🔥 Remove curator.add_validated_from (#2081)

laminlabs · Oct 18, 2024 · a7027eb · a7027eb
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commit a7027eb
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Showing 5 changed files with 82 additions and 186 deletions.
diff --git a/docs/curate-df.ipynb b/docs/curate-df.ipynb
@@ -141,50 +141,15 @@
    "source": [
     "## Register new metadata values\n",
     "\n",
-    "If you see \"non-validated\" values, you'll need to decide whether to add them to your registries or \"fix\" them in your dataset.\n",
-    "\n",
-    "Because our current registries are still empty, we'll start by populating our {class}`~bionty.CellType` registry with values from a public ontology."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "bcb388d8",
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "# this adds cell types that were validated based on a public ontology\n",
-    "curate.add_validated_from(\"cell_type\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "5bcfc09f",
-   "metadata": {},
-   "source": [
-    "If we call `validate()` again, we see that one cell type still doesn't pass validation."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "104f9932",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "curate.validate()"
+    "If you see \"non-validated\" values, you'll need to decide whether to add them to your registries or \"fix\" them in your dataset."
    ]
   },
   {
    "cell_type": "markdown",
    "id": "8c2417c7",
    "metadata": {},
    "source": [
-    "Hence, let's understand which cell type in the public ontology might be the actual match."
+    "For `cell_type`, we saw that 'cerebral pyramidal neuron' is not validated, let's understand which cell type in the public ontology might be the actual match."
    ]
   },
   {
@@ -198,7 +163,7 @@
    },
    "outputs": [],
    "source": [
-    "# use a lookup object to get the correct spelling of categories from a public ontology\n",
+    "# use a lookup object to get the correct spelling of categories from a public ontology via `public=True`\n",
     "lookup = curate.lookup(public=True)\n",
     "lookup"
    ]
@@ -231,32 +196,15 @@
    "outputs": [],
    "source": [
     "# fix the cell type\n",
-    "df.cell_type = df.cell_type.replace({\"cerebral pyramidal neuron\": cell_types.cerebral_cortex_pyramidal_neuron.name})\n",
-    "# now register curated and validated cell types\n",
-    "curate.add_validated_from(df.cell_type.name)"
+    "df.cell_type = df.cell_type.replace({\"cerebral pyramidal neuron\": cell_types.cerebral_cortex_pyramidal_neuron.name})"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "752142a1",
+   "id": "1dc1028a",
    "metadata": {},
    "source": [
-    "Now, do the same for `\"assay_ontology_id`\" and `\"donor\"`."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ede057e8",
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "# this adds assays that were validated based on a public ontology\n",
-    "curate.add_validated_from(\"assay_ontology_id\")"
+    "For donor, we want to add the new donoers: 'D0001', 'D0002', 'DOOO3'"
    ]
   },
   {
@@ -362,24 +310,6 @@
     "curate.validate()"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "71a917d1",
-   "metadata": {},
-   "source": [
-    "Save the validated genes following the instruction:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e31dabcc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "curate.add_validated_from_var_index()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "614545ea",
@@ -535,7 +465,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "WOK3vP0bNGLx",

diff --git a/docs/curate-subclass.ipynb b/docs/curate-subclass.ipynb
@@ -161,23 +161,6 @@
     "ehrcurator.validate()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "ehrcurator.add_validated_from(\"disease\")\n",
-    "ehrcurator.add_validated_from(\"phenotype\")\n",
-    "ehrcurator.add_validated_from(\"developmental_stage\")\n",
-    "\n",
-    "ehrcurator.validate()"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,