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🐛 Fix cell type curation #172

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merged 3 commits into from
Nov 25, 2024
Merged

🐛 Fix cell type curation #172

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95908c2
:bug: Fix CT curation
Zethson Nov 25, 2024
fc65f57
:art: Fix CT curation
Zethson Nov 25, 2024
bb99c7e
:art: Fix CT curation
Zethson Nov 25, 2024
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44 changes: 29 additions & 15 deletions docs/scrna2.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -193,8 +193,20 @@
"metadata": {},
"source": [
"None of the cell type names are valid.\n",
"\n",
"We'll now search the public ontology and add the name found in the dataset as a synonym to the top match found in the public ontology."
"We'll now look up the non-validated cell types using the values of the public ontology and create a mapping."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"tags": [
"hide-output"
]
},
"outputs": [],
"source": [
"curator.non_validated[\"cell_type_untrusted\"]"
]
},
{
Expand All @@ -207,23 +219,25 @@
},
"outputs": [],
"source": [
"bionty = bt.CellType.public() # access the public ontology through bionty\n",
"name_mapping = {}\n",
"for invalid_name in adata_validated.obs[\"cell_type_untrusted\"].unique():\n",
" ontology_id = bionty.search(invalid_name).index[0] # top search hit through iloc[0]\n",
" record = bt.CellType.from_source(ontology_id=ontology_id)\n",
" name_mapping[invalid_name] = record.name # map the original name to standardized name\n",
" record.save()\n",
" # record.add_synonym(name) # optionally save the invalid name as synonym so that it becomes searchable\n",
"# print the mapping\n",
"print(name_mapping)"
"ct_public_lo = bt.CellType.public().lookup()\n",
"name_mapping = {\n",
" \"Dendritic cells\": ct_public_lo.dendritic_cell.name,\n",
" \"CD19+ B\": ct_public_lo.b_cell_cd19_positive.name,\n",
" \"CD4+/CD45RO+ Memory\": ct_public_lo.effector_memory_cd45ra_positive_alpha_beta_t_cell_terminally_differentiated.name,\n",
" \"CD8+ Cytotoxic T\": ct_public_lo.cd8_positive_alpha_beta_cytotoxic_t_cell.name,\n",
" \"CD4+/CD25 T Reg\": ct_public_lo.cd4_positive_cd25_positive_alpha_beta_regulatory_t_cell.name,\n",
" \"CD14+ Monocytes\": ct_public_lo.cd14_positive_monocyte.name,\n",
" \"CD56+ NK\": ct_public_lo.cd56_positive_cd161_positive_immature_natural_killer_cell_human.name,\n",
" \"CD8+/CD45RA+ Naive Cytotoxic\": ct_public_lo.cd8_positive_alpha_beta_memory_t_cell_cd45ro_positive.name,\n",
" \"CD34+\": ct_public_lo.cd34_positive_cd56_positive_cd117_positive_common_innate_lymphoid_precursor_human.name\n",
"}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can now standardize cell type names using the search-based mapper:"
"We can now standardize cell type names using the lookup-based mapper:"
]
},
{
Expand Down Expand Up @@ -476,7 +490,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "lamindb",
"language": "python",
"name": "python3"
},
Expand All @@ -490,7 +504,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.17"
"version": "3.11.7"
},
"nbproject": {
"id": "ManDYgmftZ8C",
Expand Down