ccf-validation-tools/Liver/comments/

[giscus[bot]]

ccf-validation-tools/Liver/comments/

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

[emquardokus]

Liver_v1.2_DRAFT
https://docs.google.com/spreadsheets/d/1U1UFN1m7fkWj-UgYDNTCfGZUv-opzCjEEYypihDjjSQ/edit#gid=1694828397

Different labels
FIXED In row 32, the term CL:0001056 has different name/label in the source ontology. The name/label in the ASCT+B table is human Dendritic cell and the one in the ontology is dendritic cell, human. For reference, the given name/label by SMEs is conventional Dendritic cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

FIXED In row 30, the term CL:0002138 has different name/label in the source ontology. The name/label in the ASCT+B table is lymphatic endothelial cell and the one in the ontology is endothelial cell of lymphatic vessel. For reference, the given name/label by SMEs is hepatic lymphatic endothelial cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

FIXED In row 34, the term CL:0002399 has different name/label in the source ontology. The name/label in the ASCT+B table is CD1c+ myeloid dendritic cell and the one in the ontology is CD1c-positive myeloid dendritic cell. For reference, the given name/label by SMEs is Conventional DC 2. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

FIXED In row 39, the term CL:0001203 has different name/label in the source ontology. The name/label in the ASCT+B table is CD8 positiver alpha beta memory T cell CD45RO + and the one in the ontology is CD8-positive, alpha-beta memory T cell, CD45RO-positive. For reference, the given name/label by SMEs is CD8+ Liver-Resident Memory T cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

FIXED In row 37, the term CL:0000624 has different name/label in the source ontology. The name/label in the ASCT+B table is CD4 positive alpha beta and the one in the ontology is CD4-positive, alpha-beta T cell. For reference, the given name/label by SMEs is CD4+T cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

FIXED In row 38, the term CL:0000798 has different name/label in the source ontology. The name/label in the ASCT+B table is gamma delta T cell and the one in the ontology is gamma-delta T cell. For reference, the given name/label by SMEs is gamma delta T cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

FIXED In row 24, the term CL:0000526 has different name/label in the source ontology. The name/label in the ASCT+B table is afferent neuron cell and the one in the ontology is afferent neuron. For reference, the given name/label by SMEs is neuron cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Blank ontology ID

1. Substitute leukocyte CL:0000738 for immune cell which is listed as exact synonym
   In row 15, no term id was found for the name/label Immune cell.

2. ADD nerve UBERON:0001021 In row 24, no term id was found for the name/label nerve.
3. ADD hepatic portal fibroblast CL:0009100 In row 27, no term id was found for the name/label portal fibroblast.
4. ADD lymphatic vessel UBERON:0001473
5. ADD CT/1 CD8-positive, alpha-beta memory T cell CL:0000909 to follow pattern of recently added lung resident similar cell type In row 36, no term id was found for the name/label CD8 TRm (residence memory).
6. ADD CT/1 natural killer cell CL:0000623 In row 41, no term id was found for the name/label Eomes low Liver NK cell.
7. ADD CT/1natural killer cell CL:0000623 In row 42, no term id was found for the name/label TBet low Liver NK cell.

Blank ontology ID missing parent

1. ADDED leukocyte CL:0000738 since "immune cell" is exact synonym in ontology In row 15, the term Immune cell without ontology ID has no parent that is from the CL ontology.

2. ADDED new CL term hepatic portal fibroblast CL:0009100 In row 27, the term portal fibroblast without ontology ID has no parent that is from the CL ontology.

3. ADD CT/1 CD8-positive, alpha-beta memory T cell CL:0000909 to follow pattern of recently added lung resident similar cell type In row 36, the term CD8 TRm (residence memory) without ontology ID has no parent that is from the CL ontology.

4. ADD CT/1 CD8-positive, alpha-beta memory T cell CL:0000909 to follow pattern of recently added lung resident similar cell type In row 41, the term Eomes low Liver NK cell without ontology ID has no parent that is from the CL ontology.

5. ADD CT/1 CD8-positive, alpha-beta memory T cell CL:0000909 to follow pattern of recently added lung resident similar cell type In row 42, the term TBet low Liver NK cell without ontology ID has no parent that is from the CL ontology.

[aleixpuigb]

New terms in the ontology:
Liver : endothelial cell of central vein of liver (CL:4033061)

[emquardokus]

Liver v1.3: https://docs.google.com/spreadsheets/d/14UaKKGzb8QUUj6LgGlOyHwzz2G3RrLprPPKzm7fLt2E/edit#gid=1694828397

Different label
REMOVED SPACE at the end of label to fix. The term CL:0000909 has a different name/label in the source ontology in the following 1 row 36. The name/label in the ASCT+B table is CD8-positive, alpha-beta memory T cell _ and the one in the ontology is _CD8-positive, alpha-beta memory T cell. For reference, the given name/label by SMEs is CD8-positive, alpha-beta memory T cell . Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.