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Map blueprint ontology to CL names #983

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merged 5 commits into from
Jan 14, 2025
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Merged

Map blueprint ontology to CL names #983

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5dceeeb
add blueprint name to consensus ref
allyhawkins Jan 13, 2025
d0689c3
add cl name for blueprint to results
allyhawkins Jan 13, 2025
ccbebe2
add blueprint_annotation_cl to docs
allyhawkins Jan 13, 2025
8f83742
Merge branch 'main' into allyhawkins/map-blueprint-ontology-name
allyhawkins Jan 14, 2025
a0c7796
Merge branch 'main' into allyhawkins/map-blueprint-ontology-name
allyhawkins Jan 14, 2025
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2 changes: 1 addition & 1 deletion analyses/cell-type-consensus/README.md
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Expand Up @@ -81,7 +81,7 @@ The `scpca-consensus-celltype-assignments.tsv` file contains cell type annotatio
| `cellassign_celltype_annotation` | Cell type assigned by `CellAssign`; this term is the original term found in the `PanglaoDB` reference file |
| `panglao_ontology` | Cell type ontology term associated with the term found in `cellassign_celltype_annotation` column |
| `panglao_annotation` | Name associated with the cell type ontology term in `panglao_ontology` |
| `blueprint_annotation_fine` | Fine grained cell type annotation (`label.fine`) from `BlueprintEncodeData` associated with the `singler_celltype_ontology` term |
| `blueprint_annotation_cl` | Name associated with the cell type ontology term in `singler_celltype_ontology` |
| `consensus_ontology` | Cell type ontology term assigned as the consensus cell type |
| `consensus_annotation` | Name associated with the assigned consensus cell type in `consensus_ontology` |

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1 change: 1 addition & 0 deletions analyses/cell-type-consensus/references/README.md
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Expand Up @@ -42,6 +42,7 @@ The table includes the following columns:
| `blueprint_ontology` | Cell type ontology term for `BlueprintEncodeData` cell type |
| `blueprint_annotation_main` | Original name for the cell type as set by `BlueprintEncodeData` (main term) |
| `blueprint_annotation_fine` | Original name for the cell type as set by `BlueprintEncodeData` (fine term) |
| `blueprint_annotation_cl` | Name for the cell type defined by [Cell Ontology](https://www.ebi.ac.uk/ols4/ontologies/cl) |
| `consensus_ontology` | Cell type ontology term for consensus cell type |
| `consensus_annotation` | Human readable name for the consensus cell type |

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