ASCT+B Validation Reports for Lymph_node (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 CL:0000669 has a different name/label in the source ontology in the following 1 row 92. The name/label in the ASCT+B table is pericyte cell and the one in the ontology is pericyte. For reference, the given name/label by SMEs is Pericyte. 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 issues found.

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
7	UBERON:0001473	lymphatic vessel	Lymphatic Vessels	UBERON:0010396	afferent lymphatic vessel	Afferent lymphatic vessel	18	29.5992
8	UBERON:0001473	lymphatic vessel	Lymphatic Vessels	UBERON:0010396	afferent lymphatic vessel	Afferent lymphatic vessel	19	29.5992
14	UBERON:0034729	sympathetic nerve	Sympathetic nerve	UBERON:0035495	hilum of lymph node	Hilum	96	24.9383
37	UBERON:0010397	efferent lymphatic vessel	Efferent Lymphatics	UBERON:0035495	hilum of lymph node	Hilum	94	11.8079
38	UBERON:0010397	efferent lymphatic vessel	Efferent Lymphatics	UBERON:0035495	hilum of lymph node	Hilum	95	11.8079
46	UBERON:8410034	lymph node artery	Lymphatic Artery	UBERON:0035495	hilum of lymph node	Hilum	97	4.56793
49	UBERON:8410042	arteriole of lymph node	Arteriole	UBERON:0002194	capsule of lymph node	Capsule	13	nan
50	UBERON:8410041	venule of lymph node	Venule	UBERON:0002194	capsule of lymph node	Capsule	14	nan
51	UBERON:0002195	trabecula of lymph node	Trabeculae	UBERON:0002194	capsule of lymph node	Capsule	15	nan
52	UBERON:0002195	trabecula of lymph node	Trabeculae	UBERON:0002194	capsule of lymph node	Capsule	16	nan
53	UBERON:8410042	arteriole of lymph node	Arteriole	UBERON:0002195	trabecula of lymph node	Trabeculae	16	nan
54	UBERON:0002195	trabecula of lymph node	Trabeculae	UBERON:0002194	capsule of lymph node	Capsule	17	nan
55	UBERON:8410041	venule of lymph node	Venule	UBERON:0002195	trabecula of lymph node	Trabeculae	17	nan
56	UBERON:0010396	afferent lymphatic vessel	Afferent lymphatic vessel	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	18	nan
57	UBERON:0010396	afferent lymphatic vessel	Afferent lymphatic vessel	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	19	nan
59	UBERON:8410071	subcapsular sinus ceiling	Subcapsular sinus ceiling	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	22	nan
60	UBERON:8410072	subcapsular sinus floor	Subcapsular sinus floor	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	23	nan
61	UBERON:8410032	trabecular sinus of lymph node	Trabecular sinus	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	24	nan
63	UBERON:8410041	venule of lymph node	Venule	UBERON:0002006	cortex of lymph node	Cortex	25	nan
64	UBERON:8410042	arteriole of lymph node	Arteriole	UBERON:0002006	cortex of lymph node	Cortex	26	nan
71	UBERON:8410042	arteriole of lymph node	Arteriole	UBERON:8410066	lymph node paracortex	Paracortex	58	nan
72	UBERON:0006842	lymphatic capillary	capillaries of lymph node	UBERON:8410066	lymph node paracortex	Paracortex	59	nan
73	UBERON:8410038	high endothelial venule of lymph node	High Endothelial Venule	UBERON:8410066	lymph node paracortex	Paracortex	60	nan
84	UBERON:8410034	lymph node artery	Lymphatic Artery	UBERON:0002007	medulla of lymph node	Medulla	90	nan
85	UBERON:8410033	lymph node vein	Hilar Vein	UBERON:0002007	medulla of lymph node	Medulla	91	nan
86	UBERON:8410036	medullary venule of lymph node	Venule	UBERON:8410033	lymph node vein	Hilar Vein	91	nan
88	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	UBERON:0002007	medulla of lymph node	Medulla	93	nan
92	UBERON:8410033	lymph node vein	Hilar Vein	UBERON:0035495	hilum of lymph node	Hilum	98	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
0	CL:0000236	B cell	B Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	78	44.3425
1	CL:0000071	blood vessel endothelial cell	Blood Vessel Endothelial Cell	UBERON:0006842	lymphatic capillary	capillaries of lymph node	59	35.923
2	CL:0000451	dendritic cell	Dendritic Cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	52	35.3624
3	CL:0000451	dendritic cell	Dendritic Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	63	35.3624
4	CL:0000235	macrophage	Macrophage	UBERON:8410074	lymph node paracortical sinus	Paracortical Sinus	57	35.3006
5	CL:0000623	natural killer cell	Natural Killer Cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	50	30.8558
6	CL:0000623	natural killer cell	Natural Killer Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	74	30.8558
9	CL:0000798	gamma-delta T cell	Gamma/Delta T cells	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	69	29.5062
10	CL:0000097	mast cell	Mast Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	75	28.5401
11	CL:0000786	plasma cell	Plasma Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	76	26.2879
12	CL:0000815	regulatory T cell	T Regulatory Cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	46	26.1647
13	CL:0000815	regulatory T cell	T Regulatory Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	70	26.1647
15	CL:0000909	CD8-positive, alpha-beta memory T cell	Memory CD8+ T cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	73	23.6158
16	CL:0000909	CD8-positive, alpha-beta memory T cell	Memory CD8+ T cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	49	23.6158
17	CL:0000897	CD4-positive, alpha-beta memory T cell	Memory CD4+ T cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	42	23.2392
18	CL:0002138	endothelial cell of lymphatic vessel	Lymphatic Endothelial Cell	UBERON:8410074	lymph node paracortical sinus	Paracortical Sinus	55	23.2392
19	CL:0000897	CD4-positive, alpha-beta memory T cell	Memory CD4+ T cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	65	23.2392
20	CL:0000980	plasmablast	Plasmablast	UBERON:8410052	lymph node germinal center light zone	Light Zone	36	21.3433
21	CL:0000895	naive thymus-derived CD4-positive, alpha-beta T cell	Naive CD4+ T cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	41	20.0638
22	CL:0000895	naive thymus-derived CD4-positive, alpha-beta T cell	Naive CD4+ T cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	64	20.0638
23	CL:0000545	T-helper 1 cell	Th1 cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	66	19.4042
24	CL:0000545	T-helper 1 cell	Th1 cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	43	19.4042
25	CL:0000900	naive thymus-derived CD8-positive, alpha-beta T cell	Naive CD8+ T cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	72	19.0479
26	CL:0000900	naive thymus-derived CD8-positive, alpha-beta T cell	Naive CD8+ T cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	48	19.0479
27	CL:0000669	pericyte	Pericyte	UBERON:8410041	venule of lymph node	Venule	17	18.9743
28	CL:0000546	T-helper 2 cell	Th2 cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	67	18.2717
29	CL:0000546	T-helper 2 cell	Th2 cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	44	18.2717
30	CL:0000235	macrophage	Macrophage	UBERON:0010395	lymph node primary follicle	Primary Follicle	30	17.9089
31	CL:0000899	T-helper 17 cell	Th17 cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	45	17.3917
32	CL:0000899	T-helper 17 cell	Th17 cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	68	17.3917
33	CL:0000787	memory B cell	Memory B Cell	UBERON:0010420	lymph node germinal center mantle zone	Mantle Zone	40	17.0289
34	CL:0000910	cytotoxic T cell	T Cytotoxic Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	71	15.8024
35	CL:0000910	cytotoxic T cell	T Cytotoxic Cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	47	15.8024
36	CL:0000442	follicular dendritic cell	Follicular Dendritic Cell	UBERON:8410052	lymph node germinal center light zone	Light Zone	31	13.7038
39	CL:0002038	T follicular helper cell	T Follicular Helper Cell	UBERON:8410052	lymph node germinal center light zone	Light Zone	33	11.8079
40	CL:0000788	naive B cell	Naive B Cell	UBERON:0010420	lymph node germinal center mantle zone	Mantle Zone	39	10.2684
41	CL:0000787	memory B cell	Memory B Cell	UBERON:0010395	lymph node primary follicle	Primary Follicle	29	8.773
42	CL:0000084	T Cell	T Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	81	8.2637
43	CL:0000084	T Cell	T Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	82	8.2637
44	CL:0000236	B cell	B Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	85	8.22441
45	CL:0000186	myofibroblast cell	Myofibroblast	UBERON:0002195	trabecula of lymph node	Trabeculae	15	4.56793
47	CL:0000442	follicular dendritic cell	Follicular Dendritic Cell	UBERON:0010395	lymph node primary follicle	Primary Follicle	27	0.879988
48	CL:0000186	myofibroblast cell	Myofibroblast	UBERON:0002194	capsule of lymph node	Capsule	12	nan
58	CL:0000887	lymph node subcapsular sinus macrophage	Macrophage	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	20	nan
62	CL:0009109	lymphatic endothelial cell of trabecula	Lymphatic Endothelial Cell-Trabeculae	UBERON:8410032	trabecular sinus of lymph node	Trabecular sinus	24	nan
65	CL:0009113	T follicular regulatory cell	T Follicular Regulatory Cell	UBERON:8410052	lymph node germinal center light zone	Light Zone	34	nan
66	CL:0000888	lymph node tingible body macrophage	Tingible Body Macrophage	UBERON:8410052	lymph node germinal center light zone	Light Zone	35	nan
67	CL:0009105	T cell zone reticular cell	T Cell Zone Reticular Cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	51	nan
68	CL:0009113	T follicular regulatory cell	T Follicular Regulatory Cell	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	53	nan
69	CL:0002399	CD1c-positive myeloid dendritic cell	Conventional Dendritic Cell cDC2	UBERON:8410067	lymph node interfollicular cortex	Interfollicular Cortex	54	nan
70	CL:0009105	T cell zone reticular cell	T Cell Zone Reticular Cell	UBERON:8410074	lymph node paracortical sinus	Paracortical Sinus	56	nan
74	CL:0001058	plasmacytoid dendritic cell, human	Plasmacytoid Dendritic Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	61	nan
75	CL:0002394	CD141-positive myeloid dendritic cell	Conventional Dendritic Cell cDC1	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	62	nan
76	CL:0009114	monocytoid B Cell	Monocytoid B Cell	UBERON:8410075	lymph node paracortical cord	Paracortical Cord	77	nan
77	CL:0009106	medullary reticular cell	Medullary Reticular Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	80	nan
78	CL:0002138	endothelial cell of lymphatic vessel	Lymphatic Endothelial Cell	UBERON:0009744	lymph node medullary sinus	Medullary Sinus	83	nan
79	CL:0000786	plasma cell	Plasma Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	84	nan
80	CL:0000097	mast cell	Mast Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	86	nan
81	CL:0000235	macrophage	Macrophage	UBERON:0009745	lymph node medullary cord	Medullary Cord	87	nan
82	CL:0000980	plasmablast	Plasmablast	UBERON:0009745	lymph node medullary cord	Medullary Cord	88	nan
83	CL:0000451	dendritic cell	Dendritic Cell	UBERON:0009745	lymph node medullary cord	Medullary Cord	89	nan
87	CL:0000669	pericyte	Pericyte	UBERON:0002007	medulla of lymph node	Medulla	92	nan
89	CL:0009110	lymphatic endothelial cell of medulla ceiling	Lymphatic Endothelial Cell of Medulla Ceiling	UBERON:0005463	subcapsular sinus of lymph node	Subcapsular Sinus	93	nan
90	CL:0019017	lymphatic vessel smooth muscle cell	Smooth Muscle Cell	UBERON:0010397	efferent lymphatic vessel	Efferent Lymphatics	95	nan
91	CL:0011103	sympathetic neuron	Sympathetic Neuron	UBERON:0034729	sympathetic nerve	Sympathetic nerve	96	nan

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

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