ccf-validation-tools/Fallopian_tube/comments/

[giscus[bot]]

ccf-validation-tools/Fallopian_tube/comments/

https://hubmapconsortium.github.io/ccf-validation-tools/Fallopian_tube/comments/

[aleixpuigb]

New Term in CL
Rows 104, 108, 112, 116 and 117: Peg cell (intercalary cell) - CL:4033014

[emquardokus]

Fallopian_Tube_v1.2_DRAFT
https://docs.google.com/spreadsheets/d/16DHu7R9MC2B_fP7uRiDYcDIUvFs6SwHmZWgwpzuJwfI/edit#gid=991519552

Edits 9-13-2023 2:30 am Eastern Ellen
Different labels
Fixed In row 44, the term UBERON:0012648 has different name/label in the source ontology. The name/label in the ASCT+B table is __ and the one in the ontology is ampulla of uterine tube. For reference, the given name/label by SMEs is ampulla of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Fixed In row 83, the term UBERON:8410010 has different name/label in the source ontology. The name/label in the ASCT+B table is __ and the one in the ontology is fimbria of uterine tube. For reference, the given name/label by SMEs is fimbria of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Fixed n row 28, the term UBERON:0003889 has different name/label in the source ontology. The name/label in the ASCT+B table is __ and the one in the ontology is fallopian tube. For reference, the given name/label by SMEs is Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Fixed In row 28, the term UBERON:0016632 has different name/label in the source ontology. The name/label in the ASCT+B table is __ and the one in the ontology is isthmus of fallopian tube. For reference, the given name/label by SMEs is isthmus of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Fixed In row 76, the term UBERON:0012331 has different name/label in the source ontology. The name/label in the ASCT+B table is __ and the one in the ontology is mesosalpinx. For reference, the given name/label by SMEs is mesosalpinx. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Fixed In row 60, the term UBERON:0003984 has different name/label in the source ontology. The name/label in the ASCT+B table is __ and the one in the ontology is uterine tube infundibulum. For reference, the given name/label by SMEs is infundibulum of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Blank ontology ID
ADDED CL ID: fibroblast CL:0000057
In row 13, no term id was found for the name/label Fibroblast.
In row 29, no term id was found for the name/label Fibroblast.
In row 45, no term id was found for the name/label Fibroblast.
In row 61, no term id was found for the name/label Fibroblast.
In row 84, no term id was found for the name/label Fibroblast.

ADDED CL ID: macrophage CL:0000235
In row 15, no term id was found for the name/label macrophage.
In row 31, no term id was found for the name/label macrophage.
In row 47, no term id was found for the name/label macrophage.
In row 63, no term id was found for the name/label macrophage.
In row 86, no term id was found for the name/label macrophage.

ADDED CL ID: CD8-positive, alpha-beta T cell CL:0000625
In row 16, no term id was found for the name/label CD8+ T-cells.
In row 32, no term id was found for the name/label CD8+ T-cells.
In row 48, no term id was found for the name/label CD8+ T-cells.
In row 64, no term id was found for the name/label CD8+ T-cells.
In row 87, no term id was found for the name/label CD8+ T-cells.

ADDED CL ID: natural killer cell CL:0000623
In row 17, no term id was found for the name/label Natural killer cell.
In row 33, no term id was found for the name/label Natural killer cell.
In row 49, no term id was found for the name/label Natural killer cell.
In row 65, no term id was found for the name/label Natural killer cell.
In row 88, no term id was found for the name/label Natural killer cell.

ADDED CL ID: CD4-positive, alpha-beta T cell CL:0000624
In row 18, no term id was found for the name/label CD4+ T-cell.
In row 34, no term id was found for the name/label CD4+ T-cell.
In row 50, no term id was found for the name/label CD4+ T-cell.
In row 66, no term id was found for the name/label CD4+ T-cell.
In row 89, no term id was found for the name/label CD4+ T-cell.

ADDED CL ID: Langerhans cell CL:0000453
In row 19, no term id was found for the name/label Langerhans cell.
In row 35, no term id was found for the name/label Langerhans cell.
In row 51, no term id was found for the name/label Langerhans cell.
In row 67, no term id was found for the name/label Langerhans cell.
In row 90, no term id was found for the name/label Langerhans cell.

ADDED CL ID: monocyte CL:0000576
In row 20, no term id was found for the name/label monocyte.
In row 36, no term id was found for the name/label monocyte.
In row 52, no term id was found for the name/label monocyte.
In row 68, no term id was found for the name/label monocyte.
In row 91, no term id was found for the name/label monocyte.

ADDED CL ID: dendritic cell CL:0000451
In row 21, no term id was found for the name/label dendritic cell.
In row 37, no term id was found for the name/label dendritic cell.
In row 53, no term id was found for the name/label dendritic cell.
In row 69, no term id was found for the name/label dendritic cell.
In row 92, no term id was found for the name/label dendritic cell.

ADDED CL ID: mast cell CL:0000097
In row 22, no term id was found for the name/label mast cell.
In row 38, no term id was found for the name/label mast cell.
In row 54, no term id was found for the name/label mast cell.
In row 70, no term id was found for the name/label mast cell.
In row 93, no term id was found for the name/label mast cell.

ADDED CL ID: B cell CL:0000236
In row 23, no term id was found for the name/label B cell.
In row 39, no term id was found for the name/label B cell.
In row 55, no term id was found for the name/label B cell.
In row 71, no term id was found for the name/label B cell.
In row 94, no term id was found for the name/label B cell.

ADDED CL ID: plasma cell CL:0000786
In row 24, no term id was found for the name/label plasma cell.
In row 40, no term id was found for the name/label plasma cell.
In row 56, no term id was found for the name/label plasma cell.
In row 72, no term id was found for the name/label plasma cell.
In row 95, no term id was found for the name/label plasma cell.

ADDED CL ID: neutrophil CL:0000775
In row 25, no term id was found for the name/label neutrophil.
In row 41, no term id was found for the name/label neutrophil.
In row 57, no term id was found for the name/label neutrophil.
In row 73, no term id was found for the name/label neutrophil.
In row 96, no term id was found for the name/label neutrophil.

ADDED CL ID: endothelial cell CL:0000115
In row 27, no term id was found for the name/label Endothelial cell.
In row 43, no term id was found for the name/label Endothelial cell.
In row 59, no term id was found for the name/label Endothelial cell.
In row 75, no term id was found for the name/label Endothelial cell.
In row 98, no term id was found for the name/label Endothelial cell.

ADDED CL ID: epithelial cell CL:0000066
In row 76, no term id was found for the name/label epithelial cell.

replaced intercalary cell. with peg cell CL:4033014
In row 104, no term id was found for the name/label intercalary cell.
In row 108, no term id was found for the name/label intercalary cell.
In row 112, no term id was found for the name/label intercalary cell.
In row 116, no term id was found for the name/label intercalary cell.
In row 117, no term id was found for the name/label intercalary cell.

replaced ciliated epithelial cell with fallopian tube ciliated cell CL:4030007
In row 121, no term id was found for the name/label ciliated epithelial cell.
In row 123, no term id was found for the name/label ciliated epithelial cell.
In row 125, no term id was found for the name/label ciliated epithelial cell.
In row 127, no term id was found for the name/label ciliated epithelial cell.
In row 129, no term id was found for the name/label ciliated epithelial cell.

replaced secretory epithelial cell with fallopian tube secretory epithelial cell CL:4030006
In row 122, no term id was found for the name/label secretory epithelial cell.
In row 124, no term id was found for the name/label secretory epithelial cell.
In row 128, no term id was found for the name/label secretory epithelial cell.
In row 130, no term id was found for the name/label secretory epithelial cell.

fixed all DOIs
DOI: to doi:
Removed doi.org prefix

Mapped all genes and proteins to HGNC
CD3E CD3 epsilon subunit of T-cell receptor complex HGNC:1674
CD79A CD79a molecule HGNC:1698
CLDN5 claudin 5 HGNC:2047
DCN decorin HGNC:2705
FOXJ1 forkhead box J1 HGNC:3816
JCHAIN joining chain of multimeric IgA and IgM HGNC:5713
KLRC1 killer cell lectin like receptor C1 HGNC:6374
LYZ lysozyme HGNC:6740
PAX8 paired box 8 HGNC:8622
ACTA2 actin alpha 2, smooth muscle HGNC:130
TPSAB1 tryptase alpha/beta 1 HGNC:12019
DES desmin HGNC:2770
OVGP1 oviductal glycoprotein 1 HGNC:8524
ENG endoglin HGNC:3349 CD105
ITGAX integrin subunit alpha X HGNC:6152 CD11c
CD163 CD163 molecule HGNC:1631
CD207 CD207 molecule HGNC:17935
CD44 CD44 molecule (Indian blood group) HGNC:1681
CD56 neural cell adhesion molecule 1 HGNC:7656
FCGR1A Fc gamma receptor Ia HGNC:3613 CD64
NT5E 5'-nucleotidase ecto HGNC:8021 CD73
THY1 Thy-1 cell surface antigen HGNC:11801 CD90
EPCAM epithelial cell adhesion molecule HGNC:11529
HLA-DRA major histocompatibility complex, class II, DR alpha HGNC:4947 HLA-DR
ITGA6 integrin subunit alpha 6 HGNC:6142
VEGF vascular endothelial growth factor A HGNC:12680

[anitacaron]

Thank you so much for this effort, Ellen!

[emquardokus]

Fallopian_Tube_v1.2_DRAFT
https://docs.google.com/spreadsheets/d/16DHu7R9MC2B_fP7uRiDYcDIUvFs6SwHmZWgwpzuJwfI/edit#gid=991519552

Blank ontology ID missing parent

ADDED mesenchymal cell CL:0008019 as CT/1 In row 14, 30, 48, 62, 85 the term fibroblast-mesenchymal cell without ontology ID has no parent that is from the CL ontology.

[emquardokus]

Fallopian_Tube_v1.4_DRAFT
https://docs.google.com/spreadsheets/d/1yCfVQmd3-R8wEN6qolpBT3w7hN2ug6pHyoxnM4i-sws/edit?gid=991519552#gid=991519552

Different labels

1. Fixed 19 instances, recently updated in Uberon. The term UBERON:8410010 has a different name/label in the source ontology in the following 32 rows 83, 84, 84, 85, 86, 86, 87, 87, 88, 88, 89, 89, 90, 90, 91, 91, 92, 92, 93, 93, 94, 94, 95, 95, 96, 96, 97, 98, 98, 116, 127, 128. The name/label in the ASCT+B table is fimbria of uterine tube and the one in the ontology is fimbria of fallopian tube. For reference, the given name/label by SMEs is fimbria of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

2. Fixed 24 instances, recently updated in Uberon. The term UBERON:0012648 has a different name/label in the source ontology in the following 38 rows 44, 45, 45, 46, 46, 47, 47, 48, 48, 49, 49, 50, 50, 51, 51, 52, 52, 53, 53, 54, 54, 55, 55, 56, 56, 57, 57, 58, 59, 59, 81, 82, 112, 113, 114, 115, 125, 126. The name/label in the ASCT+B table is ampulla of uterine tube and the one in the ontology is ampulla of fallopian tube. For reference, the given name/label by SMEs is ampulla of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

[emquardokus]

Fallopian_Tube_v1.4_DRAFT
https://docs.google.com/spreadsheets/d/1yCfVQmd3-R8wEN6qolpBT3w7hN2ug6pHyoxnM4i-sws/edit?gid=991519552#gid=991519552

Different labels

1. fixed 3 additional instances fimbria of fallopian tube UBERON:8410010 The term UBERON:8410010 has a different name/label in the source ontology in the following 3 rows 116, 127, 128. The name/label in the ASCT+B table is fimbria of uterine tube and the one in the ontology is fimbria of fallopian tube. For reference, the given name/label by SMEs is fimbria of Fallopian tube. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.