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.