ASCT+B Validation Reports for Kidney (2024-11-20)

Invalid terms

These are the reports related to issues in the terms found in the ASCT+B table. We validate only CL, UBERON and PCL terms.

Terms not found

This report provides a list of terms not found neither in UBERON nor in CL. Please remove these terms from the ASCT+B table - disconsider this message if a term was recently added to the ontology.

No issues found.

Typos or punctuation mistakes

This report provides a general quality check of the terms used in the ASCT+B table. Typos, font case (upper case), punctuation mistakes in IDs: two colons, spaces, underscore instead of a colon.

No issues found.

Different labels

This report provides a list of terms having different names/labels found in the ontology and related to the one found in the ASCT+B table. Make sure to add the term's name/label in the column AS/N/LABEL or CT/N/LABEL. If the SME wants to give another name/label, please use the column AS/N or CT/N. N is the number in the column.

If the term's name/label and the name/label given by SME are too different, please make sure the term ID and its name/label are matching in OLS.

If the name/label in the ontology contains obsolete, please look into OLS, clicking on the term ID, for its replacement.

The term UBERON:8600037 has a different name/label in the source ontology in the following 2 rows 33, 33. The name/label in the ASCT+B table is long descending limb of the loop of Henle in the inner medulla and the one in the ontology is kidney loop of Henle long descending thin limb inner medulla. For reference, the given name/label by SMEs is descending thin limb of loop of Henle 3. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
The term CL:1000454 has a different name/label in the source ontology in the following 1 row 52. The name/label in the ASCT+B table is kidney collecting duct epithelial cell _ and the one in the ontology is _kidney collecting duct epithelial cell. For reference, the given name/label by SMEs is kidney collecting duct epithelial cell . Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
The term CL:0000653 has a different name/label in the source ontology in the following 2 rows 14, 20. The name/label in the ASCT+B table is glomerular visceral epithelial cell and the one in the ontology is podocyte. For reference, the given name/label by SMEs is Podocyte. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
The term CL:1000718 has a different name/label in the source ontology in the following 1 row 51. The name/label in the ASCT+B table is kidney inner medulla collecting duct and the one in the ontology is kidney inner medulla collecting duct principal cell. For reference, the given name/label by SMEs is Inner Medullary Collecting Duct Cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
The term UBERON:8600036 has a different name/label in the source ontology in the following 4 rows 17, 17, 32, 32. The name/label in the ASCT+B table is long descending limb of the loop of Henle in the outer medulla _ and the one in the ontology is _kidney loop of Henle long descending thin limb outer medulla. For reference, the given name/label by SMEs is descending thin limb of loop of Henle 2. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Blank ontology ID

This report provides a list of blank spreadsheet cells that often mean no ontology mapping found by the author. However, in some cases, a term with a synonym already exists. Please search in OLS.

You can find more information on the New CL terms or New UBERON terms reports.

No term id was found for the name/label capsule mesenchymal stromal cell in the following 1 row 12.
No term id was found for the name/label Transitional principal-intercalated cell in the following 1 row 52.
No term id was found for the name/label Kidney Lymphatic Vessel in the following 1 row 65.
No term id was found for the name/label Monocyte Derived Cell in the following 1 row 81.
No term id was found for the name/label Papillary Tip Epithelium in the following 1 row 89.

Blank ontology ID missing parent

This report provides a list of CT terms with blank ontology ID without an upper term from Cell Ontology. Please, create an upper level in the ASCT+B table and add an upper term for them. Please, make sure the term without ontology ID doesn't exist in the ontology.

No issues found.

Terms from another ontology

This report provides a list of terms from another ontologies that we do not validate. Foundational Model of Anatomy (FMA) ontology IDs are provided when an adequate term is not found in UBERON. Same case for Anatomic Ontology for Human Lung Maturation (LMHA) and Interlex IDs (ILX) from Stimulating Peripheral Activity to Relieve Conditions (SPARC). You can request cross-database request the same way a new term request. Please be sure if a term with a related synonym is already in the source ontologies CL or UBERON or PCL.

No issues found.

Relationship reports

These reports are other representations of the ASCT+B table. We split each row into pairs with adjacent terms, resulting in a table with two primary columns, object (o), left side and subject (s), right side. The experts' labels for the subject and object are in the columns user_slabel and user_olabel. The other columns are the subject label (s_label) and object label (o_label), the label from the source ontologies.

The report means it could not find a partonomy relationship in the source ontologies, but it doesn't mean this relationship is entirely invalid. In some cases, the pair is in the inverse order. In other cases, the relationship is missing in the source ontologies. Finally, how it was modelled in the ASCT+B table is not aligned with the ontologies sources and needs a more general discussion.

How to read a table entry

In the ASCT+B table

AS/2	AS/2/LABEL	AS/2/ID	AS/3	AS/3/LABEL	AS/3/ID
lens	lens	UBERON:0000965	ciliary zonules	suspensory ligament of lens	UBERON:0006762

In the Relationship Report

s	slabel	user_slabel	o	olabel	user_olabel
UBERON:0006762	suspensory ligament of lens	ciliary zonules	UBERON:0000965	lens	lens

Relationship AS-AS report

This table contains terms for anatomical structures that are related to each other according to the ASCT+B table but are not related to each other in source ontologies via one of the relation types we consider valid for ASCT+B tables. Valid relationships are: part_of, e.g. corneal endothelium part_of cornea; subClassOf, e.g. left kidney subClassOf (is_a) kidney; and overlaps (has some part in), e.g. ureter overlaps kidney; connected_to, e.g. TBA. part_of and subClassOf relationships should be specific to general, e.g. left kidney (specific) to kidney (general); corneal endothelium (specific) to cornea (general). The deltaIC score is included because a high score (>50) can indicate that this order is reversed, e.g. TBA.

	s	slabel	user_slabel	o	olabel	user_olabel	row_number	deltaIC
0	UBERON:0001986	endothelium	Endothelium (non glomerular)	UBERON:0009091	vasa recta ascending limb	Ascending Vasa Recta	64	38.4232
1	UBERON:0001986	endothelium	Endothelium (non glomerular)	UBERON:0009202	vasa recta descending limb	Descending Vasa Recta	63	38.4232
3	UBERON:0004188	glomerular epithelium	Glomerular Epithelium	UBERON:0002189	outer cortex of kidney	outer cortex of kidney	13	24.2273
4	UBERON:0004188	glomerular epithelium	Glomerular Epithelium	UBERON:0005271	juxtamedullary cortex	juxtamedullary cortex	14	24.2273
5	UBERON:0004188	glomerular epithelium	Glomerular Epithelium	UBERON:0001284	renal column	renal column (column of Bertin)	20	24.2273
6	UBERON:0004640	renal efferent arteriole	Efferent Arteriole	UBERON:0034884	juxtaglomerular arteriole	Juxtaglomerular Arteriole	61	16.3758
7	UBERON:0004639	renal afferent arteriole	Afferent Arteriole	UBERON:0034884	juxtaglomerular arteriole	Juxtaglomerular Arteriole	60	15.8024
10	UBERON:0001986	endothelium	Endothelium (non glomerular)	UBERON:0003517	kidney blood vessel	Kidney Blood Vessel	59	14.8995
11	UBERON:0001289	descending limb of loop of Henle	Loop of Henle (Thin Limb)	UBERON:0004201	kidney outer medulla inner stripe	kidney outer medulla inner stripe	17	7.83951
12	UBERON:0004203	cortical collecting duct	Collecting Duct (Cortex)	UBERON:0009883	medullary ray	medullary ray	15	4.56793
16	UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/Medulla)	UBERON:0004202	kidney outer medulla outer stripe	kidney outer medulla outer stripe	16	1.20152
17	UBERON:0002335	macula densa	Macula Densa	UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/ Cortex)	38	1.01587
18	UBERON:8600036	kidney loop of Henle long descending thin limb outer medulla	descending thin limb of loop of Henle 2	UBERON:0001289	descending limb of loop of Henle	Loop of Henle (Thin Limb)	17	nan
20	UBERON:0009202	vasa recta descending limb	Descending Vasa Recta	UBERON:0001294	inner medulla of kidney	inner medulla of kidney	18	nan
22	UBERON:0001284	renal column	renal column (column of Bertin)	UBERON:0001225	cortex of kidney	renal cortex	20	nan
23	UBERON:0009202	vasa recta descending limb	Descending Vasa Recta	UBERON:0004200	kidney pyramid	renal pyramid	21	nan
24	UBERON:0005215	kidney interstitium	Interstitium	UBERON:0001229	Renal Corpuscle	Renal Corpuscle	25	nan
25	UBERON:0005099	short descending thin limb	descending thin limb of loop of Henle 1	UBERON:0001289	descending limb of loop of Henle	Loop of Henle (Thin Limb)	31	nan
26	UBERON:8600036	kidney loop of Henle long descending thin limb outer medulla	descending thin limb of loop of Henle 2	UBERON:0001289	descending limb of loop of Henle	Loop of Henle (Thin Limb)	32	nan
28	UBERON:8600037	kidney loop of Henle long descending thin limb inner medulla	descending thin limb of loop of Henle 3	UBERON:0001289	descending limb of loop of Henle	Loop of Henle (Thin Limb)	33	nan
30	UBERON:0001232	collecting duct of renal tubule	Collecting Duct	UBERON:0001232	collecting duct of renal tubule	Tubules	47	nan
31	UBERON:0001232	collecting duct of renal tubule	Collecting Duct	UBERON:0001232	collecting duct of renal tubule	Tubules	48	nan
32	UBERON:0001232	collecting duct of renal tubule	Collecting Duct	UBERON:0001232	collecting duct of renal tubule	Tubules	52	nan
33	UBERON:0001232	collecting duct of renal tubule	Collecting Duct	UBERON:0001232	collecting duct of renal tubule	Tubules	53	nan
34	UBERON:0001232	collecting duct of renal tubule	Collecting Duct	UBERON:0001232	collecting duct of renal tubule	Tubules	54	nan
35	UBERON:0001232	collecting duct of renal tubule	Collecting Duct	UBERON:0001232	collecting duct of renal tubule	Tubules	57	nan
36	UBERON:0004726	vasa recta	Vasa Recta	UBERON:0006544	kidney vasculature	Vessels	63	nan
37	UBERON:0004726	vasa recta	Vasa Recta	UBERON:0006544	kidney vasculature	Vessels	64	nan
39	UBERON:0002303	juxtaglomerular apparatus	Juxtaglomerular Apparatus	UBERON:0003517	kidney blood vessel	Kidney Blood Vessel	68	nan

Relationship CT-CT report

In the case of the CT-CT relationship, for each couple of terms, we verify for sub class of, part of and overlaps in the source ontologies. The deltaIC score is included because a high score (>50) can indicate that this order is reversed, e.g. TBA.

No issues found.

Relationship CT-AS report

In the case of the AS-CT relationship, for each couple of terms, we verify for connected to and has part in the source ontologies.

	s	slabel	user_slabel	o	olabel	user_olabel	row_number	deltaIC
2	CL:0000499	stromal cell	stromal cell	UBERON:0002015	kidney capsule	kidney capsule	12	25.373
8	CL:0000084	T cell	T Cell	UBERON:0005215	kidney interstitium	Interstitium	82	15.5037
9	CL:0000236	B cell	B cell	UBERON:0005215	kidney interstitium	Interstitium	85	15.4644
13	CL:0000576	monocyte	Monocyte	UBERON:0005215	kidney interstitium	Interstitium	80	3.87359
14	CL:0000623	natural killer cell	Natural Killer Cell	UBERON:0005215	kidney interstitium	Interstitium	75	1.97773
15	CL:0000775	neutrophil	Neutrophil	UBERON:0005215	kidney interstitium	Interstitium	87	1.66534
19	CL:4030013	kidney loop of Henle long descending thin limb outer medulla epithelial cell	Descending Thin Limb Cell Type 2	UBERON:8600036	kidney loop of Henle long descending thin limb outer medulla	descending thin limb of loop of Henle 2	17	nan
21	CL:1000718	kidney inner medulla collecting duct principal cell	Inner Medullary Collecting Duct Cell	UBERON:0009095	tip of renal papilla	papillary tip	19	nan
27	CL:4030013	kidney loop of Henle long descending thin limb outer medulla epithelial cell	Descending Thin Limb Cell Type 2	UBERON:8600036	kidney loop of Henle long descending thin limb outer medulla	descending thin limb of loop of Henle 2	32	nan
29	CL:4030014	kidney loop of Henle long descending thin limb inner medulla epithelial cell	Descending Thin Limb Cell Type 3	UBERON:8600037	kidney loop of Henle long descending thin limb inner medulla	descending thin limb of loop of Henle 3	33	nan
38	CL:1001318	renal interstitial pericyte	Vascular Smooth Muscle Cell/Pericyte (general)	UBERON:0003517	kidney blood vessel	Kidney Blood Vessel	66	nan
40	CL:0000875	non-classical monocyte	non Classical Monocyte	UBERON:0005215	kidney interstitium	Interstitium	74	nan
41	CL:0000814	mature NK T cell	Natural Killer T Cell	UBERON:0005215	kidney interstitium	Interstitium	76	nan
42	CL:0001056	dendritic cell, human	Dendritic Cell (general)	UBERON:0005215	kidney interstitium	Interstitium	77	nan
43	CL:0001058	plasmacytoid dendritic cell, human	Dendritic Cell (plasmatoid)	UBERON:0005215	kidney interstitium	Interstitium	79	nan
44	CL:0000910	cytotoxic T cell	Cytotoxic T Cell	UBERON:0005215	kidney interstitium	Interstitium	83	nan
45	CL:0000815	regulatory T cell	regulatory T cell	UBERON:0005215	kidney interstitium	Interstitium	84	nan
46	CL:0000786	plasma cell	Plasma cell	UBERON:0005215	kidney interstitium	Interstitium	86	nan
47	CL:0000097	mast cell	Mast cell	UBERON:0005215	kidney interstitium	Interstitium	88	nan

ASCT+B Validation Reports for Kidney (2024-11-20)

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