Add HRA small-intestine NTR batch outputs and review reports

bulk_ntr_workflow/source_data/small-intestine.csv

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+tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_circular-longitudinal-muscle,circular/longitudinal muscle,,,https://purl.org/ccf/ASCTB-TEMP_muscularis-externa,muscularis externa,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_endoethlial,endoethlial,,,UBERON:0003332,submucosa of duodenum,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_epithelium,Epithelium,,,UBERON:0001213,intestinal villus,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_lamina-propria-gut-associated-lymphoid-tissue-galt-,Lamina propria/Gut associated lymphoid tissue (GALT),,,UBERON:0001213,intestinal villus,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_mucosa,mucosa,,,UBERON:0013644,duodenal ampulla,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_muscularis-externa,muscularis externa,,,UBERON:0002115,jejunum,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_muscularis-mucosa,muscularis mucosa,,,UBERON:0001213,intestinal villus,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_muscularis-propria,muscularis propria,,,UBERON:0013644,duodenal ampulla,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_myenteric-plexus-of-auerbach,myenteric plexus of Auerbach,,,UBERON:0012377,muscle layer of jejunum,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_serosa,serosa,,,UBERON:0013644,duodenal ampulla,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_submucosa,submucosa,,,UBERON:0013644,duodenal ampulla,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_submucosal-plexus-of-meissner,submucosal plexus of Meissner,,,UBERON:0003332,submucosa of duodenum,
+small-intestine,https://purl.org/ccf/ASCTB-TEMP_connective-tissue,connective tissue,,,UBERON:0003337,serosa of jejunum,"PMID: 20126587, PMID: 3310649"

src/templates/hra-small-intestine-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=|

src/templates/hra-small-intestine-reports/candidates.tsv

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+label	as_iri	uberon_id	note
+Epithelium		UBERON:0013636	confirmed_match (confidence: high)
+muscularis mucosa		UBERON:0006676	confirmed_match (confidence: high)
+muscularis externa		UBERON:0006660	confirmed_match (confidence: high)
+submucosal plexus of Meissner		UBERON:0005304	confirmed_match (confidence: high)
+connective tissue		UBERON:0002384	confirmed_match (confidence: high)
+myenteric plexus of Auerbach		UBERON:0002439	confirmed_match (confidence: high)
+mucosa		UBERON:0000344	confirmed_match (confidence: high)
+submucosa		UBERON:0000009	confirmed_match (confidence: high)
+serosa		UBERON:0000042	confirmed_match (confidence: high)
+muscularis propria		UBERON:0006660	confirmed_match (confidence: high)
+circular/longitudinal muscle		UBERON:0006660	possible_match (The term might be an informal reference to the muscularis externa/muscular coat, which typically contains both circular and longitudinal layers. However, the slash notation is non-standard and UBERON already has this parent term.)

src/templates/hra-small-intestine-reports/errors.tsv

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+label	as_iri	issue_type	parent_id	parent_label	detail
+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

src/templates/hra-small-intestine-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_circular-longitudinal-muscle	circular/longitudinal muscle		https://purl.org/ccf/ASCTB-TEMP_muscularis-externa	muscularis externa		leaf
+	https://purl.org/ccf/ASCTB-TEMP_endoethlial	endoethlial		UBERON:0003332	submucosa of duodenum		leaf
+	https://purl.org/ccf/ASCTB-TEMP_epithelium	Epithelium		UBERON:0001213	intestinal villus		leaf
+	https://purl.org/ccf/ASCTB-TEMP_lamina-propria-gut-associated-lymphoid-tissue-galt-	Lamina propria/Gut associated lymphoid tissue (GALT)		UBERON:0001213	intestinal villus		leaf
+	https://purl.org/ccf/ASCTB-TEMP_mucosa	mucosa		UBERON:0013644	duodenal ampulla		leaf
+	https://purl.org/ccf/ASCTB-TEMP_muscularis-externa	muscularis externa		UBERON:0002115	jejunum		leaf
+	https://purl.org/ccf/ASCTB-TEMP_muscularis-mucosa	muscularis mucosa		UBERON:0001213	intestinal villus		leaf
+	https://purl.org/ccf/ASCTB-TEMP_muscularis-propria	muscularis propria		UBERON:0013644	duodenal ampulla		leaf
+	https://purl.org/ccf/ASCTB-TEMP_myenteric-plexus-of-auerbach	myenteric plexus of Auerbach		UBERON:0012377	muscle layer of jejunum		leaf
+	https://purl.org/ccf/ASCTB-TEMP_serosa	serosa		UBERON:0013644	duodenal ampulla		leaf
+	https://purl.org/ccf/ASCTB-TEMP_submucosa	submucosa		UBERON:0013644	duodenal ampulla		leaf
+	https://purl.org/ccf/ASCTB-TEMP_submucosal-plexus-of-meissner	submucosal plexus of Meissner		UBERON:0003332	submucosa of duodenum		leaf
+	https://purl.org/ccf/ASCTB-TEMP_connective-tissue	connective tissue		UBERON:0003337	serosa of jejunum	PMID: 20126587, PMID: 3310649	leaf

src/templates/hra-small-intestine-reports/manual_curation.tsv

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+label	definition	reason	similar_terms	suggestion
+Lamina propria/Gut associated lymphoid tissue (GALT)	The connective tissue core of an intestinal villus containing blood vessels, a central lacteal, immune cells including lymphocytes, and in some regions gut-associated lymphoid tissue comprising organized lymphoid aggregates such as Peyer's patches and solitary lymphoid follicles.	This is a problematic compound term that conflates two related but distinct structures. Lamina propria (UBERON:0000030) is the general connective tissue layer, while GALT (UBERON:0001962) refers to specific organized lymphoid tissue. A villus-specific 'lamina propria of intestinal villus' term does not currently exist in UBERON but would be a reasonable addition. However, the compound naming with slash is non-standard and should be resolved.	UBERON:0000030=lamina propria; UBERON:0016606=lamina propria of small intestine; UBERON:0001962=gut-associated lymphoid tissue	Curator should either: (1) Create a new term 'lamina propria of intestinal villus' with intersection_of: UBERON:0000030 ! lamina propria AND part_of UBERON:0001213 ! intestinal villus, OR (2) Split this into two separate NTR entries - one for villus-specific lamina propria and maintain existing GALT term. The slash notation should not be preserved in the final ontology term name. Note that GALT is not present in all intestinal villi - it is concentrated in specific regions (ileum, Peyer's patches), so conflating it with lamina propria is anatomically imprecise.
+circular/longitudinal muscle	The combined circular and longitudinal smooth muscle layers of the muscularis externa. The inner circular layer narrows the lumen of the organ, while the outer longitudinal layer shortens its length, together enabling peristaltic movement.	Term name is non-standard. In UBERON and standard anatomical nomenclature, the circular and longitudinal muscle layers are distinct anatomical structures, not combined with a slash. UBERON has separate terms: UBERON:0012368 'circular muscle layer of muscular coat' and UBERON:0012369 'longitudinal muscle layer of muscular coat'. This term needs curator decision on whether to: (1) split into two separate NTRs for the circular and longitudinal layers, (2) treat as referring to the parent muscularis externa (UBERON:0006660) which already encompasses both layers, or (3) reject as malformed.	UBERON:0012368=circular muscle layer of muscular coat; UBERON:0012369=longitudinal muscle layer of muscular coat; UBERON:0006660=muscular coat; UBERON:0008857=stomach smooth muscle circular layer; UBERON:0008863=stomach smooth muscle outer longitudinal layer	Curator should verify the source data (ASCTB-TEMP) intent. If this refers to both layers collectively, it's redundant with UBERON:0006660 (muscular coat/muscularis externa). If it should be two separate terms, create NTRs for specific organ circular/longitudinal layers following the pattern of stomach layers shown above. The slash notation is not used in UBERON or standard anatomical nomenclature.

src/templates/hra-small-intestine-reports/name_corrections.tsv

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+source_label	corrected_label	reason
+Epithelium	epithelium of intestinal villus	The generic term 'Epithelium' (UBERON:0000483) is too broad. In the context of intestinal villus anatomy, this should be 'epithelium of intestinal villus' (UBERON:0013636), which is the specific epithelial layer covering the villus structure. Keep 'Epithelium' as an exact synonym if needed for ASCTB compatibility.
+Lamina propria/Gut associated lymphoid tissue (GALT)	Split into two separate terms OR clarify as 'lamina propria of intestinal villus (including GALT)'	This compound term with a slash represents TWO distinct but related anatomical structures: (1) lamina propria (UBERON:0000030) - the connective tissue core of the villus, and (2) gut-associated lymphoid tissue/GALT (UBERON:0001962) - organized lymphoid tissue that can be present within the lamina propria in certain intestinal regions. GALT is not universally present in all intestinal villi but is concentrated in specific areas like Peyer's patches. Standard anatomical nomenclature does not use slash notation for compound structures. Recommendation: either create separate NTR entries for 'lamina propria of intestinal villus' and maintain GALT as existing UBERON:0001962, OR clarify the term name to indicate GALT as a component that may be present within the villus lamina propria.
+endoethlial	endothelial (or more specifically, 'endothelium of [vessel type]')	The term 'endoethlial' is a non-standard spelling. The correct spelling would be 'endothelial' (adjective) or 'endothelium' (noun for the anatomical structure). However, beyond the spelling error, the term is too vague for UBERON - it needs to specify which vessel's endothelium is being described.
+circular/longitudinal muscle	Split into 'circular muscle layer' and 'longitudinal muscle layer', or map to existing 'muscular coat' (UBERON:0006660)	The slash notation combining two distinct anatomical layers is non-standard. In UBERON and TA98 (Terminologia Anatomica), the circular and longitudinal muscle layers of the muscularis externa are separate entities, each with specific structural and functional characteristics. The term should either be split into two separate NTR requests for the individual layers, or if referring to both collectively, should map to the existing 'muscular coat' term.

src/templates/hra-small-intestine-reports/out_of_scope.tsv

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+label	reason	suggestion
+muscularis mucosa	Anatomically incorrect placement. The muscularis mucosa is a smooth muscle layer located at the base of the intestinal mucosa, deep to the lamina propria and below the intestinal villi. It is NOT a component of the intestinal villus itself. Intestinal villi project upward from the mucosal surface, and the muscularis mucosa forms the deep boundary of the mucosa layer. This term should not be classified as 'part_of' intestinal villus.	Remove from this NTR group. Muscularis mucosa exists as UBERON:0006676 and has appropriate relationships to mucosa and gastrointestinal tract, but should not be linked to intestinal villus.
+endoethlial	This term is problematic for multiple reasons: (1) it appears to be a misspelling of 'endothelial', which is an adjective describing cells/tissue, not an anatomical structure; (2) even if corrected to 'endothelium', it is too vague without specifying which blood or lymphatic vessel in the submucosa; (3) UBERON requires specific anatomical structures with clear boundaries, not general cell-type descriptors; (4) if this refers to endothelial cells, those belong in the Cell Ontology (CL), not UBERON which covers anatomy.	This term should be rejected or the submitter should clarify what specific anatomical structure is intended. If they mean 'endothelium of [specific vessel type] in duodenal submucosa', that could be a valid term following UBERON's pattern (e.g., 'endothelium of capillary'). Without clarification, this is unsuitable for UBERON.

src/templates/hra-small-intestine.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=|