Update PrimeKG on 2023.07.10.

mims-harvard · Jul 13, 2023 · dd5b57b · dd5b57b
1 parent 05ac920
commit dd5b57b
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Showing 14 changed files with 5,760 additions and 772 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,19 @@
+proj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+*/.DS_Store
+
+# ignore Python cache
+__pycache__
+.ipynb_checkpoints
+
+# ignore virtual environment
+# to activate, run source primeKG/bin/activate
+primeKG_env/
+
+# ignore data files
+datasets/data/
+datasets/feature_extraction/drug/drug_bank/parsed/
+datasets/processing_scripts/test.ipynb
diff --git a/datasets/feature_extraction/drug/drug_bank/Parsed_feature.ipynb b/datasets/feature_extraction/drug/drug_bank/Parsed_feature.ipynb
@@ -10,6 +10,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -133,6 +134,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -386,6 +388,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -533,6 +536,7 @@
    ]
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -678,6 +682,7 @@
    ]
   },
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -900,6 +905,7 @@
    ]
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -1071,6 +1077,7 @@
    ]
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -1529,6 +1536,7 @@
    ]
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -1669,6 +1677,7 @@
    ]
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
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@@ -1832,6 +1841,7 @@
    ]
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -2056,6 +2066,7 @@
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+   "attachments": {},
    "cell_type": "markdown",
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    "source": [
@@ -2302,6 +2313,7 @@
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+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -2470,6 +2482,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -2716,165 +2729,6 @@
    "source": [
     "indication.to_csv('csv/indication.csv',index=False)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 73,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#chem,drugcat,state,Hl,pathway,group,atc,description,vod,pb,pharm,moa,indication"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 74,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#from functools import reduce"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 81,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#import functools"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 75,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#data_frames = [chem,drugcat,state,Hl,pathway,group,atc,description,vod,pb,pharm,moa,indication]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 76,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#df_merged = reduce(lambda  left,right: pd.merge(left,right,on=['ID'],\n",
-    "                                            how='outer'), data_frames)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 77,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#df_merged.to_csv('db_features.csv',index=False)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 78,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#df_merged['Description']"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 104,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#df=reduce(functools.partial(pd.merge,on='ID'),[chem,drugcat,state,Hl,pathway,group,atc,description,vod,pb,pharm,moa,indication])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 105,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#df.to_csv('db_features.csv',index=False)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {