Skip to content

Commit 0870164

Browse files
Anita Caronanitacaron
Anita Caron
and
anitacaron
authored
Create README.md for each table (#191)
* move logs to dirs for each table * save error log in dict and add row_number to log * generate readme template * add term reports * generate readme reports * update logs * create readme reports Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com>
1 parent 0db6728 commit 0870164

320 files changed

Lines changed: 138505 additions & 6761 deletions

File tree

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎logs/Blood/Blood_AS_CT_strict_log.tsv‎

Lines changed: 27 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
1+
row_number s slabel user_slabel o olabel user_olabel
2+
25 CL:0000767 basophil basophil UBERON:0000178 Blood Blood
3+
24 CL:0000771 eosinophil eosinophil UBERON:0000178 Blood Blood
4+
23 CL:0000775 neutrophil neutrophil UBERON:0000178 Blood Blood
5+
13 CL:0000787 memory B cell memory B cell UBERON:0000178 Blood Blood
6+
14 CL:0000788 naive B cell naive B cell UBERON:0000178 Blood Blood
7+
37 CL:0000815 regulatory T cell T regulatory UBERON:0000178 Blood Blood
8+
12 CL:0000816 immature B cell immature B cell UBERON:0000178 Blood Blood
9+
15 CL:0000818 transitional stage B cell transitional B cell UBERON:0000178 Blood Blood
10+
36 CL:0000824 mature natural killer cell mature Natural killer UBERON:0000178 Blood Blood
11+
20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) UBERON:0000178 Blood Blood
12+
26 CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell CD4 naive UBERON:0000178 Blood Blood
13+
31 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood
14+
28 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood
15+
27 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood
16+
30 CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell CD8 naive UBERON:0000178 Blood Blood
17+
35 CL:0000938 CD16-negative, CD56-bright natural killer cell, human CD56 bright Natural killer UBERON:0000178 Blood Blood
18+
32 CL:0001050 effector CD8-positive, alpha-beta T cell CD8 T cell effector memory UBERON:0000178 Blood Blood
19+
21 CL:0001054 CD14-positive monocyte CD14 monocyte UBERON:0000178 Blood Blood
20+
19 CL:0001058 plasmacytoid dendritic cell, human Plasmacytoid Dendritic Cell (pDC) UBERON:0000178 Blood Blood
21+
33 CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CD8 T cell effector memory CD45RA UBERON:0000178 Blood Blood
22+
29 CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CD4 T cell effector memory CD45RA UBERON:0000178 Blood Blood
23+
16 CL:0002394 CD141-positive myeloid dendritic cell dendritic cell type 1 (DC1) UBERON:0000178 Blood Blood
24+
22 CL:0002396 CD14-low, CD16-positive monocyte CD16 monocyte UBERON:0000178 Blood Blood
25+
17 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 2 (DC2) UBERON:0000178 Blood Blood
26+
18 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 3 (DC3) UBERON:0000178 Blood Blood
27+
34 CL:0002437 mature CD8 single-positive thymocyte mature CD8 T cell UBERON:0000178 Blood Blood

‎logs/Blood/Blood_AS_has_part_CT_log.tsv‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
row_number s slabel user_slabel o olabel user_olabel

‎logs/Blood/README.md‎

Lines changed: 89 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,89 @@
1+
2+
ASCT+B Validation Reports for Blood (2022-11-29)
3+
================================================
4+
5+
Table of contents
6+
=================
7+
8+
* [Invalid terms](#invalid-terms)
9+
* [Terms not found](#terms-not-found)
10+
* [Typos or punctuation mistakes](#typos-or-punctuation-mistakes)
11+
* [Different labels](#different-labels)
12+
* [Blank ontology ID](#blank-ontology-id)
13+
* [Terms from another ontology](#terms-from-another-ontology)
14+
* [Relationship reports](#relationship-reports)
15+
* [Relationship AS-AS report](#relationship-as-as-report)
16+
* [Relationship CT-CT report](#relationship-ct-ct-report)
17+
* [Relationship CT-AS report](#relationship-ct-as-report)
18+
* [New CL terms](#new-cl-terms)
19+
* [New UBERON terms](#new-uberon-terms)
20+
* [Informative reports (valid relationships)](#informative-reports-valid-relationships)
21+
* [Indirect relationship](#indirect-relationship)
22+
* [Relationship AS has part CT](#relationship-as-has-part-ct)
23+
24+
# Invalid terms
25+
26+
27+
These are the reports related to issues in the terms found in the ASCT+B table. We validate only [CL](https://www.ebi.ac.uk/ols/ontologies/cl), [UBERON](https://www.ebi.ac.uk/ols/ontologies/uberon) and [PCL](https://www.ebi.ac.uk/ols/ontologies/pcl) terms.
28+
## Terms not found
29+
30+
31+
This report provides a list of terms not found neither in UBERON nor in CL. Please remove these terms from the ASCT+B table.
32+
33+
- No issues found.
34+
35+
36+
## Typos or punctuation mistakes
37+
38+
39+
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.
40+
41+
- No issues found.
42+
43+
44+
## Different labels
45+
46+
47+
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.
48+
49+
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.
50+
51+
If the name/label in the ontology contains *obsolete*, please look into OLS, clicking on the term ID, for its replacement.
52+
53+
- No issues found.
54+
55+
56+
## Blank ontology ID
57+
58+
59+
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](https://www.ebi.ac.uk/ols/index).
60+
61+
- No issues found.
62+
63+
64+
## Terms from another ontology
65+
66+
67+
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. Also Anatomic Ontology for Human Lung Maturation (LMHA). You can also request cross-database request the same way a new term request.
68+
69+
- No issues found.
70+
71+
72+
# Relationship reports
73+
74+
## Relationship AS-AS report
75+
[**Report**](../logs/Blood/class_Blood_log.tsv)
76+
## Relationship CT-CT report
77+
[**Report**](../logs/Blood/class_Blood_log.tsv)
78+
## Relationship CT-AS report
79+
[**Report**](../logs/Blood/Blood_AS__CT_strict_log.tsv)
80+
# New CL terms
81+
[**Report**](../logs/Blood/new_cl_terms_Blood.tsv)
82+
# New UBERON terms
83+
[**Report**](../logs/Blood/new_uberon_terms_Blood.tsv)
84+
# Informative reports (valid relationships)
85+
86+
## Indirect relationship
87+
[**Report**](../logs/Blood/class_Blood_indirect_log.tsv)
88+
## Relationship AS has part CT
89+
[**Report**](../logs/Blood/Blood_AS_has_part_CT_log.tsv)

‎logs/Blood/class_Blood_indirect_log.tsv‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
row_number s slabel user_slabel o olabel user_olabel
2+
13 CL:0000787 memory B cell memory B cell CL:0000945 lymphocyte of B lineage B lineage
3+
14 CL:0000788 naive B cell naive B cell CL:0000945 lymphocyte of B lineage B lineage
4+
37 CL:0000815 regulatory T cell T regulatory CL:0000084 T cell T lymphocytes
5+
12 CL:0000816 immature B cell immature B cell CL:0000945 lymphocyte of B lineage B lineage
6+
15 CL:0000818 transitional stage B cell transitional B cell CL:0000945 lymphocyte of B lineage B lineage
7+
26 CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell CD4 naive CL:0000084 T cell T lymphocytes
8+
27 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory CL:0000084 T cell T lymphocytes
9+
28 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory CL:0000084 T cell T lymphocytes
10+
31 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory CL:0000084 T cell T lymphocytes
11+
30 CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell CD8 naive CL:0000084 T cell T lymphocytes
12+
32 CL:0001050 effector CD8-positive, alpha-beta T cell CD8 T cell effector memory CL:0000084 T cell T lymphocytes
13+
33 CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CD8 T cell effector memory CD45RA CL:0000084 T cell T lymphocytes
14+
29 CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CD4 T cell effector memory CD45RA CL:0000084 T cell T lymphocytes
15+
22 CL:0002396 CD14-low, CD16-positive monocyte CD16 monocyte CL:0000576 monocyte monocyte
16+
34 CL:0002437 mature CD8 single-positive thymocyte mature CD8 T cell CL:0000084 T cell T lymphocytes

‎logs/Blood/class_Blood_log.tsv‎

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
row_number s slabel user_slabel o olabel user_olabel
2+
25 CL:0000767 basophil basophil UBERON:0000178 Blood Blood
3+
24 CL:0000771 eosinophil eosinophil UBERON:0000178 Blood Blood
4+
23 CL:0000775 neutrophil neutrophil UBERON:0000178 Blood Blood
5+
23 CL:0000775 neutrophil neutrophil CL:0000775 neutrophil neutrophilic granulocyte
6+
13 CL:0000787 memory B cell memory B cell UBERON:0000178 Blood Blood
7+
14 CL:0000788 naive B cell naive B cell UBERON:0000178 Blood Blood
8+
37 CL:0000815 regulatory T cell T regulatory UBERON:0000178 Blood Blood
9+
12 CL:0000816 immature B cell immature B cell UBERON:0000178 Blood Blood
10+
15 CL:0000818 transitional stage B cell transitional B cell UBERON:0000178 Blood Blood
11+
36 CL:0000824 mature natural killer cell mature Natural killer CL:0000814 mature NK T cell NK lymphocytes
12+
36 CL:0000824 mature natural killer cell mature Natural killer UBERON:0000178 Blood Blood
13+
20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) CL:0001056 dendritic cell, human dendritic cell (DC)
14+
20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) UBERON:0000178 Blood Blood
15+
26 CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell CD4 naive UBERON:0000178 Blood Blood
16+
27 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood
17+
28 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood
18+
31 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood
19+
30 CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell CD8 naive UBERON:0000178 Blood Blood
20+
35 CL:0000938 CD16-negative, CD56-bright natural killer cell, human CD56 bright Natural killer UBERON:0000178 Blood Blood
21+
35 CL:0000938 CD16-negative, CD56-bright natural killer cell, human CD56 bright Natural killer CL:0000814 mature NK T cell NK lymphocytes
22+
32 CL:0001050 effector CD8-positive, alpha-beta T cell CD8 T cell effector memory UBERON:0000178 Blood Blood
23+
21 CL:0001054 CD14-positive monocyte CD14 monocyte UBERON:0000178 Blood Blood
24+
19 CL:0001058 plasmacytoid dendritic cell, human Plasmacytoid Dendritic Cell (pDC) UBERON:0000178 Blood Blood
25+
33 CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CD8 T cell effector memory CD45RA UBERON:0000178 Blood Blood
26+
29 CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CD4 T cell effector memory CD45RA UBERON:0000178 Blood Blood
27+
16 CL:0002394 CD141-positive myeloid dendritic cell dendritic cell type 1 (DC1) UBERON:0000178 Blood Blood
28+
16 CL:0002394 CD141-positive myeloid dendritic cell dendritic cell type 1 (DC1) CL:0001056 dendritic cell, human dendritic cell (DC)
29+
22 CL:0002396 CD14-low, CD16-positive monocyte CD16 monocyte UBERON:0000178 Blood Blood
30+
17 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 2 (DC2) CL:0001056 dendritic cell, human dendritic cell (DC)
31+
18 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 3 (DC3) UBERON:0000178 Blood Blood
32+
18 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 3 (DC3) CL:0001056 dendritic cell, human dendritic cell (DC)
33+
17 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 2 (DC2) UBERON:0000178 Blood Blood
34+
34 CL:0002437 mature CD8 single-positive thymocyte mature CD8 T cell UBERON:0000178 Blood Blood

logs/new_cl_terms_Blood.tsv renamed to logs/Blood/new_cl_terms_Blood.tsv

File renamed without changes.

logs/new_uberon_terms_Blood.tsv renamed to logs/Blood/new_uberon_terms_Blood.tsv

File renamed without changes.

logs/report_images_Blood.tsv renamed to logs/Blood/report_images_Blood.tsv

File renamed without changes.

‎logs/Blood_AS_CT_strict_log.tsv‎

Lines changed: 0 additions & 25 deletions
This file was deleted.

‎logs/Blood_AS_has_part_CT_log.tsv‎

Lines changed: 0 additions & 1 deletion
This file was deleted.

0 commit comments

Comments
 (0)