An organ part of the ovary that is located in the medial and superior region on the antimesenteric side, which is the side opposite to the hilum where the ovarian ligament attaches to the uterus via the mesovarium. https://purl.org/ccf/ASCTB-TEMP_medial-superior-antimesenteric-ovary|PMID:41886635|PMID:41430284 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovary +http://purl.obolibrary.org/obo/UBERON_9900032 medial superior mesenteric ovary An organ part of the ovary that is located in the medial and superior region on the mesenteric side, which is the side adjacent to the hilum where the ovarian ligament and mesovarium attach and through which blood vessels and nerves enter the ovary. https://purl.org/ccf/ASCTB-TEMP_medial-superior-mesenteric-ovary|PMID:41886635|PMID:41430284 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovary +http://purl.obolibrary.org/obo/UBERON_9900033 medial superior ovary A spatial subdivision of the ovary representing the superior (cranial) region of its medial (midline-facing) surface, defined by coordinate-based anatomical mapping rather than distinct histological or functional boundaries. https://purl.org/ccf/ASCTB-TEMP_medial-superior-ovary|PMID:42479259 UBERON:0000064 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovary +http://purl.obolibrary.org/obo/UBERON_9900034 multilayer ovarian follicle An ovarian follicle characterized by the presence of two or more layers of granulosa cells surrounding the oocyte, representing a stage of folliculogenesis between primary and antral follicle development. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://doi.org/10.1210/er.2018-00085|https://purl.org/ccf/ASCTB-TEMP_multilayer-ovarian-follicle|PMID:39549739|PMID:19786400 UBERON:0000036 UBERON:0000035 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900035 ovarian corticomedullary junction An anatomical junction that is the boundary between the ovarian cortex and the ovarian medulla, located in the ovary. https://purl.org/ccf/ASCTB-TEMP_ovarian-corticomedullary-junction|PMID:42376416|PMID:42041081 UBERON:0007651 UBERON:0000992 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900036 ovarian medullary vasculature A vasculature that is part of the ovarian medulla. This network of blood vessels provides vascular supply to the highly vascularized stroma of the ovarian medulla and forms the tissue of the hilum through which blood vessels enter the ovary. https://purl.org/ccf/ASCTB-TEMP_ovarian-medullary-vasculature|PMID:23204433|PMID:22479331 UBERON:0002049 UBERON:0013192 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900037 pre-selection antral follicle A tertiary ovarian follicle in the stage prior to follicle selection, characterized by continued growth but not yet exhibiting the preferential responsiveness to gonadotropins that distinguishes the dominant follicle. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle|PMID:16928805|PMID:11157797 UBERON:0000037 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovarian_follicle +http://purl.obolibrary.org/obo/UBERON_9900038 pre-selection antral follicle A tertiary ovarian follicle in the stage prior to follicle selection, characterized by continued growth but not yet exhibiting the preferential responsiveness to gonadotropins that distinguishes the dominant follicle. https://purl.org/ccf/ASCTB-TEMP_pre-selection-antral-follicle|PMID:16928805|PMID:11157797 UBERON:0000037 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovarian_follicle +http://purl.obolibrary.org/obo/UBERON_9900039 preantral follicle A maturing ovarian follicle with multiple layers of granulosa cells that has not yet developed an antral cavity. https://purl.org/ccf/ASCTB-TEMP_preantral-follicle|PMID:42460665|PMID:42447034 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 FMA:18637 +http://purl.obolibrary.org/obo/UBERON_9900040 selection antral follicle A tertiary ovarian follicle undergoing the selection process during which one follicle becomes dominant through differential expression of gonadotropin receptors and enhanced responsiveness to follicle-stimulating hormone. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://purl.org/ccf/ASCTB-TEMP_selection-antral-follicle|PMID:16928805|PMID:11157797 UBERON:0000037 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Ovarian_follicle +http://purl.obolibrary.org/obo/UBERON_9900041 transitional primary ovarian follicle A primary ovarian follicle in an intermediate stage of development, characterized by granulosa cells transitioning from flattened to cuboidal morphology, representing the developmental transition from primordial to fully established primary follicle. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://doi.org/10.1210/er.2018-00085|https://purl.org/ccf/ASCTB-TEMP_transitional-primary-ovarian-follicle|PMID:39549739|PMID:10963874 UBERON:0000035 UBERON:0003981 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900042 transitional primordial ovarian follicle A primordial ovarian follicle in an early or transitional stage of development, representing the initial activation of dormant primordial follicles toward primary follicle formation. https://doi.org/10.1093/oxfordjournals.humrep.a136365|https://doi.org/10.1210/er.2018-00085|https://purl.org/ccf/ASCTB-TEMP_transitional-primordial-ovarian-follicle|PMID:39549739|PMID:10963874 UBERON:0003981 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9900043 pancreatic extracellular matrix An acellular anatomical structure that consists of a network of extracellular macromolecules and minerals, including collagen, enzymes, and glycoproteins, that provides structural and biochemical support to pancreatic cells. https://doi.org/10.48539/HBM336.TBNP.923|https://purl.org/ccf/ASCTB-TEMP_extracellular-matrix|PMID:42466389|PMID:41129097 UBERON:0000476 UBERON:0001264 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Extracellular_matrix +http://purl.obolibrary.org/obo/UBERON_9900044 small intestine connective tissue A connective tissue that forms the structural framework and support of the small intestine, comprising the lamina propria within the mucosa, the submucosa layer containing blood vessels and nerves, the serosa covering the outer surface, and the mesentery providing vascular support. PMID: 20126587|PMID: 3310649|https://purl.org/ccf/ASCTB-TEMP_connective-tissue UBERON:0002384 UBERON:0002108 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-07-23T00:00:00Z https://orcid.org/0000-0002-7073-9172 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Small_intestine